ProSE

Identifies peptides in MS/MS spectra.

pot. predecessor tools	→ ProSE →	pot. successor tools
any signal-/preprocessing tool (in mzML, mzPeak or Bruker .d format)		IDFilter or any protein/peptide processing tool

This search engine is mainly for educational/benchmarking/prototyping use cases. It lacks behind in speed and/or quality of results when compared to state-of-the-art search engines.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

Open-search mode is automatically determined by the precursor mass tolerance: enabled when tolerance exceeds 1 Da or 1000 ppm. No explicit open-search parameter is needed. This is logged at runtime and recorded in the output search parameters as UserParam 'open_search'.

Mass tolerances are measured by default ('-Search:calibration:enabled', on in this tool; the library's ProSEAlgorithm default is off). A calibration pass over the 10 % most intense spectra, searched with at least 20 ppm precursor and fragment windows (in Da twice the configured window, up to 0.5 Da; the configured ones if wider), takes the offset (median) and the spread (robust standard deviation, 1.4826 * MAD) of the signed mass errors of its confident PSMs. The main search then uses the fragment tolerance |median| + 4 sigma ('-Search:calibration:sigma_factor'), never wider than '-Search:fragment:mass_tolerance' and never below 10 ppm (0.02 Da; 5 ppm or 0.01 Da with the m/z correction below); the precursor window stays as configured by default ('-Search:calibration:precursor_sigma_factor' 0: the precursor errors are measured and reported; a value such as 4 tightens the window to median +/- 4 sigma, asymmetric about zero when the run has an offset, within 2.5 ppm per side and the configured window). The configured tolerances are therefore the widest windows searched, and a stated window stays an upper bound. The pass takes its spectra per tenth of the run, and a fragment tolerance that covers less than 95 % of the matched peaks of the calibration PSMs (or a precursor window less than 98 % of the PSMs) is not trusted: the configured tolerance is kept, with a warning. On the 20-run benchmark at equal entrapment-estimated FDP the fragment window gains on Astral (+6 %) and ion-trap CID data (+1 %) and is neutral elsewhere, while a tightened precursor window cost 2-3 % on every Orbitrap HCD set, which is why it is off. The measured errors are also corrected: '-Search:calibration:recalibrate offset' with '-Search:calibration:recalibrate_rt_chunks 10' (the tool's defaults; the library's: none) subtracts the median error of each tenth of the run (interpolated between them; a tenth whose calibration PSMs are mostly false matches, more than a quarter of them decoy hits, takes the precursor offset of its neighbours) from the precursor and fragment m/z the search uses, before the windows are set around zero; 'linear' subtracts a line in m/z per chunk instead, and 'none' only measures. The windows then follow the residual errors, with the fragment floor of 5 ppm (0.01 Da). The PSMs report the observed precursor m/z and the residual precursor error, their fragment annotations the observed peak m/z, and the models and the errors before and after the correction are recorded in the search parameters and the run summary. At equal entrapment FDP the correction adds +0.6 % on the 20 DDA runs, +6.5 % on HeLa diaPASEF (the fragment window can tighten once the offset is gone) and +1.6 % on the Astral runs; 'linear' adds nothing over 'offset'. Set '-Search:calibration:enabled false' to search with the configured tolerances as given. The measured errors (offset, sigma and |offset| + 4 sigma, before and after the correction) are logged and recorded in the search parameters ('calibration:*') and the run summary, with a warning when a configured window is tighter than them ('calibration:precursor_measurement_trusted' / 'calibration:fragment_measurement_trusted' are false when the measured error covers less than 98 % of the calibration PSMs or 95 % of their fragment peaks, e.g. two error modes or too few peaks, or reaches the window of the calibration pass, where the errors beyond it were cut off and the value is a lower bound: such a value should not be taken as a tolerance); the errors of the final PSMs, of the m/z as observed, are reported in the run summary and the QPX provenance ('precursor_error_*', 'fragment_error_*'). '-Search:precursor:isotope_error_min' is -2 in this tool (the library: -1): a precursor may have been picked on the first or second 13C peak of its peptide, which holds for 2-4 % of the identifications of DIA pseudo-spectra and for some of DDA.

Tolerances in '-out_merged': the run of each input reports the tolerances it was searched with, which the calibration may have narrowed differently for each input. The pooled run then reports the configured tolerances, and its search parameters list those of each input as 'input_precursor_mass_tolerances' and 'input_fragment_mass_tolerances' (one entry per input, in the order of the inputs; -1 for an input that was not pooled).

Remote input: an mzML file (also .mzML.gz or .mzML.bz2) can be read from Amazon S3 or an S3-compatible server ('-in s3://bucket/run.mzML') or from an HTTP(S) or FTP server ('-in https://host/run.mzML'). It is read as one stream, without a copy on disk, so more slowly than a local file (whose parts are parsed in parallel); '-qpx_extended' reads it again. S3 needs OpenMS built with an Arrow library that has S3 support (as in the vcpkg build); the credentials and the region are those of the AWS default credential chain (e.g. the environment variables AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY and AWS_DEFAULT_REGION, or ~/.aws), and the query of the URI can set the region or the endpoint, e.g. 's3://bucket/run.mzML?region=eu-central-1' or 's3://bucket/run.mzML?endpoint_override=localhost:9000&scheme=http'. The outputs and the log name such an input without its user info and query (e.g. 's3://bucket/run.mzML'), as these can hold credentials; prefer the environment to credentials in the URI all the same, as the command line and an INI file hold the URI as given. The database ('-database'), Bruker .d, Thermo .raw and mzPeak inputs and all outputs are local files.

Search settings from a run: prose-auto (https://github.com/okohlbacher/prose-auto) proposes ProSE settings from an mzML file (label, protease, modifications, organism and mass tolerances measured from the spectra, optionally with the dataset's records and methods text), each with its source and evidence.

Decoy handling is controlled by '-Search:decoys'. The default 'generate' always builds the decoys from the targets (prefixing accessions with '-Search:decoy_prefix', default "DECOY_"; decoys in the FASTA are removed first), with '-Search:decoy_method' keep_termini (default; for a fully specific digestion with a cleaving enzyme: in every segment the first and last residue, the residues that the enzyme's cleavage rule names and P stay in place, e.g. K, R and P for Trypsin/P and F, Y, W, L and P for Chymotrypsin; semi- or non-specific digestion as 'reverse'): every target peptide, also every protein N-terminal and Met-clipped one, has a decoy of the same start, length, mass and cleavage sites, so the protein N-terminal classes are controlled by target-decoy competition like the others (with 'Acetyl (Protein N-term)' among the default variable modifications, '-Search:rescoring:terminal_features' and '-Search:rescoring:stratum_q_values', also defaults). 'auto' reuses decoys already present in the FASTA (the marker is auto-detected, prefix or suffix, e.g. from DecoyDatabase) or generates them if none are found; it reuses supplied decoys only at 0.5 to 2 decoys per target protein (target-decoy FDR needs about one decoy per target: a database with far fewer, e.g. a few 'DECOY_' entries, or far more decoys is refused with an error before the search); with reversed-protein decoys the protein N-terminal classes have almost no decoys (set '-Search:rescoring:terminal_features false' and '-Search:rescoring:stratum_q_values false' then). 'ignore' searches the targets only.

Repeated database entries: an entry whose accession and sequence an entry before it has (e.g. a FASTA file or the contaminants added twice) is searched once, with a warning; two entries of one accession with different sequences are refused with an error naming the accession and the file, before the search.

Final results vs. intermediates

'-Search:FDR:protein' decides what a run of ProSE is:

• Above 0 (e.g. 0.01): the run is the whole experiment. Its proteins are inferred on the pooled PSMs of all its inputs (also without '-out_merged'), the picked-protein FDR filters them, and the PSMs are filtered finally; every output is the final result: '-out_merged' (if set) the pooled result, each per-input output ('-out_idxml', '-out_qpx' with its runs/ files and quantms.*, '-out_parquet') that input's part of it, with the same PSMs and the proteins (with their pooled protein q-values, score type 'q-value', and protein groups) that they reference. Only the best hit of each spectrum is kept. (The modification analysis of an open search, '-out_mod_analysis_dir' and the report, covers the PSMs at '-Search:FDR:PSM', before the protein FDR.) The order of the filters:
  1. per input: the search, Percolator on the input (or, if it cannot rescore the input alone, the model trained on a sample of the other inputs, see the note on rescoring below), PSM q-values and PEPs per run;
  2. per input: the reported PSMs (q-value ≤ '-Search:FDR:PSM', the final PSM FDR, e.g. 0.01) and, kept aside for the protein inference only, those up to '-Search:FDR:protein_inference_PSM' (default 0.1);
  3. all inputs pooled: protein inference on both sets (the loose set gives the picked-protein FDR its decoy proteins);
  4. the picked-protein FDR ('-Search:FDR:protein') on the complete protein set;
  5. final: the reported PSMs without those all of whose proteins fail the protein FDR (as in ProteomicsLFQ), decoys removed unless '-keep_decoys', the inference-only PSMs dropped; each input gets its part back.
• 0 (the default): the run is one part of a larger experiment, e.g. a shard of the files searched on one compute node. Only steps 1 and 2 above happen, with '-Search:FDR:PSM' as the loose threshold (e.g. 0.1, not the final FDR) and no inference-only set; steps 3 to 5 happen downstream (e.g. in ProteomicsLFQ, which applies its final PSM FDR on the PEPs of all runs pooled). Every output is a per-input intermediate: the PSM q-values and PEPs of each run (Percolator's), the decoy PSMs and the proteins the search indexed for the run's PSMs kept, no protein inference and no protein filter. Finish the experiment downstream on the intermediates of all parts together: ProteomicsLFQ (its PSM and protein FDR, e.g. 0.01, and quantification), or IDMerger → ProteinInference / Epifany → FalseDiscoveryRate → IDFilter. Search every part with the same parameters and the same FASTA, with its decoys in it (e.g. from DecoyDatabase), which the downstream tools get as well, so that every part and the downstream FDR see the same decoys. With several inputs, '-out_merged' then writes the pooled PSMs with a protein inference across the inputs but without protein FDR (an intermediate too).

The per-input PSM q-values and PEPs come from Percolator's rescoring of each input ('-Search:rescore', see below); ProSE's intermediates carry the q-value as main score and the PEP as meta value MS:1001493, which ProteomicsLFQ takes as its main score itself. So keep the rescoring on for intermediates that ProteomicsLFQ finishes: it needs a PEP for every PSM and stops with "expects a Posterior Error Probability score" for an input without (with '-Search:rescore' false, or a file that Percolator could not rescore at all, not even with the model of the other inputs). '-out_pin' always holds the PSMs before the rescoring and before any FDR filter. Outputs by mode:

output	FDR:protein > 0 (final result)	FDR:protein 0 (intermediate)
-out_idxml, -out_parquet, -out_qpx (per input)	the input's part of the pooled result: PSMs at FDR:PSM whose proteins pass the protein FDR, the proteins (with q-values and groups) they reference, without decoys unless -keep_decoys	the input's PSMs at FDR:PSM with run-level q-values and PEPs, target and decoy, the proteins the search indexed for its PSMs, no protein q-values
quantms.* of -out_qpx	the PSMs of all inputs as above, quantms.pg.parquet: the pooled protein groups with their q-values	the PSMs of all inputs as above; with several inputs and -out_merged the pooled groups (no FDR), else one group per protein of each input
-out_merged (several inputs)	the pooled final result	the pooled PSMs with a protein inference across inputs, no protein FDR
'peptide q-value' of the PSMs	per-input outputs: the q-value among the input's peptides; -out_merged: among the peptides of all inputs (the same computation across them, see the note on peptide-level q-values)
-out_pin	the PSMs before rescoring and FDR, with ProSE's own scores (input for an external Percolator)

Note

Peptide-level q-values: each rescored PSM carries the q-value of its peptide as meta value 'peptide q-value' (the name FalseDiscoveryRate writes and EntrapmentEvaluator reads). A list of peptides at an FDR is the target peptides with 'peptide q-value' at most that FDR; the distinct peptides of the PSMs at an FDR are not FDR-controlled at the peptide level. ProSE computes it with the peptide-level target-decoy FDR of OpenMS (FalseDiscoveryRate::applyBasicPeptideLevel()): a peptide is an unmodified sequence, its best PSM competes with its label, and q = (decoy peptides + 1) / target peptides at the thresholds that accept it, with the PSMs ranked by their Percolator PEP (the PEP only ranks; the q-values come from target-decoy competition). In a per-input output it is computed on the input's PSMs (before '-Search:FDR:PSM'), an FDR of that input's peptides. Such per-input lists do not pool: true peptides recur across inputs, false ones rarely do, so the union of the inputs' lists at 1 % has a higher FDR. '-out_merged' therefore carries the same computation on the pooled PSMs of all inputs (those at '-Search:FDR:PSM', all with 0; before decoys are removed), with the same peptide definition; the PEPs of the inputs are on one scale, the scores of their separate models are not. None is written without rescoring, with '-Search:rescore_method reset' (its 'RESET:peptide_q_value' stays per input), or in '-out_merged' if Percolator could not rescore every input (a warning says so). Percolator's own peptide level ('-Search:rescoring:peptide_level') writes 'percolator_peptide_q_value' and 'percolator_peptide_pep' besides, on modified sequences.

Protein-level FDR scope: picked-protein FDR does not compose across runs, so it is applied to a complete protein set only: a single input, or the pooled inputs of a run (see above). ProSE never filters the proteins of one input of several on their own.

Protein inference of the protein FDR: as in ProteomicsLFQ, the inference and the picked-protein FDR use the PSMs up to a looser q-value than '-Search:FDR:PSM', '-Search:FDR:protein_inference_PSM' (default 0.1), which leaves more decoy proteins for the picked-protein FDR, and a protein scores with the best posterior error probability of its PSMs (Percolator's PEP; without rescoring the best HyperScore). The proteins and the protein groups are filtered at '-Search:FDR:protein', each by its own q-value (the picked FDR of the groups counts a group once, however many targets it holds, so a group can be above the threshold while its proteins are not), and only the proteins of the groups that pass are kept. The reported PSMs are those that pass '-Search:FDR:PSM', but for the PSMs all of whose proteins fail the protein FDR, which are removed (as in ProteomicsLFQ), so that every reported PSM maps to a reported protein; proteins and protein groups without a reported PSM are removed after the protein FDR.

PSM FDR: '-Search:FDR:PSM' filters the PSMs of each input on their q-values (Percolator's, or target-decoy competition of ProSE's score). It is never lifted: if no PSM of an input matched a decoy, the q-value of its T PSMs is the conservative 1/T (target-decoy competition with +1, where the uncorrected 0/T would pass every PSM), so a lower threshold reports no PSM, as an unattainable protein FDR reports no protein. Only a search without decoys ('-Search:decoys ignore') skips the filter, with a warning. The proteins of a per-file intermediate ('-Search:FDR:protein' 0) are those the search indexed for its PSMs (also for the PSMs that the PSM FDR removed); a final result holds the proteins its reported PSMs reference (see "Final results vs. intermediates").

Percolator rescoring: by default ('-Search:rescore true'), the PSMs of each input file are rescored separately with OpenMS' built-in (in-process) Percolator implementation, the same backend PercolatorAdapter uses by default. No percolator executable is needed (the former '-percolator_executable' parameter and '-rescore' flag were removed). Training uses the standard Percolator feature set plus ProSE's search engine features, '-train_best_positive' and target-decoy competition ('-post_processing_tdc'), so q-values and PEPs come from target-decoy competition without a pi0 estimate, as with the percolator executable's -Y; Percolator q-values become the main score (the SVM score and PEP are kept as meta values MS:1001492/MS:1001493, the HyperScore as meta value 'ln(hyperscore)'), only the best hit per spectrum is kept, and the runs report 'Percolator' as search engine. The PSM and protein FDR thresholds are then applied on the rescored PSMs. A file with fewer than 100 PSMs or without decoys, or for which Percolator fails, is not rescored on its own: ProSE prints a warning and continues. Searched alone, such a file keeps its HyperScores (FDR is then computed from them); in a multi-file search, it gets the scores of a model trained on other inputs (see below) and keeps its HyperScores only if that fails too. The end-of-search report states how many files were rescored, and with '-qpx_extended' the run view has 'rescoring_applied' and 'rescoring_skipped_reason' per input. In a multi-file search, the inputs that Percolator rescores on their own keep exactly these results, whatever other inputs are searched with them. An input that it cannot rescore on its own (e.g. a small file next to large ones) gets the scores of a Percolator model trained on the PSMs of the inputs it rescored on their own, applied on the scale of that model's training PSMs: a PSM gets the score it would get among them and their PEP at that score (the score-to-PEP function is not estimated again on the few PSMs of the input); its q-values are those of target-decoy competition of the input's PSMs on that score (FDR per run, as for every input), on which '-Search:FDR:PSM' filters, and the run view's 'rescoring_warning' says that the scores come from a model trained on the other inputs. So every PSM has a Percolator PEP, and '-out_merged' ranks the proteins of all inputs by PEP. If Percolator can rescore no input on its own, the PSMs of all inputs are rescored together, with one model. Only if that fails too (e.g. fewer than 100 PSMs in all), such inputs keep their search engine scores, and the pooled evaluation ('-Search:FDR:protein' > 0 or '-out_merged') then scores the proteins of all inputs by ProSE's score 'ln(hyperscore)' (as without rescoring) instead of Percolator's PEP, which only the rescored PSMs have (every pooled PSM has a q-value as main score). '-Search:percolator:max_train_psms' (default 500000) caps the PSMs a model is trained on, and so the PSMs a multi-file search keeps for the model of the inputs too small for their own (see there). Set '-Search:rescore false' to report ProSE's own scores. '-out_pin' always holds ProSE's own scores (see there).

Search:peptide:clip_nterm_methionine=true also searches the mature N-terminal peptide after loss of exactly the initial methionine of an M-leading protein. Both forms are searched with the configured length, mass and missed-cleavage limits. Protein N-terminal variable modifications also apply after clipping. Set false to restore the previous search space; internal methionines are not clipped. Generated decoys retain the initial M when enabled; supplied decoys are searched as provided.

Local peak filtering: Search:peaks:window_type=auto retains up to Search:peaks:window_top peaks in every 100 Da window, including the short final window, for high-resolution fragments (tolerance <= 0.1 Da or <= 100 ppm). Low-resolution auto retains the legacy width-scaled final quota. Use jump for legacy filtering at every resolution, or jump_full to always retain the full quota. This changes high-resolution preprocessing, not the scoring formula.

Self-trained fragment ion priors: with Search:annotate:self_trained_ion_priors (on by default) each file learns how its fragment ions appear: presence, intensity rank among all peaks after deisotoping (before the Search:peaks:window_top and Search:peaks:keep_n filters) and mass error, per ion series (a/b, x/y, c and z apart: the c and z+1 ions of electron-activated spectra, see Search:ions:by_activation, have statistics of their own), precursor and fragment charge, relative cleavage position, residues at the cleavage site (before P, after D or E) and presence of the complementary ion (Search:annotate:ion_prior_model 'rich'; 'basic' keeps series, charges and position, and the rank only). The model learns from the confident target PSMs (target-decoy competition q <= Search:annotate:ion_prior_train_fdr of the native score) against their reversed sequences on the same spectra. The spectra are split into two halves by scan parity, and every PSM is scored by the model of the other half (cross-fitting), so a PSM's own spectrum and label never enter the model that scores it. Every PSM gets the Percolator features of Search:annotate:ion_prior_features (ion_prior_llr and ion_prior_explained); native scores and the reported candidates are unchanged. Nothing is pre-trained: a file with fewer than Search:annotate:ion_prior_min_psms confident PSMs in either half gets zeros (and a warning); at that boundary a single label decides between the features and zeros for the whole file. Target-only searches (Search:decoys ignore) learn and write nothing. The peak lists are kept in a compact form (m/z and rank, 5 bytes per peak) until the PSMs are annotated.

Ion mobility: the drift time of an MS2 spectrum is written to its identification. An ion mobility (e.g. 1/K0 of Bruker timsTOF DDA-PASEF data) is written as meta value 'IM', with its unit as 'IM' on the run; a FAIMS compensation voltage (Thermo FAIMS data, from .raw or mzML) is written as 'FAIMS_CV', which the FAIMS-aware tools (e.g. ProteomicsLFQ, MS1LabeledWorkflow, FeatureFinderIdentification) read.

Extended QPX output: '-qpx_extended' (with '-out_qpx') adds optional columns to the QPX psm view and writes the QPX mz, run, sample and provenance views, so that a viewer can show a search from the QPX files alone. QPX readers ignore columns and keys they do not know; the names are those proposed in bigbio/qpx#355 and #259. Each row of the per-input psm.parquet files and of quantms.psm.parquet gets: 'additional_scores' with every numeric score and meta value of the PSM in snake_case instead of the known scores only ('global_qvalue': the PSM-level q-value, from target-decoy competition or Percolator, computed over the PSMs of the input file; 'ln_hyperscore'; Percolator's 'percolator_score', 'percolator_qvalue', 'percolator_pep'; 'precursor_mz_error_ppm' (corrected for the isotope error), 'isotope_error' (as the column), 'delta_mass' (open search) and the Percolator features), with 'higher_better' where it is known; 'spectrum_reference' (string, the native ID of the spectrum; null if the mz view has no row of it, see below); 'isotope_error' (int16: the 13C peaks from the monoisotopic to the selected precursor peak, i.e. observed minus theoretical, whatever 'Search:report:isotope_error_convention' says); 'protein_mappings' (list of struct accession, start, end, aa_before, aa_after: each protein of the peptide with the peptide's 1-based first and last position and the residues before and after it, '-' at a protein terminus). The per-input psm files also get 'predicted_ion_type_array', 'predicted_mz_array', 'predicted_intensity_array': the b and y ions of charge 1 and (for precursors of charge 2 or more) 2, named as in 'ion_type_array' ("b3+", "y5++"), with their theoretical m/z and the intensity PeptDeep predicts, relative to the most intense of them; ions of 0.01 or less are left out. The predictions use the settings of 'Search:peptdeep:*' (models, instrument) at the normalised collision energy of the file: the one PeptDeep rescoring used ('Search:peptdeep:enable'; predicted again at that NCE), else 'Search:peptdeep:nce' if set, else the one PeptDeep rescoring would select for the written PSMs (its selection alone, without its features); PSMs of precursor charge 1 to 6 are predicted, others get null. Each input is read once more after its search for the spectra of its PSMs (as the search reads it: in one pass, parsed in parallel); a failed re-read is a warning and leaves out its mz view (and the 'spectrum_reference' of its PSMs null), a failed prediction a warning and null prediction columns; without ONNX Runtime the prediction columns are null. The work of each input is logged in phase lines, each written at once when its phase starts, for a progress display: "-qpx_extended: INPUT: reading spectra", "-qpx_extended: INPUT: selecting NCE" (only if the NCE is selected), "-qpx_extended: INPUT: predicting N peptides at NCE X (SOURCE)" (N the distinct peptide and charge pairs, SOURCE 'from PeptDeep rescoring', 'set' or 'selected'; not without ONNX Runtime or without PSMs) and "-qpx_extended: INPUT: writing" (the outputs of the input), INPUT the path of the input as given; other lines of that prefix are summaries or warnings. The NCE selection logs no "[PeptDeepRescoring]" lines of its own (except warnings about its input), so they stand for PeptDeep rescoring only. Each input gets the QPX mz view (runs/BASENAME.mz.parquet, BASENAME the input's basename) of the MS2 spectra of its written PSMs only (one row per spectrum, in the order of its first PSM; of several spectra of one native ID only the first, as 'id' is the view's key, so the PSMs of the others have no spectrum there and a null 'spectrum_reference': they are unresolved, as a join on their native ID would give the first spectrum, and a reader must not look them up by 'scan' either; 'id' the native ID, 'run_file_name', 'scan', 'ms_level', 'centroid', 'scan_start_time' (minutes), 'inverse_ion_mobility', 'ion_injection_time' (null if unknown), 'total_ion_current' (of all its peaks), 'precursors', 'cv_params' (null)), whose 'mz' and 'intensity' are filtered: the '-qpx_peak_top' most intense peaks of each '-qpx_peak_window' Th window (jumping windows: each starts at its first peak; the last one too keeps '-qpx_peak_top' peaks) and the peaks of the fragment annotations 'mz_array' of its PSMs ('-qpx_peak_top 0' keeps all); of deisotoped spectra, whose annotation has every fragment at its 1+ m/z, also the peak of the fragment at its own charge 2 or 3, so that every annotated fragment keeps its peak (the charges the search's deisotoping tried: up to 3, and with 'Search:fragment:deisotope_charge_cap precursor' at most the spectrum's recorded precursor charge, whatever the charge of the PSM; up to 3 if that is unknown). Its footer records the filter: 'prose_peak_window', 'prose_peak_top', 'prose_peak_annotated' (kept). A PSM's spectrum is the mz row whose 'id' is its 'spectrum_reference'; a null one means no stored spectrum (the re-read failed, the spectrum was not found again, or another spectrum of its native ID has the row). A per-input mz view is written while the PSMs of the input are predicted, its psm and pg files right after the input's other outputs, each file on a thread of its own while the run goes on (an mz view whose psm file cannot be written is removed again); psm and mz files are in row groups of 256 rows, so that a viewer can read the spectrum and the prediction of one PSM alone; the psm file's footer has the keys of its prediction columns: 'prose_prediction_ms2_model', 'prose_prediction_instrument'. quantms.psm.parquet has the rows of the inputs whose psm file was written, in input order, without the prediction columns (and no rows if there are none). The output directory is one QPX dataset (prefix 'quantms'): the quantms.* files of the whole run on top, the per-input files (BASENAME.psm/mz/pg.parquet) in its subfolder runs/, so an input may be named 'quantms' too; two inputs of one basename are still refused, as they would share runs/BASENAME.*. At the end of the run three QPX metadata views describe it: quantms.run.parquet (one row per input, in input order): 'run_accession' and 'run_file_name' (the input's stem), 'file_name', 'samples' (one sample per run: the stem, label 'LFQ'; ProSE knows no design), 'fraction', 'instrument', 'dissociation_method', 'acquisition_method', 'additional_terms' (null: unknown to ProSE), 'enzymes', 'modification_parameters' (the search's fixed and variable modifications: UNIMOD accession, name, fixed, position, target residue); and the optional columns 'search_status' (EXECUTION_OK, INPUT_FILE_EMPTY, UNEXPECTED_RESULT, UNKNOWN_ERROR, ILLEGAL_PARAMETERS), 'ms2_spectra_count' (0 for an input without MS2 spectra, e.g. MS1 only), 'profile_spectra_count' (of these, the spectra recorded as profile spectra, which ProSE searches as they are; it warns, as they should be centroided first), 'charge_out_of_range_spectra_count' (of these, the spectra not searched because their recorded precursor charge is outside '-Search:precursor:min_charge' to '-Search:precursor:max_charge'), 'identified_spectra_count' (target PSMs after the FDR filters), 'decoy_psm_count', 'psm_rows' (its rows in quantms.psm.parquet), int64; 'psm_fdr_applied' (bool: whether '-Search:FDR:PSM' filtered its PSMs, false if the filter was skipped for lack of decoys; null without '-Search:FDR:PSM' or for a failed search); 'rescoring_applied' (bool; null: the search did not rescore), 'rescoring_skipped_reason', 'rescoring_warning' (string); 'prediction_nce' (double; null: no prediction); 'precursor_error_median_ppm', 'precursor_error_mad_ppm', 'precursor_tolerance_recommended_ppm', 'fragment_error_median_ppm', 'fragment_error_mad_ppm', 'fragment_tolerance_recommended_ppm' (double; null: no estimate, fewer than 10 PSMs): the mass errors of the best hits of the run's target PSMs after the FDR filters (decoys, and hits without a target/decoy annotation, left out), signed, observed minus theoretical m/z in ppm: of the precursor, its m/z corrected by the hit's isotope error (the 13C peak the search matched), in an open search of the PSMs without a delta mass (within 0.05 Da of zero) only; of the fragments, every annotated b and y peak (without neutral losses) of these PSMs. The median is that of the signed errors (the bias of the run), the MAD their median absolute deviation from the median (unscaled), and the recommended tolerance the symmetric one that covers the bias and three standard deviations of a normal distribution estimated robustly: ceil(|median| + 3 * 1.4826 * MAD). The fragment errors are those of the matched peaks, so within the searched fragment tolerance: a recommended fragment tolerance near it says that the searched one may be too narrow rather than right (the report's "Tolerance estimate" is the same); 'search_seconds' (double). quantms.sample.parquet: the sample of each run ('sample_accession' the stem; 'organism' and 'organism_part' "not available", as SDRF has an unknown value). quantms.provenance.parquet: one row per step, in order: 'database_search' 'peptide_search' (tool ProSE; parameters database_file, enzyme, enzyme_specificity, missed_cleavages, peptide_min_length, peptide_max_length, precursor_mass_tolerance_lower, precursor_mass_tolerance_upper, precursor_mass_tolerance_unit, fragment_mass_tolerance, fragment_mass_tolerance_unit, min_charge, max_charge, fixed_modifications, variable_modifications, clip_nterm_methionine, decoy_mode, decoy_string, decoy_position, open_search, calibration, chunked, isotope_error_convention (the sign of ProSE's own isotope_error meta value, which Percolator saw: observed_minus_theoretical or theoretical_minus_observed), extra_features (the Percolator features beyond the standard ones, by their names in 'additional_scores'), db_target_proteins, db_decoy_proteins, indexed_peptides, indexed_fragments, seconds_index_build, seconds_total, and in open search with -out_mod_analysis_dir mod_analysis_delta_masses and mod_analysis_ptms, the file names of the run's tables in that directory; 'config': every parameter of this tool as one JSON object); 'rescoring' 'spectrum_prediction' (tool OpenMS, PeptDeep's models; only if some input was predicted; parameters method, ms2_model, instrument, rescoring_features); 'rescoring' 'psm_rescoring' (tool OpenMS, its Percolator; with 'Search:rescore'; parameter method); 'fdr_filtering' 'target_decoy_fdr' (tool ProSE; psm_fdr, protein_fdr, psm_fdr_method, protein_fdr_method, psm_fdr_applied: the PSM FDR filtered the PSMs of every input that was searched (see the run view's psm_fdr_applied), protein_fdr_applied: the protein FDR was applied to a complete protein set, one input or the pooled set of -out_merged); 'protein_inference' 'protein_grouping' (tool ProSE; algorithm, pooled). 'tool_version' is the version of OpenMS. Protein groups: with '-qpx_extended' a run without protein inference gets one group per protein in its pg.parquet (without a global_qvalue). With several inputs and the pooled evaluation ('-Search:FDR:protein' > 0 or '-out_merged'), quantms.pg.parquet holds the groups of the pooled inference (with its protein FDR; a row per group and run, the view's key), also without '-qpx_extended'.

Decoys: '-keep_decoys' keeps the decoy PSMs and decoy proteins that pass the FDR thresholds in a final result, e.g. for showing target and decoy score distributions (see "Final results vs. intermediates").

Several input files: give all files that share the database and the search parameters to one call ('-in a.mzML b.mzML ...'). The fragment index is then built once instead of once per file, and with more than one thread the next mzML file is read while the current one is searched. Each file's outputs depend on '-Search:FDR:protein' (see "Final results vs. intermediates"), and the whole run usually takes less time than one call per file. Compare search engines in the same mode.

Threads: '-threads' sets the threads of the search ('-threads 0': the physical cores the process may use, without their hardware threads); an mzML file read while the search runs takes its threads from these if they are fewer than the physical cores the process may use (otherwise it reads with threads of its own). For many files on a machine with many cores, several processes at 16-32 threads, each searching a share of the files, finish sooner than one process at 64 threads. With many threads on a shared machine, set the environment variable OMP_WAIT_POLICY=passive: idle OpenMP threads then sleep instead of spinning, which saves CPU time at about the same wall time. Do not bind threads (OMP_PROC_BIND), which made ProSE slower.

Memory in chunked multi-file runs: '-Search:database:chunk_size' bounds the fragment-index memory only. With multiple '-in' files and chunking active, the chunk-major schedule keeps every input file's preprocessed MS2 spectra in memory for the whole search (each chunk's index is built once and scored against all files). Budget roughly the sum of all files' MS2 peak data on top of one chunk's index, or split very large cohorts across separate invocations (see the sharded-FDR workflow below).

Memory: on Linux with glibc, ProSE sets glibc's malloc top pad to 64 MiB (mallopt M_TOP_PAD), so that the heap of a thread's arena is made writable at once instead of page by page (with many threads the latter kept the kernel busy; no change of results). Not if the environment sets the top pad itself (GLIBC_TUNABLES=glibc.malloc.top_pad=...), nor with OPENMS_MALLOC_DEFAULTS=0. Huge pages for glibc's malloc, which cut the page faults of a large search (a 64-thread HeLa search was 8 % faster), can be requested with GLIBC_TUNABLES=glibc.malloc.hugetlb=1 (glibc 2.35 or later, transparent huge pages 'madvise' or 'always').

Exit: on Linux, ProSE hands the release of its memory at the end to a short-lived helper process, so that its caller sees the end earlier (40-80 ms for a small search, about 0.8 s for a 250,000-spectrum run; exit code and outputs unchanged). OPENMS_FAST_EXIT=0 (or false, no, off) turns this off. Caveat: the helper is a process of its own for that moment, so a parent that does not reap the children it adopts (an init process or subreaper that waits only for its own child) keeps one zombie process per run; shells, systemd, Slurm and Apptainer reap it. Not used under a debugger or tracer, nor under a seccomp filter (as in some container runtimes and systemd services).

Distributed (sharded) searches: '-Search:FDR:protein' 0 on each node, then ProteomicsLFQ ('-psmFDR' and '-proteinFDR' 0.01, '-picked_proteinFDR' true, the same FASTA) on the intermediates of all shards (see "Final results vs. intermediates").

The command line parameters of this tool are:

ProSE -- Annotates bottom-up MS/MS spectra using ProSE.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_ProSE.html
Version: 3.7.0-pre-nightly-2026-11-13 Nov 14 2026, 01:17:51, Revision: 339429f
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  ProSE <options>

Options (mandatory options marked with '*'):
  -in <files>*                                             Input spectrum file(s). Multiple files are searche
                                                           d against the same database; the fragment index 
                                                           is built once and reused. An mzML file may also 
                                                           be given as a remote location (s3://bucket/run.mzM
                                                           L, http://, https:// or ftp://): it is streamed, 
                                                           not downloaded to disk. (valid formats: 'mzML', 
                                                           'mzpeak', 'd', 'raw')
  -database <file>*                                        Input protein sequence database in FASTA format. 
                                                           (valid formats: 'fasta', 'fa', 'faa')
  -out <files>                                             Output identification file(s), one per -in: idXML 
                                                           or an idparquet directory bundle (format by extens
                                                           ion). Must have the same number of entries as -in.
                                                            (valid formats: 'idXML', 'idparquet')
  -out_merged <file>                                       Optional output of all PSMs pooled across the inpu
                                                           t files, with a protein inference across them (Bas
                                                           icProteinInferenceAlgorithm) and, with 'Search:FDR
                                                           :protein' > 0, the picked-protein FDR (see the 
                                                           tool documentation, 'Final results vs. intermediat
                                                           es'). Only useful with multiple -in files. idXML 
                                                           or an idparquet directory bundle (format by extens
                                                           ion). (valid formats: 'idXML', 'idparquet')

Search:
  -Search:enzyme <choice>                                  The enzyme used for peptide digestion. (default: 
                                                           'Trypsin') (valid: 'Chymotrypsin/P', 'CNBr', 'Form
                                                           ic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA', 
                                                           'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'leukoc
                                                           yte elastase', 'proline endopeptidase', 'Trypsin',
                                                            'glutamyl endopeptidase', 'Alpha-lytic protease',
                                                            '2-iodobenzoate', 'iodosobenzoate', 'staphylococc
                                                           al protease/D', 'proline-endopeptidase/HKR', 'Glu-
                                                           C+P', 'PepsinA + P', 'cyanogen-bromide', 'Clostrip
                                                           ...
                                                           'Asp-N', 'Asp-N/B', 'Asp-N_ambic', 'Chymotrypsin')

  -Search:decoys <choice>                                  Decoy handling for target-decoy FDR. 'auto': ensur
                                                           e decoys are available — reuse decoys already 
                                                           present in the database (marker auto-detected, 
                                                           prefix or suffix) or generate them if none are 
                                                           found. Supplied decoys are reused only at 0.5 to 
                                                           2 decoys per target protein: target-decoy FDR need
                                                           s about one decoy per target, so a database with 
                                                           far fewer or more is refused (use 'generate'). 
                                                           ...
                                                           present in the database are removed. (default: 
                                                           'generate') (valid: 'auto', 'generate', 'ignore')
  -Search:low_memory                                       Non-specific searches (peptide:enzyme_specificity=
                                                           none; ignored otherwise): index the peptide masses
                                                           , as the prefixes of one mother peptide per protei
                                                           n position, instead of the fragments of every pept
                                                           idoform, and generate the fragments of the peptido
                                                           forms in the precursor window at query time. Finds
                                                            the same candidates with a fraction of the memory
                                                            (e.g. for immunopeptidomics against a human datab
                                                           ase), but takes more time per spectrum, the more 
                                                           the wider the precursor window.
  -Search:rescore <choice>                                 Rescore the PSMs of every search run (input file) 
                                                           in-process with Percolator (OpenMS' built-in imple
                                                           mentation, as PercolatorAdapter uses by default) 
                                                           before the FDR filters: Percolator q-values become
                                                            the main score (the SVM score and PEP are kept 
                                                           as meta values), Percolator rescores the top 'resc
                                                           oring:top_hits' hits of each spectrum and only 
                                                           its best one per spectrum is kept, and FDR:PSM 
                                                           ...
                                                           score and stops for an input without PEPs. (defaul
                                                           t: 'true') (valid: 'true', 'false')

Precursor (Parent Ion) Options. mass_tolerance_lower/_upper are positive magnitudes applied as [-lower, +uppe
r] around the precursor mass.:
  -Search:precursor:mass_tolerance_lower <value>           Lower-side precursor-mass tolerance (positive magn
                                                           itude; effective window is [-lower, +upper] around
                                                            the precursor). When strongly asymmetric, also 
                                                           review precursor:isotope_error_min. (default: '10.
                                                           0') (min: '0.0')
  -Search:precursor:mass_tolerance_upper <value>           Upper-side precursor-mass tolerance (positive magn
                                                           itude). (default: '10.0') (min: '0.0')
  -Search:precursor:mass_tolerance_unit <choice>           Unit of precursor mass tolerance. (default: 'ppm')
                                                            (valid: 'ppm', 'Da')
  -Search:precursor:min_charge <number>                    Minimum precursor charge to be considered. Spectra
                                                            without a precursor charge are searched with ever
                                                           y charge of the range; spectra whose recorded char
                                                           ge lies outside of it are searched at that charge,
                                                            or not at all with precursor:recorded_charge_outs
                                                           ide_range 'skip'. (default: '2') (min: '1' max: 
                                                           '20')
  -Search:precursor:max_charge <number>                    Maximum precursor charge to be considered (see 
                                                           precursor:min_charge). (default: '5') (min: '1' 
                                                           max: '20')
  -Search:precursor:isotope_error_min <number>             Minimum precursor isotope error searched, in 13C 
                                                           spacings (1.00336 Da) added to the observed precur
                                                           sor mass: -1 finds a peptide whose first 13C isoto
                                                           pe peak was selected as the precursor. The PSM 
                                                           meta value 'isotope_error' reports the opposite 
                                                           sign by default (see report:isotope_error_conventi
                                                           on). (default: '-2') (min: '-5' max: '5')
  -Search:precursor:isotope_error_max <number>             Maximum precursor isotope error searched, with 
                                                           the sign of precursor:isotope_error_min: +1 finds 
                                                           a peptide whose precursor was selected one 13C 
                                                           spacing below its monoisotopic peak. (default: 
                                                           '1') (min: '-5' max: '5')

Fragments (Product Ion) Options:
  -Search:fragment:mass_tolerance <value>                  Fragment mass tolerance (default: '20.0')
  -Search:fragment:mass_tolerance_unit <choice>            Unit of fragment m (default: 'ppm') (valid: 'ppm',
                                                            'Da')
  -Search:fragment:deisotope <choice>                      MS2 deisotoping (single-charge deconvolution) befo
                                                           re searching. 'auto' deisotopes only when the frag
                                                           ment tolerance is within the high-resolution deiso
                                                           toper range (<= 0.1 Da / <= 100 ppm) and skips it 
                                                           for low-resolution (e.g. ion-trap CID) data; 'true
                                                           ' always deisotopes (requires a high-resolution 
                                                           fragment tolerance); 'false' never deisotopes. 
                                                           (default: 'auto') (valid: 'auto', 'true', 'false')

  -Search:fragment:min_mz <number>                         Minimal fragment mz for database (default: '150') 
                                                           (min: '0')
  -Search:fragment:max_mz <number>                         Maximal fragment mz for database (default: '2000')
                                                            (min: '0')
  -Search:fragment:min_ion_index <number>                  Ions with index less than or equal to this value 
                                                           are not added to the fragment index (use 0 to incl
                                                           ude all ions; 2 skips b1/b2/y1/y2). Low-index ions
                                                            are often noisy and unreliable. (default: '2') 
                                                           (min: '0')
  -Search:fragment:min_matched_ions <number>               Minimal number of matched ions to report a PSM 
                                                           (default: '5') (min: '0' max: '1000')
  -Search:fragment:max_charge <number>                     Max fragment charge (default: '2') (min: '1' max: 
                                                           '10')

Modifications Options:
  -Search:modifications:fixed <list>                       Fixed modifications, specified using UniMod (www.u
                                                           nimod.org) terms, e.g. 'Carbamidomethyl (C)' (defa
                                                           ult: '[Carbamidomethyl (C)]') (valid: '15N-oxobuta
                                                           noic (N-term C)', '15N-oxobutanoic (Protein N-term
                                                            S)', '15N-oxobutanoic (Protein N-term T)', '2-dim
                                                           ethylsuccinyl (C)', '2-methylbutyryl (K)', '2-mono
                                                           methylsuccinyl (C)', '2-nitrobenzyl (Y)', '2-succi
                                                           nyl (C)', '2HPG (R)', '2PCA-triazole-ethanethiol 
                                                           (N-term)', '3-deoxyglucosone (R)', '3-hydroxy-3-me
                                                           thylglutaryl (K)', '3-hydroxybenzyl-phosphate (K)'
                                                           ...
                                                           'ZGB (N-term)', 'ZQG (K)')
  -Search:modifications:variable <list>                    Variable modifications, specified using UniMod 
                                                           (www.unimod.org) terms, e.g. 'Oxidation (M)'. A 
                                                           terminus and a residue carry one modification each
                                                           : a variable terminal modification (e.g. 'Acetyl 
                                                           (Protein N-term)', 'Gln->pyro-Glu (N-term Q)') is 
                                                           not searched where a fixed one sits on that termin
                                                           us (e.g. 'TMT6plex (N-term)'), and a variable resi
                                                           due modification (e.g. 'Glutathione (C)') is not 
                                                           searched where a fixed one sits on that residue 
                                                           (e.g. 'Carbamidomethyl (C)'). (default: '[Oxidatio
                                                           n (M) Acetyl (Protein N-term)]') (valid: '15N-oxob
                                                           utanoic (N-term C)', '15N-oxobutanoic (Protein 
                                                           N-term S)', '15N-oxobutanoic (Protein N-term T)', 
                                                           '2-dimethylsuccinyl (C)', '2-methylbutyryl (K)', 
                                                           '2-monomethylsuccinyl (C)', '2-nitrobenzyl (Y)', 
                                                           '2-succinyl (C)', '2HPG (R)', '2PCA-triazole-ethan
                                                           ethiol (N-term)', '3-deoxyglucosone (R)', '3-hydro
                                                           xy-3-methylglutaryl (K)', '3-hydroxybenzyl-phospha
                                                           ...
                                                           'ZGB (N-term)', 'ZQG (K)')
  -Search:modifications:variable_max_per_peptide <number>  Maximum number of residues carrying a variable 
                                                           modification per candidate peptide (default: '2') 
                                                           (min: '0' max: '5')

Annotation Options:
  -Search:annotate:PSM <list>                              Annotations added to each PSM. (default: '[ALL]') 
                                                           (valid: 'ALL', 'fragment_mz_error_median_ppm', 
                                                           'precursor_mz_error_ppm', 'matched_prefix_ions_fra
                                                           ction', 'matched_suffix_ions_fraction', 'num_match
                                                           ed_peaks', 'matched_prefix_ions', 'matched_suffix_
                                                           ions', 'longest_peptide_ion_sequence', 'matched_io
                                                           n_current', 'fragment_annotation', 'hyperscore_zsc
                                                           ore', 'ln_num_candidates', 'matched_ion_current_fr
                                                           action', 'complementary_ions_fraction')

PeptDeep (ONNX) prediction-based rescoring features:
  -Search:peptdeep:enable                                  Add PeptDeep prediction-based rescoring features 
                                                           (ms2_cosine, ms2_spectral_angle, ms2_pearson, ms2_
                                                           frac_pred_found, rt_abs_error) to every PSM. Uses 
                                                           the models shipped in OpenMS' 'share/OpenMS/models
                                                           ' unless 'peptdeep:ms2_model'/'peptdeep:rt_model' 
                                                           name others. Requires an OpenMS built with ONNX 
                                                           support.
  -Search:peptdeep:ms2_model <text>                        PeptDeep MS2 fragment-intensity ONNX model, used 
                                                           when 'peptdeep:enable' is true. A relative name 
                                                           is resolved against OpenMS' shared-data directory;
                                                            an absolute path is used as given. (default: 'mod
                                                           els/peptdeep_ms2_dynamic.onnx')
  -Search:peptdeep:rt_model <text>                         PeptDeep retention-time ONNX model. See 'peptdeep:
                                                           ms2_model'. (default: 'models/peptdeep_rt_dynamic.
                                                           onnx')
  -Search:peptdeep:instrument <choice>                     Instrument class passed to the PeptDeep MS2 model.
                                                            An instrument that is not in this list is best 
                                                           approximated by the closest one that is. (default:
                                                            'QE') (valid: 'QE', 'Lumos', 'timsTOF', 'SciexTOF
                                                           ', 'ThermoTOF')
  -Search:peptdeep:nce <value>                             Normalised collision energy for the PeptDeep MS2 
                                                           model. Negative selects it automatically from the 
                                                           collision energy recorded in the spectra, refined 
                                                           by scoring a small grid on confident PSMs. (defaul
                                                           t: '-1.0')

Peptide Options:
  -Search:peptide:min_size <number>                        Minimum size a peptide must have after digestion 
                                                           to be considered in the search. (default: '7') 
                                                           (min: '0')
  -Search:peptide:max_size <number>                        Maximum size a peptide must have after digestion 
                                                           to be considered in the search (0 = disabled). 
                                                           (default: '40') (min: '0')
  -Search:peptide:missed_cleavages <number>                Number of missed cleavages. (default: '1') (min: 
                                                           '0')
  -Search:peptide:clip_nterm_methionine <choice>           Also search protein N-terminal peptides after remo
                                                           val of their initial methionine. The retained-M 
                                                           form is still searched; length, mass and missed-cl
                                                           eavage limits apply to each form. Set false for 
                                                           the previous search space. (default: 'true') (vali
                                                           d: 'true', 'false')
  -Search:peptide:enzyme_specificity <choice>              Enzyme cleavage specificity required for both pept
                                                           ide termini.
                                                             'full' : both termini must be enzyme-specific 
                                                           (canonical, e.g. tryptic).
                                                             'semi' : only one terminus needs to be enzyme-sp
                                                           ecific (semi-tryptic).
                                                             'none' : no enzyme constraint at either terminus
                                                           ; every substring of length
                                                           ...
                                                           max_size'. (default: 'full') (valid: 'full', 'semi
                                                           ', 'none')
  -Search:peptide:motif <text>                             If set, only peptides whose unmodified sequence 
                                                           (one-letter codes) contains a match of this regula
                                                           r expression are searched, target and decoy peptid
                                                           es alike, e.g. 'N[^P][ST]' for N-glycosylation 
                                                           sequons or 'C' for cysteine-containing peptides; 
                                                           '^' and '$' anchor it to the peptide termini.
  -Search:peptide:min_mass <number>                        Minimal peptide mass for database (default: '100')
                                                            (min: '0')
  -Search:peptide:max_mass <number>                        Maximal peptide mass for database (default: '9000'
                                                           ) (min: '0')

Reporting Options:
  -Search:report:top_hits <number>                         Maximum number of top scoring hits per spectrum 
                                                           that are reported. With 'rescore', only the best 
                                                           hit per spectrum is reported after the rescoring, 
                                                           and the hits that Percolator rescores are set by 
                                                           'rescoring:top_hits' (report:top_hits then applies
                                                            to a run that is not rescored and to -out_pin). 
                                                           FDR:PSM > 0 and the protein FDR (FDR:protein > 0) 
                                                           also keep the best hit of each spectrum only, so 
                                                           values above 1 apply with 'rescore' false, FDR:PSM
                                                            0 and FDR:protein 0. (default: '1') (min: '1' 
                                                           max: '100')

False Discovery Rate control (requires decoys):
  -Search:FDR:PSM <value>                                  Filter PSMs based on q-value (e.g., 0.05 = 5% FDR;
                                                            0 disables the filter). Target and decoy PSMs 
                                                           are filtered alike by the threshold; decoys that 
                                                           pass are kept (no decoy-specific stripping here 
                                                           — decoys are removed only at protein-FDR finaliz
                                                           ation). With 'rescore' (the default), the threshol
                                                           d applies to the Percolator q-values, the main 
                                                           score of the rescored PSMs. Without rescoring ('re
                                                           ...
                                                            FDR:protein 0 (e.g. 0.1; see there). (default: 
                                                           '0.0') (min: '0.0' max: '1.0')
  -Search:FDR:protein <value>                              Picked-protein FDR threshold (e.g. 0.01 = 1 %), 
                                                           and the switch between the two modes of a search. 
                                                           Above 0, the search is the whole experiment: its 
                                                           proteins are inferred on the pooled PSMs of all 
                                                           its inputs, filtered at this protein FDR, and the 
                                                           PSMs filtered finally, so every output is the fina
                                                           l result (the decoys removed, see the ProSE tool's
                                                            -keep_decoys). With 0 (the default), the search 
                                                           ...
                                                           decoys ('decoys' auto or generate). (default: '0.0
                                                           ') (min: '0.0' max: '1.0')

Search/Scoring Limits:
  -Search:scoring:max_candidates_per_spectrum <number>     The number of initial hits for which we calculate 
                                                           a score (default: '50') (min: '1')

Theoretical ion series toggles:
  -Search:ions:add_y_ions <choice>                         Add peaks of y-ions to the spectrum (default: 'tru
                                                           e') (valid: 'true', 'false')
  -Search:ions:add_b_ions <choice>                         Add peaks of b-ions to the spectrum (default: 'tru
                                                           e') (valid: 'true', 'false')
  -Search:ions:add_a_ions                                  Add peaks of a-ions to the spectrum
  -Search:ions:add_c_ions                                  Add peaks of c-ions to the spectrum
  -Search:ions:add_x_ions                                  Add peaks of  x-ions to the spectrum
  -Search:ions:add_z_ions                                  Add peaks of z-ions (y - NH3) to the spectrum. 
                                                           These are not the z+1 ions of ETD-type spectra; 
                                                           see ions:by_activation and ions:add_zp1_ions.
  -Search:ions:add_zp1_ions                                Add peaks of z+1 ions (z-dot, y - NH2) to the spec
                                                           trum, the main C-terminal fragments of ETD, EThcD 
                                                           and ETciD spectra, for all spectra. ions:by_activa
                                                           tion adds them (with c ions) for spectra recorded 
                                                           as electron-activated; set this, typically with 
                                                           ions:add_c_ions, for ETD-type data without activat
                                                           ion information.
  -Search:ions:by_activation <choice>                      Score spectra whose precursor was activated by 
                                                           electrons (ETD, ECD, EThcD or ETciD, as recorded 
                                                           in the input file) with c and z+1 ions in addition
                                                            to the ion series above. Other spectra, and spect
                                                           ra without activation information, use the ion 
                                                           series above. (default: 'true') (valid: 'true', 
                                                           'false')

Automatic mass tolerances (two-pass search). A fast first pass on the most intense spectra measures the offse
t and spread of the precursor and fragment mass errors of the run; the main search uses windows derived from 
them, never wider than the configured tolerances.:
  -Search:calibration:enabled <choice>                     Measure the mass error of the run and search with 
                                                           windows derived from it: a fast calibration pass 
                                                           on the most intense spectra (calibration:subset_ra
                                                           tio), searched with at least 20 ppm (in Da: twice 
                                                           the configured window, up to 0.5 Da) precursor 
                                                           and fragment windows (the configured ones if wider
                                                           ) so the error is measured and not censored, takes
                                                            the offset (median) and the spread (robust standa
                                                           ...
                                                           configured tolerances as given. (default: 'true') 
                                                           (valid: 'true', 'false')
  -Search:calibration:subset_ratio <value>                 Fraction of spectra (by TIC, highest first) used 
                                                           for the calibration pass (0.0-1.0). (default: '0.1
                                                           ') (min: '0.01' max: '1.0')
  -Search:calibration:min_psms <number>                    Minimum number of confident PSMs required for cali
                                                           bration. If fewer are found, calibration is skippe
                                                           d and the user-configured tolerances are used. 
                                                           (default: '50') (min: '1')
  -Search:calibration:sigma_factor <value>                 Half-width of the calibrated fragment tolerance 
                                                           in robust standard deviations (1.4826 * MAD) of 
                                                           the signed errors of the matched fragment peaks 
                                                           of the calibration PSMs: |median| + k sigma. 4 
                                                           covers practically all correct matches of a normal
                                                            error distribution. (default: '4.0') (min: '1.0')

  -Search:calibration:precursor_sigma_factor <value>       Half-width of the calibrated precursor window in 
                                                           robust standard deviations of the precursor errors
                                                            of the calibration PSMs, around their median (asy
                                                           mmetric about zero when the run has an offset). 0 
                                                           keeps the configured precursor window and only 
                                                           measures and reports the errors: precursor yields 
                                                           are flat from 5 to 50 ppm, and a tightened precurs
                                                           or window cost identifications on every Orbitrap 
                                                           ...
                                                           98 % of the calibration PSMs. (default: '0.0') 
                                                           (min: '0.0')
  -Search:calibration:min_precursor_tolerance <value>      Smallest calibrated precursor tolerance per side, 
                                                           in precursor:mass_tolerance_unit (0: 2.5 ppm or 
                                                           0.005 Da). The calibrated window never exceeds 
                                                           the configured one. (default: '0.0') (min: '0.0')
  -Search:calibration:min_fragment_tolerance <value>       Smallest calibrated fragment tolerance, in fragmen
                                                           t:mass_tolerance_unit (0: 10 ppm or 0.02 Da; 5 
                                                           ppm or 0.01 Da with calibration:recalibrate). The 
                                                           calibrated tolerance never exceeds the configured 
                                                           one. (default: '0.0') (min: '0.0')
  -Search:calibration:recalibrate <choice>                 Correct the m/z of the spectra by the mass errors 
                                                           the calibration pass measures, before the main 
                                                           search: 'offset' subtracts the median error, 'line
                                                           ar' a line in m/z fitted to the errors (precursor 
                                                           errors against the precursor m/z, fragment errors 
                                                           against the fragment m/z), each per retention-time
                                                            chunk (calibration:recalibrate_rt_chunks) and 
                                                           interpolated between the chunks; a chunk of the 
                                                           ...
                                                           measures only. (default: 'offset') (valid: 'none',
                                                            'offset', 'linear')
  -Search:calibration:recalibrate_rt_chunks <number>       Retention-time chunks of the recalibration models 
                                                           (calibration:recalibrate): the calibration PSMs 
                                                           are split in acquisition order into this many grou
                                                           ps of equal size (fewer when a group would hold 
                                                           less than calibration:min_psms PSMs), one model 
                                                           each, interpolated between the groups' median rete
                                                           ntion times. 1: one model for the run; 10 follows 
                                                           an offset that changes over the run (the pass samp
                                                           les each tenth of it). (default: '10') (min: '1')

Search:database:
  -Search:database:chunk_size <number>                     Split the protein database into chunks of at most 
                                                           this many proteins for fragment index building. 0 
                                                           = disabled (load entire database at once). Enable 
                                                           for very large databases (e.g. MHC-II immunopeptid
                                                           omics with variants) that exceed available memory.
                                                            Each chunk builds its own fragment index; results
                                                            are merged across chunks before post-processing. 
                                                           Calibration (when enabled) runs on a strided, size
                                                           ...
                                                           cohorts across separate ProSE invocations. (defaul
                                                           t: '0') (min: '0')

Search of precursors co-isolated with the selected one (chimeric spectra).:
  -Search:chimeric:enabled                                 Also identify precursors co-isolated with the sele
                                                           cted one (after the andes chimeric cascade). The 
                                                           survey scan of each MS2 spectrum is searched for 
                                                           isotope envelopes in its isolation window that 
                                                           fit averagine (needs centroided MS1 spectra in 
                                                           the input and isolation windows on the precursors)
                                                           . After the search, the peaks the best hit of the 
                                                           spectrum explains are removed, and the rest is 
                                                           ...
                                                           with database:chunk_size > 0.
  -Search:chimeric:max_coisolated <number>                 At most this many co-isolated precursors per spect
                                                           rum, the most intense first. (default: '4') (min: 
                                                           '1')
  -Search:chimeric:max_kl <value>                          Largest Kullback-Leibler divergence of an isotope 
                                                           envelope in the survey scan from averagine (first 
                                                           four isotope peaks) to accept it as a co-isolated 
                                                           precursor. (default: '0.3') (min: '0.0')
  -Search:chimeric:top_hits <number>                       At most this many hits of a co-isolated precursor 
                                                           are reported (and at most report:top_hits). Each 
                                                           takes about as much memory as a hit of a spectrum.
                                                            (default: '3') (min: '1')
  -Search:chimeric:mz_tolerance <value>                    Tolerance (ppm) for the m/z of the isotope peaks 
                                                           in the survey scan. (default: '10.0') (min: '0.0')


                                                           
Common TOPP options:
  -ini <file>                                              Use the given TOPP INI file
  -threads <n>                                             Sets the number of threads allowed to be used by 
                                                           the TOPP tool (0 = all available cores) (default: 
                                                           '1')
  -write_ini <file>                                        Writes the default configuration file
  --help                                                   Shows options
  --helphelp                                               Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

• Name The identifier used in configuration files and on the command line.
• Default value The value used if the parameter is not explicitly specified.
• Description A short explanation describing the purpose and behavior of the parameter.
• Tags Additional metadata associated with the parameter.
• Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+ProSEAnnotates bottom-up MS/MS spectra using ProSE.

version3.7.0-pre-nightly-2026-11-13 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ProSE'

in[] Input spectrum file(s). Multiple files are searched against the same database; the fragment index is built once and reused. An mzML file may also be given as a remote location (s3://bucket/run.mzML, http://, https:// or ftp://): it is streamed, not downloaded to disk.input file*.mzML, *.mzpeak, *.d, *.raw

database Input protein sequence database in FASTA format.input file*.fasta, *.fa, *.faa

out[] Output identification file(s), one per -in: idXML or an idparquet directory bundle (format by extension). Must have the same number of entries as -in.output file*.idXML, *.idparquet

out_idxml[] Deprecated alias of -out (same behaviour, idXML or idparquet by extension). Cannot be combined with -out.output file*.idXML, *.idparquet

out_qpx Output directory for QPX exchange format Parquet files. Writes per-input runs/.psm.parquet and runs/.pg.parquet, and quantms.psm.parquet and quantms.pg.parquet of the whole run (see also -qpx_extended): the folder is one QPX dataset (prefix quantms). The pg files are written only when protein groups were actually inferred, which needs 'FDR:protein' > 0 (with decoys), or '-out_merged' with more than one input; an identification-only run produces no pg file rather than an empty one. The Parquet files of an earlier run in the folder (quantms.*.parquet, runs/*.parquet) are removed.output dir

out_parquet Output directory for OpenMS internal format Parquet files. Writes per-input runs/.psm/proteins/pg/search_params.parquet, and openms.psm/proteins/pg/search_params.parquet of the whole run: the folder is one dataset (prefix openms). With several inputs and 'FDR:protein' > 0 or -out_merged also merged.proteins.parquet and merged.pg.parquet (the pooled proteins). The Parquet files of an earlier run in the folder (openms.*.parquet, merged.*.parquet, runs/*.parquet) are removed.output dir

out_merged Optional output of all PSMs pooled across the input files, with a protein inference across them (BasicProteinInferenceAlgorithm) and, with 'Search:FDR:protein' > 0, the picked-protein FDR (see the tool documentation, 'Final results vs. intermediates'). Only useful with multiple -in files. idXML or an idparquet directory bundle (format by extension).output file*.idXML, *.idparquet

out_pin[] Output Percolator input (.pin/.tsv) file(s) for external rescoring. Must have the same number of entries as -in. It holds the PSMs before the rescoring and before any FDR filter, with ProSE's own scores and all reported hits: 'Search:rescore' and 'Search:FDR:*' apply to the other outputs only.output file*.tsv

out_mod_analysis_dir Optional directory to write modification-analysis tables (delta-mass, PTM stats) when running in open-search mode. When set, per-file tables are written using each input file's basename and an additional aggregate table is written across all input files. The analysis covers the PSMs of each input that pass 'Search:FDR:PSM', before the protein FDR (the evidence for the mass shifts, also of PSMs whose proteins the protein FDR removes). Has no effect in closed-search mode.output dir

summary_out Optional YAML file capturing the end-of-search report (per-file identification statistics, shared configuration/database/index facts, timing and output manifest) for pipeline ingestion. The same information is printed to the command line unless -no_summary is set.output file*.yaml

no_summaryfalse Suppress the end-of-search report printed to the command line. The -summary_out YAML file (if requested) is still written.true, false

qpx_extendedfalse With -out_qpx: add optional columns to the QPX psm view (all scores in 'additional_scores', 'spectrum_reference', 'isotope_error', 'protein_mappings'; in the per-input files also PeptDeep's predicted b/y intensities) and write the QPX mz view of the spectra of each input's PSMs (filtered peaks, see -qpx_peak_top) and the QPX run, sample and provenance views (quantms.run/sample/provenance.parquet: the inputs with their statistics, the steps of the search with their parameters); a run without protein inference gets one protein group per protein. See the tool documentation.true, false

qpx_peak_window100.0 -qpx_extended: the m/z window of the peak filter of the mz view.1.0:∞

qpx_peak_top100 -qpx_extended: the most intense peaks kept per -qpx_peak_window (with every annotated peak); 0 keeps all peaks.0:∞

keep_decoysfalse Keep the decoy PSMs and proteins that pass the FDR thresholds in the outputs of a final result (Search:FDR:protein > 0; see the tool documentation, 'Final results vs. intermediates').true, false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool (0 = all available cores)

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false

+++Search

enzymeTrypsin The enzyme used for peptide digestion.Chymotrypsin/P, CNBr, Formic_acid, Lys-C, Lys-N, Lys-C/P, PepsinA, TrypChymo, Trypsin/P, V8-DE, V8-E, leukocyte elastase, proline endopeptidase, Trypsin, glutamyl endopeptidase, Alpha-lytic protease, 2-iodobenzoate, iodosobenzoate, staphylococcal protease/D, proline-endopeptidase/HKR, Glu-C+P, PepsinA + P, cyanogen-bromide, Clostripain/P, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage, Arg-C, Arg-C/P, Asp-N, Asp-N/B, Asp-N_ambic, Chymotrypsin

decoysgenerate Decoy handling for target-decoy FDR. 'auto': ensure decoys are available — reuse decoys already present in the database (marker auto-detected, prefix or suffix) or generate them if none are found. Supplied decoys are reused only at 0.5 to 2 decoys per target protein: target-decoy FDR needs about one decoy per target, so a database with far fewer or more is refused (use 'generate'). 'generate': always (re)generate decoys from the target proteins (any pre-existing decoys are removed first to avoid decoy-of-decoy entries). 'ignore': search the target proteins only — any decoys present in the database are removed.auto, generate, ignore

decoy_prefixDECOY_ Accession prefix prepended to decoy proteins when ProSE generates them (modes 'auto' without existing decoys, and 'generate'). Pre-existing decoys in the database are detected automatically (any common marker, used as prefix or suffix) and do not require this setting.

decoy_methodkeep_termini How ProSE generates decoys (decoys 'generate', or 'auto' with a database without decoys). 'reverse' (ProSEAlgorithm's default; the ProSE tool's default is 'keep_termini'): every enzymatic segment of the protein is reversed except its last residue (the last segment entirely), an initial Met stays first with peptide:clip_nterm_methionine. 'keep_termini': the construction of OpenMS DecoyDatabase (method reverse, Decoy:keepPeptideNTerm/keepPeptideCTerm true) with the search enzyme and as Decoy:non_shuffle_pattern the residues that the enzyme's cleavage rule names and P (K, R, X and P for Trypsin and Trypsin/P, for Trypsin/P the decoys of 'K,P,R'; F, Y, W, L, J, X and P for Chymotrypsin): in every segment of a digest without missed cleavages, the first and the last residue and every one of these residues stay in place and the rest is reversed. The decoys then have the cleavage sites of their targets, and every target peptide has a decoy with the same start, length, mass and cleavage sites: also every protein N-terminal and Met-clipped one, so that peptide:clip_nterm_methionine and protein N-terminal modifications add the same number of target and decoy candidates (except peptides that equal their decoy, e.g. made of short segments or of residues kept in place only; and modifications specific to a peptide's first residue, e.g. pyro-Glu on an N-terminal Q, apply to the target and its decoy alike only where that residue is kept in place). Semi- or non-specific digestion: as 'reverse'. A warning names the decoys whose cleavage sites differ from the target's (none with the enzymes of OpenMS). No effect on decoys taken from the database (decoys 'auto' with decoys in it). The results differ from 'reverse'.reverse, keep_termini

decoy_parity_reportfalse Diagnostic: log the candidate counts of the fragment index per label (target, decoy) and subclass (internal, protein N-terminal with and without initial M, Met-clipped; and their protein N-terminally acetylated occurrences, none with a fixed N-terminal modification such as TMT, which leaves no room for a variable one), and a checksum of generated decoys. Output unchanged.true, false

low_memoryfalse Non-specific searches (peptide:enzyme_specificity=none; ignored otherwise): index the peptide masses, as the prefixes of one mother peptide per protein position, instead of the fragments of every peptidoform, and generate the fragments of the peptidoforms in the precursor window at query time. Finds the same candidates with a fraction of the memory (e.g. for immunopeptidomics against a human database), but takes more time per spectrum, the more the wider the precursor window.true, false

rescoretrue Rescore the PSMs of every search run (input file) in-process with Percolator (OpenMS' built-in implementation, as PercolatorAdapter uses by default) before the FDR filters: Percolator q-values become the main score (the SVM score and PEP are kept as meta values), Percolator rescores the top 'rescoring:top_hits' hits of each spectrum and only its best one per spectrum is kept, and FDR:PSM and FDR:protein are applied to the rescored PSMs. Needs decoys (see 'decoys') and at least 100 PSMs: a run without them, or for which Percolator fails, is not rescored and keeps its search engine scores, which the FDR filters then use (the ProSE tool warns). If that happens to some files of a multi-file search, the files rescored on their own keep their results, and the others get the scores of a model trained on the PSMs of those (on the scale of its training PSMs, with their PEP at the same score; q-values by target-decoy competition of each file's PSMs on that score); if Percolator can rescore no file on its own, all files are rescored together with one model. Only if that fails too, the files keep their search engine scores, and the pooled evaluation of the files (the ProSE tool's -out_merged) scores the proteins by ProSE's score 'ln(hyperscore)' of all PSMs instead of Percolator's PEP. See percolator:max_train_psms for the training PSMs. Set to 'false' to report the search engine scores. Keep it on for intermediates (FDR:protein 0) that ProteomicsLFQ finishes: it takes the PEP (meta value MS:1001493) as main score and stops for an input without PEPs.true, false

rescore_solvernewton Solver of Percolator's SVMs with 'rescore' (Percolator's parameter 'solver'): 'newton' (default; explicit-Hessian Newton method with exact line search and warm starts: the same SVM optimum for a given training set as TRON, within the solver tolerance, much faster on large runs; as the earlier iterations of the cross-validation stop at a looser tolerance, they may choose slightly different training sets, so the models can differ from TRON's), 'tron' (Percolator's trust region Newton method, the solver of the percolator executable and of earlier ProSE versions) or 'lda' (Fisher's linear discriminant instead of the SVM: fastest, an approximation).newton, tron, lda

rescore_methodpercolator With 'rescore': 'percolator' = Percolator's PSM-level FDR (default); 'reset' = Percolator-RESET (Freestone et al., J Proteome Res 2025): half of the decoy peptides (stems = unmodified sequences, by a random coin per stem) train the model, the other half estimates the FDR, which is controlled at the peptide (stem) level: every rescored hit gets the q-value of its stem as meta value 'RESET:peptide_q_value'. The main score (q-value) stays PSM-level, but under RESET it is a heuristic (not FDR-controlled): 2 (estimating decoy PSMs + 1) / target PSMs. Experimental.percolator, reset

++++precursorPrecursor (Parent Ion) Options. mass_tolerance_lower/_upper are positive magnitudes applied as [-lower, +upper] around the precursor mass.

mass_tolerance_lower10.0 Lower-side precursor-mass tolerance (positive magnitude; effective window is [-lower, +upper] around the precursor). When strongly asymmetric, also review precursor:isotope_error_min.0.0:∞

mass_tolerance_upper10.0 Upper-side precursor-mass tolerance (positive magnitude).0.0:∞

mass_tolerance_unitppm Unit of precursor mass tolerance.ppm, Da

min_charge2 Minimum precursor charge to be considered. Spectra without a precursor charge are searched with every charge of the range; spectra whose recorded charge lies outside of it are searched at that charge, or not at all with precursor:recorded_charge_outside_range 'skip'.1:20

max_charge5 Maximum precursor charge to be considered (see precursor:min_charge).1:20

recorded_charge_outside_rangeskip A spectrum whose recorded precursor charge lies outside of precursor:min_charge..max_charge: 'skip' (the default, as OpenMS develop since #10713) does not search it; 'search' (the behaviour before #10713) searches it at its recorded charge, up to charge 20. Spectra without a recorded charge are searched with every charge of the range.search, skip

isotope_error_min-2 Minimum precursor isotope error searched, in 13C spacings (1.00336 Da) added to the observed precursor mass: -1 finds a peptide whose first 13C isotope peak was selected as the precursor. The PSM meta value 'isotope_error' reports the opposite sign by default (see report:isotope_error_convention).-5:5

isotope_error_max1 Maximum precursor isotope error searched, with the sign of precursor:isotope_error_min: +1 finds a peptide whose precursor was selected one 13C spacing below its monoisotopic peak.-5:5

++++fragmentFragments (Product Ion) Options

mass_tolerance20.0 Fragment mass tolerance

mass_tolerance_unitppm Unit of fragment mppm, Da

deisotopeauto MS2 deisotoping (single-charge deconvolution) before searching. 'auto' deisotopes only when the fragment tolerance is within the high-resolution deisotoper range (<= 0.1 Da / <= 100 ppm) and skips it for low-resolution (e.g. ion-trap CID) data; 'true' always deisotopes (requires a high-resolution fragment tolerance); 'false' never deisotopes.auto, true, false

deisotope_min_peaks2 Minimum number of peaks, the monoisotopic peak included, of an isotope envelope that MS2 deisotoping collapses into its monoisotopic peak. With 2 (Sage-like), an ion whose M+2 peak is lost in the noise loses its M+1 peak too, so the M+1 peak no longer takes a place in the per-window peak quota, and a multiply charged ion seen with two isotope peaks is converted to charge 1; in dense spectra (e.g. timsTOF) more of the two-peak multiply charged envelopes are chance pairs. 3 is the earlier behaviour.2:10

deisotope_charge_capprecursor Fragment charges that MS2 deisotoping tries. 'precursor' tries charges up to the precursor charge, but at most 3 (1-3 when the precursor charge is unknown): a fragment cannot carry more charges than its precursor, so a chance peak 1/3 Th above an ion of a 2+ precursor cannot turn the ion into a '3+' envelope at a wrong m/z. This is Sage-like; Sage caps at the precursor charge without the limit of 3 and counts an unknown charge as 3. 'none' tries charges 1-3 in every spectrum (the earlier behaviour).precursor, none

deisotope_sum_intensitytrue Give the monoisotopic peak of each isotope envelope the summed intensity of the envelope (Sage-like). 'false' keeps the monoisotopic peak's own intensity (the earlier behaviour).true, false

min_mz150 Minimal fragment mz for database0:∞

max_mz2000 Maximal fragment mz for database0:∞

min_ion_index2 Ions with index less than or equal to this value are not added to the fragment index (use 0 to include all ions; 2 skips b1/b2/y1/y2). Low-index ions are often noisy and unreliable.0:∞

query_spectrumauto Spectrum used for candidate retrieval. 'raw' queries the fragment index with all positive-intensity peaks, before deisotoping and local/top-N filtering, so that spectra whose matching fragments are not among the retained peaks still get candidates; it costs an additional peak list per spectrum and more fragment matches. 'processed' queries with the scoring peak list. 'auto' uses 'raw' for high-resolution fragments (<= 0.1 Da / <= 100 ppm) and 'processed' otherwise: at low resolution, the unfiltered peaks match many random fragments and crowd out the correct candidates. Scoring always uses the processed spectrum.auto, raw, processed

min_matched_ions5 Minimal number of matched ions to report a PSM0:1000

max_charge2 max fragment charge1:10

++++peaks

keep_n0 Maximum number of MS2 peaks kept per spectrum (NLargest) before scoring. 0 = auto: a resolution-aware cap (~400 for high-res, ~80 at 0.5 Da, floor 60) that avoids the spurious low-resolution fragment matching which otherwise inflates HyperScore for targets and decoys alike. Set an explicit value to override (e.g. 400 for the legacy behavior).0:∞

window_top20 Maximum number of MS2 peaks kept per 100 Da window (WindowMower) before scoring.1:∞

window_typeauto Local peak filtering. 'auto' uses jump_full for high-resolution fragments (<= 0.1 Da / <= 100 ppm), preserving the strongest peaks even in a short final 100 Da window, and legacy jump filtering otherwise. 'jump' scales the last window's peak quota by its observed width; 'jump_full' keeps the full quota in every window.auto, jump, jump_full

++++modificationsModifications Options

fixed[Carbamidomethyl (C)] Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'15N-oxobutanoic (N-term C), 15N-oxobutanoic (Protein N-term S), 15N-oxobutanoic (Protein N-term T), 2-dimethylsuccinyl (C), 2-methylbutyryl (K), 2-monomethylsuccinyl (C), 2-nitrobenzyl (Y), 2-succinyl (C), 2HPG (R), 2PCA-triazole-ethanethiol (N-term), 3-deoxyglucosone (R), 3-hydroxy-3-methylglutaryl (K), 3-hydroxybenzyl-phosphate (K), 3-hydroxybenzyl-phosphate (S), 3-hydroxybenzyl-phosphate (T), 3-hydroxybenzyl-phosphate (Y), 3-methylglutaconyl (K), 3-methylglutaryl (K), 3-phosphoglyceryl (K), 3sulfo (N-term), 4-ONE (C), 4-ONE (H), 4-ONE (K), 4-ONE+Delta:H(-2)O(-1) (C), 4-ONE+Delta:H(-2)O(-1) (H), 4-ONE+Delta:H(-2)O(-1) (K), 4AcAllylGal (C), 6C-CysPAT (C), 6C-CysPAT (D), 6C-CysPAT (E), 6C-CysPAT (H), 6C-CysPAT (K), 6C-CysPAT (N-term), 6C-CysPAT (S), 6C-CysPAT (T), 6C-CysPAT (Y), a-type-ion (C-term), AccQTag (K), AccQTag (N-term), Acetoacetyl (K), Acetyl (C), Acetyl (H), Acetyl (K), Acetyl (N-term), Acetyl (Protein N-term), Acetyl (R), Acetyl (S), Acetyl (T), Acetyl (Y), Acetyl:13C(2) (K), Acetyl:13C(2) (Protein N-term), Acetyl:2H(3) (H), Acetyl:2H(3) (K), Acetyl:2H(3) (N-term), Acetyl:2H(3) (Protein N-term), Acetyl:2H(3) (S), Acetyl:2H(3) (T), Acetyl:2H(3) (Y), Acetyldeoxyhypusine (K), Acetylhypusine (K), ADP-Ribosyl (C), ADP-Ribosyl (D), ADP-Ribosyl (E), ADP-Ribosyl (K), ADP-Ribosyl (N), ADP-Ribosyl (R), ADP-Ribosyl (S), ADP-Ribosyl (T), AEBS (H), AEBS (K), AEBS (Protein N-term), AEBS (S), AEBS (Y), AEC-MAEC (S), AEC-MAEC (T), AEC-MAEC:2H(4) (S), AEC-MAEC:2H(4) (T), AFB1_Dialdehyde (K), AHA-Alkyne (M), AHA-Alkyne-KDDDD (M), AHA-SS (M), AHA-SS_CAM (M), Ahx2+Hsl (C-term), Ala->Arg (A), Ala->Asn (A), Ala->Asp (A), Ala->Cys (A), Ala->Gln (A), Ala->Glu (A), Ala->Gly (A), Ala->His (A), Ala->Lys (A), Ala->Met (A), Ala->Phe (A), Ala->Pro (A), Ala->Ser (A), Ala->Thr (A), Ala->Trp (A), Ala->Tyr (A), Ala->Val (A), Ala->Xle (A), Amidated (C-term), Amidated (Protein C-term), Amidine (K), Amidine (N-term), Amidino (C), Amino (Y), Ammonia-loss (N), Ammonia-loss (N-term C), Ammonia-loss (Protein N-term S), Ammonia-loss (Protein N-term T), Ammonium (C-term), Ammonium (D), Ammonium (E), AMTzHexNAc2 (N), AMTzHexNAc2 (S), AMTzHexNAc2 (T), Andro-H2O (C), Archaeol (C), Arg (N-term), Arg->Ala (R), Arg->Asn (R), Arg->Asp (R), Arg->Cys (R), Arg->Gln (R), Arg->Glu (R), Arg->GluSA (R), Arg->Gly (R), Arg->His (R), Arg->Lys (R), Arg->Met (R), Arg->Npo (R), Arg->Orn (R), Arg->Phe (R), Arg->Pro (R), Arg->Ser (R), Arg->Thr (R), Arg->Trp (R), Arg->Tyr (R), Arg->Val (R), Arg->Xle (R), Arg-loss (C-term R), Arg2PG (R), Argbiotinhydrazide (R), AROD (C), Asn->Ala (N), Asn->Arg (N), Asn->Asp (N), Asn->Cys (N), Asn->Gln (N), Asn->Glu (N), Asn->Gly (N), Asn->His (N), Asn->Lys (N), Asn->Met (N), Asn->Phe (N), Asn->Pro (N), Asn->Ser (N), Asn->Thr (N), Asn->Trp (N), Asn->Tyr (N), Asn->Val (N), Asn->Xle (N), Asp->Ala (D), Asp->Arg (D), Asp->Asn (D), Asp->Cys (D), Asp->Gln (D), Asp->Glu (D), Asp->Gly (D), Asp->His (D), Asp->Lys (D), Asp->Met (D), Asp->Phe (D), Asp->Pro (D), Asp->Ser (D), Asp->Thr (D), Asp->Trp (D), Asp->Tyr (D), Asp->Val (D), Asp->Xle (D), Aspartylurea (H), Atto495Maleimide (C), AzidoF (F), azole (C), azole (S), Bacillosamine (N), BADGE (C), BDMAPP (H), BDMAPP (K), BDMAPP (Protein N-term), BDMAPP (W), BDMAPP (Y), BEMAD_C (C), BEMAD_C:2H(6) (C), BEMAD_ST (S), BEMAD_ST (T), BEMAD_ST:2H(6) (S), BEMAD_ST:2H(6) (T), Benzoyl (K), Benzoyl (N-term), benzylguanidine (K), betaFNA (C), betaFNA (K), BHT (C), BHT (H), BHT (K), BHTOH (C), BHTOH (H), BHTOH (K), Biotin (K), Biotin (N-term), Biotin-HPDP (C), Biotin-PEG-PRA (M), Biotin-PEO-Amine (D), Biotin-PEO-Amine (E), Biotin-PEO-Amine (Protein C-term), Biotin-phenacyl (C), Biotin-phenacyl (H), Biotin-phenacyl (S), Biotin-tyramide (C), Biotin-tyramide (W), Biotin-tyramide (Y), Biotin:Aha-DADPS (M), Biotin:Aha-PC (M), Biotin:Cayman-10013 (C), Biotin:Cayman-10141 (C), Biotin:Invitrogen-M1602 (C), Biotin:Sigma-B1267 (C), Biotin:Thermo-21325 (K), Biotin:Thermo-21328 (K), Biotin:Thermo-21328 (N-term), Biotin:Thermo-21330 (K), Biotin:Thermo-21330 (N-term), Biotin:Thermo-21345 (Q), Biotin:Thermo-21360 (X), Biotin:Thermo-21901+2H2O (C), Biotin:Thermo-21901+H2O (C), Biotin:Thermo-21911 (C), Biotin:Thermo-33033 (X), Biotin:Thermo-33033-H (X), Biotin:Thermo-88310 (K), Biotin:Thermo-88317 (S), Biotin:Thermo-88317 (Y), biotinAcrolein298 (C), biotinAcrolein298 (H), biotinAcrolein298 (K), biotinAcrolein298 (Protein N-term), BisANS (K), bisANS-sulfonates (K), bisANS-sulfonates (S), bisANS-sulfonates (T), BITC (C), BITC (K), BITC (N-term), BMP-piperidinol (C), BMP-piperidinol (M), Brij35 (N-term), Brij58 (N-term), Bromo (F), Bromo (H), Bromo (W), Bromo (Y), Bromobimane (C), Butyryl (K), C8-QAT (K), C8-QAT (N-term), CAF (N-term), CAMthiopropanoyl (K), CAMthiopropanoyl (Protein N-term), Can-FP-biotin (S), Can-FP-biotin (T), Can-FP-biotin (Y), Carbamidomethyl (C), Carbamidomethyl (D), Carbamidomethyl (E), Carbamidomethyl (H), Carbamidomethyl (K), Carbamidomethyl (M), Carbamidomethyl (N-term), Carbamidomethyl (S), Carbamidomethyl (T), Carbamidomethyl (U), Carbamidomethyl (Y), CarbamidomethylDTT (C), Carbamyl (C), Carbamyl (K), Carbamyl (M), Carbamyl (N-term), Carbamyl (Protein N-term), Carbamyl (R), Carbamyl (S), Carbamyl (T), Carbamyl (Y), Carbofuran (S), Carbonyl (A), Carbonyl (E), Carbonyl (I), Carbonyl (L), Carbonyl (Q), Carbonyl (R), Carbonyl (S), Carbonyl (V), Carboxy (D), Carboxy (E), Carboxy (K), Carboxy (Protein N-term M), Carboxy (W), Carboxy->Thiocarboxy (Protein C-term G), Carboxyethyl (H), Carboxyethyl (K), Carboxyethylpyrrole (K), Carboxymethyl (C), Carboxymethyl (K), Carboxymethyl (N-term), Carboxymethyl (U), Carboxymethyl (W), Carboxymethyl:13C(2) (C), CarboxymethylDMAP (N-term), CarboxymethylDTT (C), Cation:Ag (C-term), Cation:Ag (D), Cation:Ag (E), Cation:Al[III] (C-term), Cation:Al[III] (D), Cation:Al[III] (E), Cation:Ca[II] (C-term), Cation:Ca[II] (D), Cation:Ca[II] (E), Cation:Cu[I] (C-term), Cation:Cu[I] (D), Cation:Cu[I] (E), Cation:Cu[I] (H), Cation:Fe[II] (C-term), Cation:Fe[II] (D), Cation:Fe[II] (E), Cation:Fe[III] (C-term), Cation:Fe[III] (D), Cation:Fe[III] (E), Cation:K (C-term), Cation:K (D), Cation:K (E), Cation:Li (C-term), Cation:Li (D), Cation:Li (E), Cation:Mg[II] (C-term), Cation:Mg[II] (D), Cation:Mg[II] (E), Cation:Na (C-term), Cation:Na (D), Cation:Na (E), Cation:Ni[II] (C-term), Cation:Ni[II] (D), Cation:Ni[II] (E), Cation:Zn[II] (C-term), Cation:Zn[II] (D), Cation:Zn[II] (E), Cation:Zn[II] (H), cGMP (C), cGMP (S), cGMP+RMP-loss (C), cGMP+RMP-loss (S), CHDH (D), Chlorination (W), Chlorination (Y), Cholesterol (Protein C-term), CIGG (K), CLIP_TRAQ_2 (K), CLIP_TRAQ_2 (N-term), CLIP_TRAQ_2 (Y), CLIP_TRAQ_3 (K), CLIP_TRAQ_3 (N-term), CLIP_TRAQ_3 (Y), CLIP_TRAQ_4 (K), CLIP_TRAQ_4 (N-term), CLIP_TRAQ_4 (Y), CoenzymeA (C), Cresylphosphate (H), Cresylphosphate (K), Cresylphosphate (R), Cresylphosphate (S), Cresylphosphate (T), Cresylphosphate (Y), CresylSaligeninPhosphate (H), CresylSaligeninPhosphate (K), CresylSaligeninPhosphate (R), CresylSaligeninPhosphate (S), CresylSaligeninPhosphate (T), CresylSaligeninPhosphate (Y), Crotonaldehyde (C), Crotonaldehyde (H), Crotonaldehyde (K), Crotonyl (K), CuSMo (C), CUSTOM0 (A), CUSTOM0 (C), CUSTOM0 (C-term), CUSTOM0 (D), CUSTOM0 (E), CUSTOM0 (F), CUSTOM0 (G), CUSTOM0 (H), CUSTOM0 (I), CUSTOM0 (K), CUSTOM0 (L), CUSTOM0 (M), CUSTOM0 (N), CUSTOM0 (N-term), CUSTOM0 (P), CUSTOM0 (Q), CUSTOM0 (R), CUSTOM0 (S), CUSTOM0 (T), CUSTOM0 (V), CUSTOM0 (W), CUSTOM0 (Y), CUSTOM1 (A), CUSTOM1 (C), CUSTOM1 (C-term), CUSTOM1 (D), CUSTOM1 (E), CUSTOM1 (F), CUSTOM1 (G), CUSTOM1 (H), CUSTOM1 (I), CUSTOM1 (K), CUSTOM1 (L), CUSTOM1 (M), CUSTOM1 (N), CUSTOM1 (N-term), CUSTOM1 (P), CUSTOM1 (Q), CUSTOM1 (R), CUSTOM1 (S), CUSTOM1 (T), CUSTOM1 (V), CUSTOM1 (W), CUSTOM1 (Y), CUSTOM2 (A), CUSTOM2 (C), CUSTOM2 (C-term), CUSTOM2 (D), CUSTOM2 (E), CUSTOM2 (F), CUSTOM2 (G), CUSTOM2 (H), CUSTOM2 (I), CUSTOM2 (K), CUSTOM2 (L), CUSTOM2 (M), CUSTOM2 (N), CUSTOM2 (N-term), CUSTOM2 (P), CUSTOM2 (Q), CUSTOM2 (R), CUSTOM2 (S), CUSTOM2 (T), CUSTOM2 (V), CUSTOM2 (W), CUSTOM2 (Y), CUSTOM3 (A), CUSTOM3 (C), CUSTOM3 (C-term), CUSTOM3 (D), CUSTOM3 (E), CUSTOM3 (F), CUSTOM3 (G), CUSTOM3 (H), CUSTOM3 (I), CUSTOM3 (K), CUSTOM3 (L), CUSTOM3 (M), CUSTOM3 (N), CUSTOM3 (N-term), CUSTOM3 (P), CUSTOM3 (Q), CUSTOM3 (R), CUSTOM3 (S), CUSTOM3 (T), CUSTOM3 (V), CUSTOM3 (W), CUSTOM3 (Y), CUSTOM4 (A), CUSTOM4 (C), CUSTOM4 (C-term), CUSTOM4 (D), CUSTOM4 (E), CUSTOM4 (F), CUSTOM4 (G), CUSTOM4 (H), CUSTOM4 (I), CUSTOM4 (K), CUSTOM4 (L), CUSTOM4 (M), CUSTOM4 (N), CUSTOM4 (N-term), CUSTOM4 (P), CUSTOM4 (Q), CUSTOM4 (R), CUSTOM4 (S), CUSTOM4 (T), CUSTOM4 (V), CUSTOM4 (W), CUSTOM4 (Y), CUSTOM5 (A), CUSTOM5 (C), CUSTOM5 (C-term), CUSTOM5 (D), CUSTOM5 (E), CUSTOM5 (F), CUSTOM5 (G), CUSTOM5 (H), CUSTOM5 (I), CUSTOM5 (K), CUSTOM5 (L), CUSTOM5 (M), CUSTOM5 (N), CUSTOM5 (N-term), CUSTOM5 (P), CUSTOM5 (Q), CUSTOM5 (R), CUSTOM5 (S), CUSTOM5 (T), CUSTOM5 (V), CUSTOM5 (W), CUSTOM5 (Y), CUSTOM6 (A), CUSTOM6 (C), CUSTOM6 (C-term), CUSTOM6 (D), CUSTOM6 (E), CUSTOM6 (F), CUSTOM6 (G), CUSTOM6 (H), CUSTOM6 (I), CUSTOM6 (K), CUSTOM6 (L), CUSTOM6 (M), CUSTOM6 (N), CUSTOM6 (N-term), CUSTOM6 (P), CUSTOM6 (Q), CUSTOM6 (R), CUSTOM6 (S), CUSTOM6 (T), CUSTOM6 (V), CUSTOM6 (W), CUSTOM6 (Y), CUSTOM7 (A), CUSTOM7 (C), CUSTOM7 (C-term), CUSTOM7 (D), CUSTOM7 (E), CUSTOM7 (F), CUSTOM7 (G), CUSTOM7 (H), CUSTOM7 (I), CUSTOM7 (K), CUSTOM7 (L), CUSTOM7 (M), CUSTOM7 (N), CUSTOM7 (N-term), CUSTOM7 (P), CUSTOM7 (Q), CUSTOM7 (R), CUSTOM7 (S), CUSTOM7 (T), CUSTOM7 (V), CUSTOM7 (W), CUSTOM7 (Y), CUSTOM8 (A), CUSTOM8 (C), CUSTOM8 (C-term), CUSTOM8 (D), CUSTOM8 (E), CUSTOM8 (F), CUSTOM8 (G), CUSTOM8 (H), CUSTOM8 (I), CUSTOM8 (K), CUSTOM8 (L), CUSTOM8 (M), CUSTOM8 (N), CUSTOM8 (N-term), CUSTOM8 (P), CUSTOM8 (Q), CUSTOM8 (R), CUSTOM8 (S), CUSTOM8 (T), CUSTOM8 (V), CUSTOM8 (W), CUSTOM8 (Y), CUSTOM9 (A), CUSTOM9 (C), CUSTOM9 (C-term), CUSTOM9 (D), CUSTOM9 (E), CUSTOM9 (F), CUSTOM9 (G), CUSTOM9 (H), CUSTOM9 (I), CUSTOM9 (K), CUSTOM9 (L), CUSTOM9 (M), CUSTOM9 (N), CUSTOM9 (N-term), CUSTOM9 (P), CUSTOM9 (Q), CUSTOM9 (R), CUSTOM9 (S), CUSTOM9 (T), CUSTOM9 (V), CUSTOM9 (W), CUSTOM9 (Y), Cy3-maleimide (C), Cy3b-maleimide (C), Cyano (C), CyDye-Cy3 (C), CyDye-Cy5 (C), Cys->Ala (C), Cys->Arg (C), Cys->Asn (C), Cys->Asp (C), Cys->CamSec (C), Cys->Dha (C), Cys->ethylaminoAla (C), Cys->Gln (C), Cys->Glu (C), Cys->Gly (C), Cys->His (C), Cys->Lys (C), Cys->Met (C), Cys->methylaminoAla (C), Cys->Oxoalanine (C), Cys->Phe (C), Cys->Pro (C), Cys->PyruvicAcid (Protein N-term C), Cys->SecNEM (C), Cys->SecNEM:2H(5) (C), Cys->Ser (C), Cys->Thr (C), Cys->Trp (C), Cys->Tyr (C), Cys->Val (C), Cys->Xle (C), Cysteinyl (C), cysTMT (C), cysTMT6plex (C), Cytopiloyne (C), Cytopiloyne (K), Cytopiloyne (N-term), Cytopiloyne (P), Cytopiloyne (R), Cytopiloyne (S), Cytopiloyne (Y), Cytopiloyne+water (C), Cytopiloyne+water (K), Cytopiloyne+water (N-term), Cytopiloyne+water (R), Cytopiloyne+water (S), Cytopiloyne+water (T), Cytopiloyne+water (Y), DABCYL-C2-maleimide (C), DABCYL-C2-maleimide (K), DAET (S), DAET (T), Dansyl (K), Dansyl (N-term), Dap-DSP (A), Dap-DSP (E), Dap-DSP (K), DBIA (C), DCP (C), Deamidated (N), Deamidated (Protein N-term F), Deamidated (Q), Deamidated (R), Deamidated:18O(1) (N), Deamidated:18O(1) (Q), Decanoyl (S), Decanoyl (T), Decarboxylation (D), Decarboxylation (E), DEDGFLYMVYASQETFG (K), Dehydrated (D), Dehydrated (N-term C), Dehydrated (Protein C-term N), Dehydrated (Protein C-term Q), Dehydrated (S), Dehydrated (T), Dehydrated (Y), Dehydro (C), Delta:H(-1)N(-1)18O(1) (N), Delta:H(-4)O(2) (W), Delta:H(-4)O(3) (W), Delta:H(10)C(8)O(1) (K), Delta:H(2)C(2) (H), Delta:H(2)C(2) (K), Delta:H(2)C(2) (N-term), Delta:H(2)C(2) (Protein N-term), Delta:H(2)C(3) (K), Delta:H(2)C(3)O(1) (K), Delta:H(2)C(3)O(1) (R), Delta:H(2)C(5) (K), Delta:H(4)C(2) (H), Delta:H(4)C(2) (K), Delta:H(4)C(2) (N-term), Delta:H(4)C(2)O(-1)S(1) (S), Delta:H(4)C(3) (H), Delta:H(4)C(3) (K), Delta:H(4)C(3) (Protein N-term), Delta:H(4)C(3)O(1) (C), Delta:H(4)C(3)O(1) (H), Delta:H(4)C(3)O(1) (K), Delta:H(4)C(3)O(1) (R), Delta:H(4)C(3)O(2) (K), Delta:H(4)C(5)O(1) (R), Delta:H(4)C(6) (K), Delta:H(5)C(2) (P), Delta:H(6)C(3)O(1) (C), Delta:H(6)C(3)O(1) (H), Delta:H(6)C(3)O(1) (K), Delta:H(6)C(3)O(1) (Protein N-term), Delta:H(6)C(6)O(1) (K), Delta:H(6)C(7)O(4) (R), Delta:H(8)C(6)O(1) (K), Delta:H(8)C(6)O(1) (Protein N-term), Delta:H(8)C(6)O(2) (K), Delta:Hg(1) (C), Delta:O(4) (W), Delta:S(-1)Se(1) (C), Delta:S(-1)Se(1) (M), Delta:Se(1) (C), Deoxy (D), Deoxy (S), Deoxy (T), Deoxyhypusine (K), Deoxyhypusine (Q), DeStreak (C), Dethiomethyl (M), dHex (N), dHex (S), dHex (T), dHex(1)Hex(1) (S), dHex(1)Hex(1) (T), dHex(1)Hex(1)HexA(1)HexNAc(3) (S), dHex(1)Hex(1)HexA(1)HexNAc(3) (T), dHex(1)Hex(1)HexNAc(1)Kdn(1) (S), dHex(1)Hex(1)HexNAc(1)Kdn(1) (T), dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S), dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T), dHex(1)Hex(1)HexNAc(2)Kdn(1) (S), dHex(1)Hex(1)HexNAc(2)Kdn(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T), dHex(1)Hex(1)HexNAc(2)Sulf(1) (S), dHex(1)Hex(1)HexNAc(2)Sulf(1) (T), dHex(1)Hex(1)HexNAc(3) (S), dHex(1)Hex(1)HexNAc(3) (T), dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S), dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T), dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S), dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T), dHex(1)Hex(1)HexNAc(3)Sulf(1) (S), dHex(1)Hex(1)HexNAc(3)Sulf(1) (T), dHex(1)Hex(1)HexNAc(4) (S), dHex(1)Hex(1)HexNAc(4) (T), dHex(1)Hex(2) (S), dHex(1)Hex(2) (T), dHex(1)Hex(2)HexA(1) (S), dHex(1)Hex(2)HexA(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(1) (S), dHex(1)Hex(2)HexA(1)HexNAc(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S), dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(2) (S), dHex(1)Hex(2)HexA(1)HexNAc(2) (T), dHex(1)Hex(2)HexNAc(1) (S), dHex(1)Hex(2)HexNAc(1) (T), dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S), dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T), dHex(1)Hex(2)HexNAc(1)Sulf(1) (S), dHex(1)Hex(2)HexNAc(1)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T), dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S), dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T), dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S), dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T), dHex(1)Hex(2)HexNAc(2)Pent(1) (N), dHex(1)Hex(2)HexNAc(2)Sulf(1) (S), 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dHex(2)Hex(4)HexNAc(2) (N), dHex(2)Hex(4)HexNAc(2) (S), dHex(2)Hex(4)HexNAc(2) (T), dHex(2)Hex(4)HexNAc(3) (N), dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N), dHex(2)Hex(4)HexNAc(3)Pent(1) (N), dHex(2)Hex(4)HexNAc(4) (N), dHex(2)Hex(4)HexNAc(4) (S), dHex(2)Hex(4)HexNAc(4) (T), dHex(2)Hex(4)HexNAc(4)Pent(1) (N), dHex(2)Hex(4)HexNAc(4)Sulf(1) (N), dHex(2)Hex(4)HexNAc(5) (N), dHex(2)Hex(4)HexNAc(5) (S), dHex(2)Hex(4)HexNAc(5) (T), dHex(2)Hex(5)HexNAc(2)Me(1) (S), dHex(2)Hex(5)HexNAc(2)Me(1) (T), dHex(2)Hex(5)HexNAc(3)Pent(1) (N), dHex(2)Hex(5)HexNAc(4) (N), dHex(2)HexNAc(2)Kdn(1) (S), dHex(2)HexNAc(2)Kdn(1) (T), dHex(2)HexNAc(5) (S), dHex(2)HexNAc(5) (T), dHex(2)HexNAc(7) (S), dHex(2)HexNAc(7) (T), dHex(3)Hex(1)HexNAc(2)Kdn(1) (S), dHex(3)Hex(1)HexNAc(2)Kdn(1) (T), dHex(3)Hex(1)HexNAc(3)Kdn(1) (S), dHex(3)Hex(1)HexNAc(3)Kdn(1) (T), dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S), dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T), dHex(3)Hex(2)HexNAc(2) (S), dHex(3)Hex(2)HexNAc(2) (T), dHex(3)Hex(2)HexNAc(2)Kdn(1) (S), dHex(3)Hex(2)HexNAc(2)Kdn(1) (T), dHex(3)Hex(2)HexNAc(3) (S), dHex(3)Hex(2)HexNAc(3) (T), dHex(3)Hex(2)HexNAc(3)Kdn(1) (S), dHex(3)Hex(2)HexNAc(3)Kdn(1) (T), dHex(3)Hex(2)HexNAc(4) (S), dHex(3)Hex(2)HexNAc(4) (T), dHex(3)Hex(2)HexNAc(4)Sulf(2) (S), dHex(3)Hex(2)HexNAc(4)Sulf(2) (T), dHex(3)Hex(3)HexNAc(1) (S), dHex(3)Hex(3)HexNAc(1) (T), dHex(3)Hex(3)HexNAc(2) (S), dHex(3)Hex(3)HexNAc(2) (T), dHex(3)Hex(3)HexNAc(3) (S), dHex(3)Hex(3)HexNAc(3) (T), dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S), dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T), dHex(3)Hex(3)HexNAc(3)Pent(1) (N), dHex(3)Hex(3)HexNAc(4) (N), dHex(3)Hex(3)HexNAc(4)Pent(1) (N), dHex(3)Hex(4)HexNAc(4) (N), dHex(3)Hex(4)HexNAc(4) (S), dHex(3)Hex(4)HexNAc(4) (T), dHex(3)Hex(4)HexNAc(4)Sulf(1) (N), dHex(3)HexNAc(3)Kdn(1) (S), dHex(3)HexNAc(3)Kdn(1) (T), dHex(4)Hex(1)HexNAc(1)Kdn(2) (S), dHex(4)Hex(1)HexNAc(1)Kdn(2) (T), dHex(4)Hex(1)HexNAc(2)Kdn(1) (S), dHex(4)Hex(1)HexNAc(2)Kdn(1) (T), dHex(4)Hex(1)HexNAc(3)Kdn(1) (S), dHex(4)Hex(1)HexNAc(3)Kdn(1) (T), dHex(4)Hex(2)HexNAc(2)Kdn(1) (S), dHex(4)Hex(2)HexNAc(2)Kdn(1) (T), dHex(4)Hex(2)HexNAc(3) (S), dHex(4)Hex(2)HexNAc(3) (T), dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S), dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T), dHex(4)Hex(3)HexNAc(3) (S), dHex(4)Hex(3)HexNAc(3) (T), dHex(4)HexNAc(3)Kdn(1) (S), dHex(4)HexNAc(3)Kdn(1) (T), DHP (C), Di_L-Gln_Ngamma-propargyl-L-Gln_desthiobiotin (D), Di_L-Gln_Ngamma-propargyl-L-Gln_desthiobiotin (E), Di_L-Glu_Ngamma-propargyl-L-Gln_desthiobiotin (D), Di_L-Glu_Ngamma-propargyl-L-Gln_desthiobiotin (E), Diacylglycerol (C), DiART6plex (K), DiART6plex (N-term), DiART6plex (Protein N-term), DiART6plex (Y), DiART6plex115 (K), DiART6plex115 (N-term), DiART6plex115 (Protein N-term), DiART6plex115 (Y), DiART6plex116/119 (K), DiART6plex116/119 (N-term), DiART6plex116/119 (Protein N-term), DiART6plex116/119 (Y), DiART6plex117 (K), DiART6plex117 (N-term), DiART6plex117 (Protein N-term), DiART6plex117 (Y), DiART6plex118 (K), DiART6plex118 (N-term), DiART6plex118 (Protein N-term), DiART6plex118 (Y), Dibromo (Y), Dicarbamidomethyl (C), Dicarbamidomethyl (H), Dicarbamidomethyl (K), Dicarbamidomethyl (N-term), Dicarbamidomethyl (R), dichlorination (C), dichlorination (Y), Didehydro (C-term K), Didehydro (S), Didehydro (T), Didehydro (Y), Didehydroretinylidene (K), Diethyl (K), Diethyl (N-term), Diethylphosphate (C), Diethylphosphate (H), Diethylphosphate (K), Diethylphosphate (N-term), Diethylphosphate (S), Diethylphosphate (T), Diethylphosphate (Y), Diethylphosphothione (C), Diethylphosphothione (H), Diethylphosphothione (K), Diethylphosphothione (S), Diethylphosphothione (T), Diethylphosphothione (Y), Difuran (Y), Dihydroxyimidazolidine (R), Diiodo (H), Diiodo (Y), Diironsubcluster (C), Diisopropylphosphate (K), Diisopropylphosphate (N-term), Diisopropylphosphate (S), Diisopropylphosphate (T), Diisopropylphosphate (Y), DiLeu4plex (K), DiLeu4plex (N-term), DiLeu4plex (Y), DiLeu4plex115 (K), DiLeu4plex115 (N-term), DiLeu4plex115 (Y), DiLeu4plex117 (K), DiLeu4plex117 (N-term), DiLeu4plex117 (Y), DiLeu4plex118 (K), DiLeu4plex118 (N-term), DiLeu4plex118 (Y), Dimethyl (K), Dimethyl (N), Dimethyl (N-term), Dimethyl (Protein N-term P), Dimethyl (Protein N-term), Dimethyl (R), Dimethyl:2H(2)13C (K), Dimethyl:2H(2)13C (N), Dimethyl:2H(2)13C (N-term), Dimethyl:2H(2)13C (Protein N-term P), Dimethyl:2H(2)13C (R), Dimethyl:2H(4) (K), Dimethyl:2H(4) (N-term), Dimethyl:2H(4) (Protein N-term), Dimethyl:2H(4) (R), Dimethyl:2H(4)13C(2) (K), Dimethyl:2H(4)13C(2) (N-term), Dimethyl:2H(4)13C(2) (Protein N-term), Dimethyl:2H(4)13C(2) (R), Dimethyl:2H(6) (K), Dimethyl:2H(6) (N-term), Dimethyl:2H(6) (R), Dimethyl:2H(6)13C(2) (K), Dimethyl:2H(6)13C(2) (N-term), Dimethyl:2H(6)13C(2) (Protein N-term), Dimethyl:2H(6)13C(2) (R), DimethylamineGMBS (C), Dimethylaminoethyl (C), DimethylArsino (C), Dimethylphosphothione (C), Dimethylphosphothione (H), Dimethylphosphothione (K), Dimethylphosphothione (S), Dimethylphosphothione (T), Dimethylphosphothione (Y), DimethylpyrroleAdduct (K), Dioxidation (C), Dioxidation (E), Dioxidation (F), Dioxidation (I), Dioxidation (K), Dioxidation (L), Dioxidation (M), Dioxidation (P), Dioxidation (R), Dioxidation (U), Dioxidation (V), Dioxidation (W), Dioxidation (Y), Diphthamide (H), Dipyridyl (C), Dipyrrolylmethanemethyl (C), DMPO (C), DMPO (H), DMPO (Y), DNCB_hapten (C), DNCB_hapten (H), DNCB_hapten (K), DNCB_hapten (Y), dNIC (K), dNIC (N-term), DNPS (C), DNPS (W), DPIA (C), DTT (C), DVFQQQTGG (K), DyLight-maleimide (C), DYn-2 (C), EDEDTIDVFQQQTGG (K), EDT-iodoacetyl-PEO-biotin (S), EDT-iodoacetyl-PEO-biotin (T), EDT-maleimide-PEO-biotin (S), EDT-maleimide-PEO-biotin (T), EEEDVIEVYQEQTGG (K), EGCG1 (C), EGCG2 (C), EHD-diphenylpentanone (C), EHD-diphenylpentanone (M), EQAT (C), EQAT:2H(5) (C), EQIGG (K), ESP (K), ESP (N-term), ESP:2H(10) (K), ESP:2H(10) (N-term), Ethanedithiol (S), Ethanedithiol (T), Ethanolamine (C), Ethanolamine (C-term), Ethanolamine (D), Ethanolamine (E), Ethanolyl (C), Ethanolyl (K), Ethanolyl (R), Ethyl (C-term), Ethyl (D), Ethyl (E), Ethyl (K), Ethyl (N-term), Ethyl (Protein N-term), Ethyl+Deamidated (N), Ethyl+Deamidated (Q), ethylamino (S), ethylamino (T), Ethylphosphate (K), Ethylphosphate (N-term), Ethylphosphate (S), Ethylphosphate (T), Ethylphosphate (Y), ethylsulfonylethyl (C), ethylsulfonylethyl (H), ethylsulfonylethyl (K), Ethynyl (C), ExacTagAmine (K), ExacTagThiol (C), FAD (C), FAD (H), FAD (Y), Farnesyl (C), Fluorescein (C), Fluorescein-tyramine (Y), Fluoro (A), Fluoro (F), Fluoro (W), Fluoro (Y), FMN (S), FMN (T), FMNC (C), FMNH (C), FMNH (H), FNEM (C), Formyl (K), Formyl (N-term), Formyl (Protein N-term), Formyl (S), Formyl (T), Formylasparagine (H), FormylMet (Protein N-term), FP-Biotin (K), FP-Biotin (S), FP-Biotin (T), FP-Biotin (Y), FTC (C), FTC (K), FTC (P), FTC (R), FTC (S), Furan (Y), G-H1 (R), Galactosyl (K), Galactosyl (N-term), GEE (Q), GeranylGeranyl (C), GG (C), GG (K), GG (Protein N-term), GG (S), GG (T), GGQ (K), GIST-Quat (K), GIST-Quat (N-term), GIST-Quat:2H(3) (K), GIST-Quat:2H(3) (N-term), GIST-Quat:2H(6) (K), GIST-Quat:2H(6) (N-term), GIST-Quat:2H(9) (K), GIST-Quat:2H(9) (N-term), Gln->Ala (Q), Gln->Arg (Q), Gln->Asn (Q), Gln->Asp (Q), Gln->Cys (Q), Gln->Glu (Q), Gln->Gly (Q), Gln->His (Q), Gln->Lys (Q), Gln->Met (Q), Gln->Phe (Q), Gln->Pro (Q), Gln->pyro-Glu (N-term Q), Gln->Ser (Q), Gln->Thr (Q), Gln->Trp (Q), Gln->Tyr (Q), Gln->Val (Q), Gln->Xle (Q), Glu (E), Glu (Protein C-term), Glu+O(2) (H), Glu->Ala (E), Glu->Arg (E), Glu->Asn (E), Glu->Asp (E), Glu->Cys (E), Glu->Gln (E), Glu->Gly (E), Glu->His (E), Glu->Lys (E), Glu->Met (E), Glu->Phe (E), Glu->Pro (E), Glu->pyro-Glu (N-term E), Glu->pyro-Glu+Methyl (N-term E), Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E), Glu->Ser (E), Glu->Thr (E), Glu->Trp (E), Glu->Tyr (E), Glu->Val (E), Glu->Xle (E), glucosone (R), Glucosylgalactosyl (K), Glucuronyl (Protein N-term), Glucuronyl (S), Glucuronyl (T), GluGlu (E), GluGlu (Protein C-term), GluGluGlu (E), GluGluGlu (Protein C-term), GluGluGluGlu (E), GluGluGluGlu (Protein C-term), Gluratylation (K), Glutathione (C), Gly (K), Gly (S), Gly (T), Gly+O(2) (H), Gly->Ala (G), Gly->Arg (G), Gly->Asn (G), Gly->Asp (G), Gly->Cys (G), Gly->Gln (G), Gly->Glu (G), Gly->His (G), Gly->Lys (G), Gly->Met (G), Gly->Phe (G), Gly->Pro (G), Gly->Ser (G), Gly->Thr (G), Gly->Trp (G), Gly->Tyr (G), Gly->Val (G), Gly->Xle (G), Gly-loss+Amide (C-term G), Glycerophospho (S), Glyceroyl (K), Glyceroyl (Protein N-term), GlycerylPE (E), glycidamide (K), glycidamide (N-term), Glycosyl (P), glyoxalAGE (R), Glyoxylyl (K), GNLLFLACYCIGG (K), GPIanchor (Protein C-term), Guanidinyl (K), Guanidinyl (N-term), Haloxon (C), Haloxon (H), Haloxon (K), Haloxon (S), Haloxon (T), Haloxon (Y), HCysteinyl (C), HCysThiolactone (K), Heme (C), Heme (H), Hep (K), Hep (N), Hep (Q), Hep (R), Hep (S), Hep (T), Hex (C), Hex (K), Hex (N), Hex (N-term), Hex (R), Hex (S), Hex (T), Hex (W), Hex (Y), Hex(1)HexA(1) (S), Hex(1)HexA(1) (T), Hex(1)HexA(1)HexNAc(1) (S), Hex(1)HexA(1)HexNAc(1) (T), Hex(1)HexA(1)HexNAc(2) (S), Hex(1)HexA(1)HexNAc(2) (T), Hex(1)HexNAc(1) (N), Hex(1)HexNAc(1) (S), Hex(1)HexNAc(1) (T), Hex(1)HexNAc(1)dHex(1) (N), Hex(1)HexNAc(1)dHex(1) (S), Hex(1)HexNAc(1)dHex(1) (T), Hex(1)HexNAc(1)dHex(1)Me(1) (S), Hex(1)HexNAc(1)dHex(1)Me(1) (T), Hex(1)HexNAc(1)dHex(1)Me(2) (S), Hex(1)HexNAc(1)dHex(1)Me(2) (T), Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S), Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T), Hex(1)HexNAc(1)NeuAc(1) (N), Hex(1)HexNAc(1)NeuAc(1) (S), Hex(1)HexNAc(1)NeuAc(1) (T), Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S), Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T), Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S), Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T), Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S), Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T), Hex(1)HexNAc(1)NeuAc(2) (N), Hex(1)HexNAc(1)NeuAc(2) (S), Hex(1)HexNAc(1)NeuAc(2) (T), Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S), Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T), Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S), Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T), Hex(1)HexNAc(1)NeuAc(3) (S), Hex(1)HexNAc(1)NeuAc(3) (T), Hex(1)HexNAc(1)NeuGc(1) (S), Hex(1)HexNAc(1)NeuGc(1) (T), Hex(1)HexNAc(1)NeuGc(2) (S), Hex(1)HexNAc(1)NeuGc(2) (T), Hex(1)HexNAc(1)NeuGc(3) (S), Hex(1)HexNAc(1)NeuGc(3) (T), Hex(1)HexNAc(1)NeuGc(4) (S), Hex(1)HexNAc(1)NeuGc(4) (T), Hex(1)HexNAc(1)NeuGc(5) (S), Hex(1)HexNAc(1)NeuGc(5) (T), Hex(1)HexNAc(1)Phos(1) (S), Hex(1)HexNAc(1)Phos(1) (T), Hex(1)HexNAc(1)Sulf(1) (S), Hex(1)HexNAc(1)Sulf(1) (T), Hex(1)HexNAc(2) (N), Hex(1)HexNAc(2) (S), Hex(1)HexNAc(2) (T), Hex(1)HexNAc(2)dHex(1) (N), Hex(1)HexNAc(2)dHex(1) (S), Hex(1)HexNAc(2)dHex(1) (T), Hex(1)HexNAc(2)dHex(1)Pent(1) (N), Hex(1)HexNAc(2)dHex(2) (N), Hex(1)HexNAc(2)dHex(2) (S), Hex(1)HexNAc(2)dHex(2) (T), Hex(1)HexNAc(2)dHex(2)Sulf(1) (S), Hex(1)HexNAc(2)dHex(2)Sulf(1) (T), Hex(1)HexNAc(2)NeuAc(1) (S), Hex(1)HexNAc(2)NeuAc(1) (T), Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S), Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T), Hex(1)HexNAc(2)NeuAc(2) (S), Hex(1)HexNAc(2)NeuAc(2) (T), Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S), Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T), Hex(1)HexNAc(2)NeuGc(1) (S), Hex(1)HexNAc(2)NeuGc(1) (T), Hex(1)HexNAc(2)Pent(1) (N), Hex(1)HexNAc(2)Sulf(1) (S), Hex(1)HexNAc(2)Sulf(1) (T), Hex(1)HexNAc(3) (S), Hex(1)HexNAc(3) (T), Hex(1)HexNAc(3)NeuAc(1) (S), Hex(1)HexNAc(3)NeuAc(1) (T), Hex(1)HexNAc(3)NeuAc(2) (S), Hex(1)HexNAc(3)NeuAc(2) (T), Hex(1)HexNAc(3)NeuGc(1) (S), Hex(1)HexNAc(3)NeuGc(1) (T), Hex(1)HexNAc(3)Sulf(1) (S), Hex(1)HexNAc(3)Sulf(1) (T), Hex(1)HexNAc(4)dHex(1)Sulf(1) (S), Hex(1)HexNAc(4)dHex(1)Sulf(1) (T), Hex(1)NeuAc(1) (S), Hex(1)NeuAc(1) (T), Hex(1)NeuAc(1)Pent(1) (S), Hex(1)NeuAc(1)Pent(1) (T), Hex(1)NeuGc(1) (S), Hex(1)NeuGc(1) (T), Hex(1)Pent(1) (S), Hex(1)Pent(1) (T), Hex(1)Pent(2) (S), Hex(1)Pent(2) (T), Hex(1)Pent(2)Me(1) (S), Hex(1)Pent(2)Me(1) (T), Hex(1)Pent(3) (S), Hex(1)Pent(3) (T), Hex(1)Pent(3)Me(1) (S), Hex(1)Pent(3)Me(1) (T), Hex(10)HexNAc(1) (N), Hex(10)Phos(3) (S), Hex(10)Phos(3) (T), Hex(2) (K), Hex(2) (R), Hex(2) (S), Hex(2) (T), Hex(2)HexA(1)HexNAc(1)Sulf(1) (S), Hex(2)HexA(1)HexNAc(1)Sulf(1) (T), Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S), Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T), Hex(2)HexA(1)Pent(1)Sulf(1) (S), Hex(2)HexA(1)Pent(1)Sulf(1) (T), Hex(2)HexNAc(1) (N), Hex(2)HexNAc(1) (S), Hex(2)HexNAc(1) (T), Hex(2)HexNAc(1)Me(1) (S), Hex(2)HexNAc(1)Me(1) (T), Hex(2)HexNAc(1)NeuGc(1) (S), Hex(2)HexNAc(1)NeuGc(1) (T), Hex(2)HexNAc(1)NeuGc(2) (S), Hex(2)HexNAc(1)NeuGc(2) (T), Hex(2)HexNAc(1)NeuGc(3) (S), Hex(2)HexNAc(1)NeuGc(3) (T), Hex(2)HexNAc(1)NeuGc(4) (S), Hex(2)HexNAc(1)NeuGc(4) (T), Hex(2)HexNAc(1)Pent(1)HexA(1) (S), Hex(2)HexNAc(1)Pent(1)HexA(1) (T), Hex(2)HexNAc(1)Sulf(1) (S), Hex(2)HexNAc(1)Sulf(1) (T), Hex(2)HexNAc(2) (N), Hex(2)HexNAc(2) (S), Hex(2)HexNAc(2) (T), Hex(2)HexNAc(2)dHex(1) (N), Hex(2)HexNAc(2)dHex(1) (S), Hex(2)HexNAc(2)dHex(1) (T), Hex(2)HexNAc(2)NeuAc(1) (N), Hex(2)HexNAc(2)NeuAc(1) (S), Hex(2)HexNAc(2)NeuAc(1) (T), Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S), Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T), Hex(2)HexNAc(2)NeuAc(2) (S), Hex(2)HexNAc(2)NeuAc(2) (T), Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S), Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T), Hex(2)HexNAc(2)NeuGc(1) (S), Hex(2)HexNAc(2)NeuGc(1) (T), Hex(2)HexNAc(2)Pent(1) (N), Hex(2)HexNAc(2)Sulf(1) (S), Hex(2)HexNAc(2)Sulf(1) (T), Hex(2)HexNAc(3) (N), Hex(2)HexNAc(3) (S), Hex(2)HexNAc(3) (T), Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S), Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T), Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S), Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T), Hex(2)HexNAc(3)NeuAc(2) (S), Hex(2)HexNAc(3)NeuAc(2) (T), Hex(2)HexNAc(3)NeuAc(3) (S), Hex(2)HexNAc(3)NeuAc(3) (T), Hex(2)HexNAc(3)NeuGc(1) (S), Hex(2)HexNAc(3)NeuGc(1) (T), Hex(2)HexNAc(3)NeuGc(2) (S), Hex(2)HexNAc(3)NeuGc(2) (T), Hex(2)HexNAc(3)NeuGc(3) (S), Hex(2)HexNAc(3)NeuGc(3) (T), Hex(2)HexNAc(3)Sulf(1) (S), Hex(2)HexNAc(3)Sulf(1) (T), Hex(2)HexNAc(4) (N), Hex(2)HexNAc(4) (S), Hex(2)HexNAc(4) (T), Hex(2)HexNAc(4)NeuAc(1) (S), Hex(2)HexNAc(4)NeuAc(1) (T), Hex(2)HexNAc(5) (S), Hex(2)HexNAc(5) (T), Hex(2)NeuAc(1) (S), Hex(2)NeuAc(1) (T), Hex(2)Pent(2) (S), Hex(2)Pent(2) (T), Hex(2)Pent(2)Me(1) (S), Hex(2)Pent(2)Me(1) (T), Hex(2)Sulf(1) (S), Hex(2)Sulf(1) (T), Hex(3) (N), Hex(3) (S), Hex(3) (T), Hex(3)HexNAc(1) (N), Hex(3)HexNAc(1) (S), Hex(3)HexNAc(1) (T), Hex(3)HexNAc(1)HexA(1) (S), Hex(3)HexNAc(1)HexA(1) (T), Hex(3)HexNAc(1)Me(1) (S), Hex(3)HexNAc(1)Me(1) (T), Hex(3)HexNAc(1)Pent(1) (N), Hex(3)HexNAc(2) (N), Hex(3)HexNAc(2) (S), Hex(3)HexNAc(2) (T), Hex(3)HexNAc(2)NeuAc(1) (N), Hex(3)HexNAc(2)NeuAc(2) (S), Hex(3)HexNAc(2)NeuAc(2) (T), Hex(3)HexNAc(2)Pent(1) (N), Hex(3)HexNAc(2)Phos(1) (N), Hex(3)HexNAc(3) (N), Hex(3)HexNAc(3) (S), Hex(3)HexNAc(3) (T), Hex(3)HexNAc(3)NeuAc(1) (S), Hex(3)HexNAc(3)NeuAc(1) (T), Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S), Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T), Hex(3)HexNAc(3)NeuAc(2) (S), Hex(3)HexNAc(3)NeuAc(2) (T), Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S), Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T), Hex(3)HexNAc(3)NeuAc(3) (S), Hex(3)HexNAc(3)NeuAc(3) (T), Hex(3)HexNAc(3)NeuGc(1) (S), Hex(3)HexNAc(3)NeuGc(1) (T), Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S), Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T), Hex(3)HexNAc(3)Pent(1) (N), Hex(3)HexNAc(3)Sulf(1) (N), Hex(3)HexNAc(3)Sulf(1) (S), Hex(3)HexNAc(3)Sulf(1) (T), Hex(3)HexNAc(4) (N), Hex(3)HexNAc(4) (S), Hex(3)HexNAc(4) (T), Hex(3)HexNAc(4)NeuAc(1) (N), Hex(3)HexNAc(4)NeuAc(2) (N), Hex(3)HexNAc(4)Pent(1) (N), Hex(3)HexNAc(4)Sulf(1) (N), Hex(3)HexNAc(5) (N), Hex(3)HexNAc(5) (S), Hex(3)HexNAc(5) (T), Hex(3)HexNAc(5)NeuAc(1) (N), Hex(3)HexNAc(5)Sulf(1) (N), Hex(3)HexNAc(6) (N), Hex(3)HexNAc(6) (S), Hex(3)HexNAc(6) (T), Hex(3)HexNAc(6)NeuAc(1) (N), Hex(3)HexNAc(6)Sulf(1) (N), Hex(3)HexNAc(6)Sulf(2) (N), Hex(3)HexNAc(7) (N), Hex(3)HexNAc(7)Sulf(1) (N), Hex(4) (S), Hex(4) (T), Hex(4)HexA(1) (S), Hex(4)HexA(1) (T), Hex(4)HexA(1)HexNAc(1) (S), Hex(4)HexA(1)HexNAc(1) (T), Hex(4)HexNAc(1) (N), Hex(4)HexNAc(1) (S), Hex(4)HexNAc(1) (T), Hex(4)HexNAc(2) (N), Hex(4)HexNAc(2)NeuAc(1) (N), Hex(4)HexNAc(2)NeuAc(1) (S), Hex(4)HexNAc(2)NeuAc(1) (T), Hex(4)HexNAc(2)Pent(1) (N), Hex(4)HexNAc(3) (N), Hex(4)HexNAc(3) (S), Hex(4)HexNAc(3) (T), Hex(4)HexNAc(3)NeuAc(1) (N), Hex(4)HexNAc(3)NeuAc(1) (S), Hex(4)HexNAc(3)NeuAc(1) (T), Hex(4)HexNAc(3)NeuAc(2) (N), Hex(4)HexNAc(3)NeuGc(1) (N), Hex(4)HexNAc(3)Pent(1) (N), Hex(4)HexNAc(4) (N), Hex(4)HexNAc(4) (S), Hex(4)HexNAc(4) (T), Hex(4)HexNAc(4)Me(2)Pent(1) (N), Hex(4)HexNAc(4)NeuAc(1) (N), Hex(4)HexNAc(4)NeuAc(1) (S), Hex(4)HexNAc(4)NeuAc(1) (T), Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S), Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T), Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S), Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T), Hex(4)HexNAc(4)NeuGc(1) (N), Hex(4)HexNAc(4)NeuGc(1) (S), Hex(4)HexNAc(4)NeuGc(1) (T), Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S), Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T), Hex(4)HexNAc(4)Pent(1) (N), Hex(4)HexNAc(4)Sulf(1) (N), Hex(4)HexNAc(4)Sulf(2) (S), Hex(4)HexNAc(4)Sulf(2) (T), Hex(4)HexNAc(5) (N), Hex(4)HexNAc(5)NeuAc(1) (N), Hex(4)HexNAc(5)Sulf(1) (N), Hex(4)HexNAc(6) (N), Hex(4)Phos(1) (S), Hex(4)Phos(1) (T), Hex(5) (S), Hex(5) (T), Hex(5)HexA(1) (S), Hex(5)HexA(1) (T), Hex(5)HexNAc(1) (N), Hex(5)HexNAc(1) (S), Hex(5)HexNAc(1) (T), Hex(5)HexNAc(2) (N), Hex(5)HexNAc(2)Phos(1) (N), Hex(5)HexNAc(3) (N), Hex(5)HexNAc(3)Pent(1) (N), Hex(5)HexNAc(4) (N), Hex(5)HexNAc(4) (S), Hex(5)HexNAc(4) (T), Hex(5)HexNAc(4)Me(2)Pent(1) (N), Hex(5)HexNAc(4)NeuAc(1) (N), Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N), Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N), Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N), Hex(5)HexNAc(4)NeuAc(2) (N), Hex(5)HexNAc(4)NeuGc(1) (N), Hex(5)HexNAc(4)Sulf(1) (N), Hex(5)HexNAc(5) (N), Hex(5)HexNAc(5) (S), Hex(5)HexNAc(5) (T), Hex(5)Phos(1) (S), Hex(5)Phos(1) (T), Hex(5)Phos(3) (S), Hex(5)Phos(3) (T), Hex(6)HexNAc(1) (N), Hex(6)HexNAc(2) (N), Hex(6)HexNAc(2)Phos(1) (N), Hex(6)HexNAc(3) (N), Hex(6)HexNAc(3)Phos(1) (N), Hex(6)HexNAc(4) (N), Hex(6)HexNAc(4) (S), Hex(6)HexNAc(4) (T), Hex(6)HexNAc(4)Me(3) (N), Hex(6)HexNAc(4)Me(3)Pent(1) (N), Hex(6)HexNAc(5) (N), Hex(6)HexNAc(5)NeuAc(3) (N), Hex(6)Phos(1) (S), Hex(6)Phos(1) (T), Hex(6)Phos(3) (S), Hex(6)Phos(3) (T), Hex(7)HexNAc(1) (N), Hex(7)HexNAc(2) (N), Hex(7)HexNAc(2)Phos(1) (N), Hex(7)HexNAc(2)Phos(2) (N), Hex(7)HexNAc(3) (N), Hex(7)HexNAc(3)Phos(1) (N), Hex(7)HexNAc(4) (N), Hex(7)HexNAc(6) (N), Hex(7)HexNAc(6) (S), Hex(7)HexNAc(6) (T), Hex(7)Phos(3) (S), Hex(7)Phos(3) (T), Hex(8)HexNAc(1) (N), Hex(8)HexNAc(2) (N), Hex(8)Phos(3) (S), Hex(8)Phos(3) (T), Hex(9) (N), Hex(9)HexNAc(1) (N), Hex(9)HexNAc(2) (N), Hex(9)Phos(3) (S), Hex(9)Phos(3) (T), HexA(2)HexNAc(3) (S), HexA(2)HexNAc(3) (T), Hexanoyl (K), HexN (K), HexN (N), HexN (S), HexN (T), HexN (W), HexNAc (C), HexNAc (N), HexNAc (S), HexNAc (T), HexNAc(1)dHex(1) (N), HexNAc(1)dHex(1) (S), HexNAc(1)dHex(1) (T), HexNAc(1)dHex(2) (N), HexNAc(1)Kdn(2) (S), HexNAc(1)Kdn(2) (T), HexNAc(1)NeuAc(1) (S), HexNAc(1)NeuAc(1) (T), HexNAc(1)NeuGc(1) (S), HexNAc(1)NeuGc(1) (T), HexNAc(1)NeuGc(2) (S), HexNAc(1)NeuGc(2) (T), HexNAc(2) (N), HexNAc(2) (S), HexNAc(2) (T), HexNAc(2)dHex(1) (N), HexNAc(2)dHex(2) (N), HexNAc(2)NeuAc(1) (S), HexNAc(2)NeuAc(1) (T), HexNAc(2)NeuAc(1)Sulf(1) (S), HexNAc(2)NeuAc(1)Sulf(1) (T), HexNAc(2)NeuGc(1) (S), HexNAc(2)NeuGc(1) (T), HexNAc(2)Sulf(1) (S), HexNAc(2)Sulf(1) (T), HexNAc(3) (S), HexNAc(3) (T), HexNAc(3)Sulf(1) (S), HexNAc(3)Sulf(1) (T), HexNAc(4) (S), HexNAc(4) (T), HexNAc(5) (S), HexNAc(5) (T), His+O(2) (H), His->Ala (H), His->Arg (H), His->Asn (H), His->Asp (H), His->Cys (H), His->Gln (H), His->Glu (H), His->Gly (H), His->Lys (H), His->Met (H), His->Phe (H), His->Pro (H), His->Ser (H), His->Thr (H), His->Trp (H), His->Tyr (H), His->Val (H), His->Xle (H), HMVK (C), HN2_mustard (C), HN2_mustard (H), HN2_mustard (K), HN3_mustard (C), HN3_mustard (H), HN3_mustard (K), HNE (A), HNE (C), HNE (H), HNE (K), HNE (L), HNE (R), HNE+Delta:H(2) (C), HNE+Delta:H(2) (H), HNE+Delta:H(2) (K), HNE-BAHAH (C), HNE-BAHAH (H), HNE-BAHAH (K), HNE-Delta:H(2)O (C), HNE-Delta:H(2)O (H), HNE-Delta:H(2)O (K), Homocysteic_acid (M), HPG (R), Hydroxamic_acid (D), Hydroxamic_acid (E), Hydroxycinnamyl (C), Hydroxyfarnesyl (C), Hydroxyheme (E), hydroxyisobutyryl (K), Hydroxymethyl (N), HydroxymethylOP (K), Hydroxytrimethyl (K), Hypusine (K), IASD (C), IBTP (C), ICAT-C (C), ICAT-C:13C(9) (C), ICAT-D (C), ICAT-D:2H(8) (C), ICAT-G (C), ICAT-G:2H(8) (C), ICAT-H (C), ICAT-H:13C(6) (C), ICDID (C), ICDID:2H(6) (C), ICPL (K), ICPL (N-term), ICPL (Protein N-term), ICPL:13C(6) (K), ICPL:13C(6) (N-term), ICPL:13C(6) (Protein N-term), ICPL:13C(6)2H(4) (K), ICPL:13C(6)2H(4) (N-term), ICPL:13C(6)2H(4) (Protein N-term), ICPL:2H(4) (K), ICPL:2H(4) (N-term), ICPL:2H(4) (Protein N-term), IDEnT (C), IED-Biotin (C), IGBP (C), IGBP:13C(2) (C), IMEHex(2)NeuAc(1) (K), IMID (K), IMID:2H(4) (K), Iminobiotin (K), Iminobiotin (N-term), Iodo (H), Iodo (Y), Iodoacetanilide (C), Iodoacetanilide (K), Iodoacetanilide (N-term), Iodoacetanilide:13C(6) (C), Iodoacetanilide:13C(6) (K), Iodoacetanilide:13C(6) (N-term), iodoTMT (C), iodoTMT (D), iodoTMT (E), iodoTMT (H), iodoTMT (K), iodoTMT6plex (C), iodoTMT6plex (D), iodoTMT6plex (E), iodoTMT6plex (H), iodoTMT6plex (K), IodoU-AMP (F), IodoU-AMP (W), IodoU-AMP (Y), ISD_z+2_ion (N-term), Isopropylphospho (S), Isopropylphospho (T), Isopropylphospho (Y), Isovaleryl (K), iST-NHS specific cysteine modification (C), Itaconatyl (C), Itaconyl (K), iTRAQ4plex (C), iTRAQ4plex (H), iTRAQ4plex (K), iTRAQ4plex (N-term), iTRAQ4plex (Protein N-term), iTRAQ4plex (S), iTRAQ4plex (T), iTRAQ4plex (Y), iTRAQ4plex114 (C), iTRAQ4plex114 (K), iTRAQ4plex114 (N-term), iTRAQ4plex114 (Y), iTRAQ4plex115 (C), iTRAQ4plex115 (K), iTRAQ4plex115 (N-term), iTRAQ4plex115 (Y), iTRAQ8plex (C), iTRAQ8plex (H), iTRAQ8plex (K), iTRAQ8plex (N-term), iTRAQ8plex (Protein N-term), iTRAQ8plex (S), iTRAQ8plex (T), iTRAQ8plex (Y), iTRAQ8plex:13C(6)15N(2) (C), iTRAQ8plex:13C(6)15N(2) (K), iTRAQ8plex:13C(6)15N(2) (N-term), iTRAQ8plex:13C(6)15N(2) (Y), L-Gln (D), L-Gln (E), Label:13C(1)2H(3) (M), Label:13C(1)2H(3)+Oxidation (M), Label:13C(2)15N(1) (G), Label:13C(2)15N(2) (K), Label:13C(3) (A), Label:13C(3)15N(1) (A), Label:13C(3)15N(1) (S), Label:13C(4) (M), Label:13C(4)+Oxidation (M), Label:13C(4)15N(1) (D), Label:13C(4)15N(2)+GG (K), Label:13C(5) (P), Label:13C(5)15N(1) (E), Label:13C(5)15N(1) (M), Label:13C(5)15N(1) (P), Label:13C(5)15N(1) (V), Label:13C(6) (I), Label:13C(6) (K), Label:13C(6) (L), Label:13C(6) (R), Label:13C(6)+Acetyl (K), Label:13C(6)+Dimethyl (K), Label:13C(6)+GG (K), Label:13C(6)15N(1) (I), Label:13C(6)15N(1) (L), Label:13C(6)15N(2) (K), Label:13C(6)15N(2)+Acetyl (K), Label:13C(6)15N(2)+Dimethyl (K), Label:13C(6)15N(2)+GG (K), Label:13C(6)15N(2)+TMT6plex (K), Label:13C(6)15N(2)+TMTpro (K), Label:13C(6)15N(4) (R), Label:13C(6)15N(4)+Dimethyl (R), Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R), Label:13C(6)15N(4)+Methyl (R), Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R), Label:13C(9) (F), Label:13C(9) (Y), Label:13C(9)+Phospho (Y), Label:13C(9)15N(1) (F), Label:15N(1) (A), Label:15N(1) (C), Label:15N(1) (D), Label:15N(1) (E), Label:15N(1) (F), Label:15N(1) (G), Label:15N(1) (I), Label:15N(1) (L), Label:15N(1) (M), Label:15N(1) (P), Label:15N(1) (S), Label:15N(1) (T), Label:15N(1) (V), Label:15N(1) (Y), Label:15N(2) (K), Label:15N(2) (N), Label:15N(2) (Q), Label:15N(2) (W), Label:15N(2)2H(9) (K), Label:15N(3) (H), Label:15N(4) (R), Label:18O(1) (C-term), Label:18O(1) (S), Label:18O(1) (T), Label:18O(1) (Y), Label:18O(2) (C-term), Label:2H(10) (L), Label:2H(3) (L), Label:2H(3) (M), Label:2H(3)+Oxidation (M), Label:2H(4) (A), Label:2H(4) (F), Label:2H(4) (K), Label:2H(4) (U), Label:2H(4) (Y), Label:2H(4)+Acetyl (K), Label:2H(4)+GG (K), Label:2H(4)13C(1) (R), Label:2H(6)15N(1) (P), Label:2H(7)15N(4) (R), Label:2H(9)13C(6)15N(2) (K), Lactylation (K), lapachenole (C), Leu->MetOx (L), LG-anhydrolactam (K), LG-anhydrolactam (N-term), LG-anhyropyrrole (K), LG-anhyropyrrole (N-term), LG-Hlactam-K (K), LG-Hlactam-K (Protein N-term), LG-Hlactam-R (R), LG-lactam-K (K), LG-lactam-K (Protein N-term), LG-lactam-R (R), LG-pyrrole (C), LG-pyrrole (K), LG-pyrrole (N-term), Lipoyl (K), LRGG (K), LRGG+dimethyl (K), LRGG+methyl (K), LTX+Lophotoxin (Y), Lys (N-term), Lys+O(2) (H), Lys->Ala (K), Lys->Allysine (K), Lys->AminoadipicAcid (K), Lys->Arg (K), Lys->Asn (K), Lys->Asp (K), Lys->CamCys (K), Lys->Cys (K), Lys->Gln (K), Lys->Glu (K), Lys->Gly (K), Lys->His (K), Lys->Met (K), Lys->MetOx (K), Lys->Phe (K), Lys->Pro (K), Lys->Ser (K), Lys->Thr (K), Lys->Trp (K), Lys->Tyr (K), Lys->Val (K), Lys->Xle (K), Lys-loss (K), Lys-loss (Protein C-term K), Lysbiotinhydrazide (K), maleimide (C), maleimide (K), Maleimide-PEO2-Biotin (C), maleimide3 (C), maleimide3 (K), maleimide5 (C), maleimide5 (K), Malonyl (C), Malonyl (K), Malonyl (S), MBS+peptide (C), MDCC (C), MeMePhosphorothioate (S), Menadione (C), Menadione (K), Menadione-HQ (C), Menadione-HQ (K), MercaptoEthanol (S), MercaptoEthanol (T), MesitylOxide (H), MesitylOxide (K), MesitylOxide (Protein N-term), Met+O(2) (H), Met->Aha (M), Met->Ala (M), Met->Arg (M), Met->Asn (M), Met->Asp (M), Met->AspSA (M), Met->Cys (M), Met->Gln (M), Met->Glu (M), Met->Gly (M), Met->His (M), Met->Hpg (M), Met->Hse (C-term M), Met->Hsl (C-term M), Met->Lys (M), Met->Phe (M), Met->Pro (M), Met->Ser (M), Met->Thr (M), Met->Trp (M), Met->Tyr (M), Met->Val (M), Met->Xle (M), Met-loss (Protein N-term M), Met-loss+Acetyl (Protein N-term M), Methamidophos-O (C), Methamidophos-O (H), Methamidophos-O (K), Methamidophos-O (S), Methamidophos-O (T), Methamidophos-O (Y), Methamidophos-S (C), Methamidophos-S (H), Methamidophos-S (K), Methamidophos-S (S), Methamidophos-S (T), Methamidophos-S (Y), Methyl (C), Methyl (C-term), Methyl (D), Methyl (E), Methyl (H), Methyl (I), Methyl (K), Methyl (L), Methyl (N), Methyl (N-term), Methyl (Protein N-term), Methyl (Q), Methyl (R), Methyl (S), Methyl (T), Methyl+Acetyl:2H(3) (K), Methyl+Deamidated (N), Methyl+Deamidated (Q), Methyl-PEO12-Maleimide (C), Methyl:2H(2) (K), Methyl:2H(2) (N-term), Methyl:2H(2)13C (C), Methyl:2H(2)13C (C-term), Methyl:2H(2)13C (D), Methyl:2H(2)13C (E), Methyl:2H(2)13C (H), Methyl:2H(2)13C (I), Methyl:2H(2)13C (K), Methyl:2H(2)13C (L), Methyl:2H(2)13C (N), Methyl:2H(2)13C (N-term), Methyl:2H(2)13C (Protein N-term), Methyl:2H(2)13C (Q), Methyl:2H(2)13C (R), Methyl:2H(2)13C (S), Methyl:2H(2)13C (T), Methyl:2H(3) (D), Methyl:2H(3) (E), Methyl:2H(3) (K), Methyl:2H(3) (R), Methyl:2H(3) (X), Methyl:2H(3)+Acetyl:2H(3) (K), Methyl:2H(3)13C(1) (K), Methyl:2H(3)13C(1) (N-term), Methyl:2H(3)13C(1) (R), Methylamine (S), Methylamine (T), Methylmalonylation (S), methylol (K), methylol (W), methylol (Y), Methylphosphonate (S), Methylphosphonate (T), Methylphosphonate (Y), Methylpyrroline (K), methylsulfonylethyl (C), methylsulfonylethyl (H), methylsulfonylethyl (K), Methylthio (C), Methylthio (D), Methylthio (K), Methylthio (N), Methylthio (N-term), MG-H1 (R), Microcin (Protein C-term), MicrocinC7 (Protein C-term), MM-diphenylpentanone (C), Molybdopterin (C), MolybdopterinGD (C), MolybdopterinGD (D), MolybdopterinGD (U), MolybdopterinGD+Delta:S(-1)Se(1) (C), Mono_Ngamma-propargyl-L-Gln_desthiobiotin (C), monomethylphosphothione (C), monomethylphosphothione (H), monomethylphosphothione (K), monomethylphosphothione (S), monomethylphosphothione (T), monomethylphosphothione (Y), mTRAQ (H), mTRAQ (K), mTRAQ (N-term), mTRAQ (S), mTRAQ (T), mTRAQ (Y), mTRAQ:13C(3)15N(1) (H), mTRAQ:13C(3)15N(1) (K), mTRAQ:13C(3)15N(1) (N-term), mTRAQ:13C(3)15N(1) (S), mTRAQ:13C(3)15N(1) (T), mTRAQ:13C(3)15N(1) (Y), mTRAQ:13C(6)15N(2) (H), mTRAQ:13C(6)15N(2) (K), mTRAQ:13C(6)15N(2) (N-term), mTRAQ:13C(6)15N(2) (S), mTRAQ:13C(6)15N(2) (T), mTRAQ:13C(6)15N(2) (Y), MTSL (C), MurNAc (A), Myristoleyl (Protein N-term G), Myristoyl (C), Myristoyl (K), Myristoyl (N-term G), Myristoyl+Delta:H(-4) (Protein N-term G), N-dimethylphosphate (S), N6pAMP (S), N6pAMP (T), N6pAMP (Y), NA-LNO2 (C), NA-LNO2 (H), NA-OA-NO2 (C), NA-OA-NO2 (H), NBF (C), NBF (K), NBF (R), NBS (W), NBS:13C(6) (W), NDA (K), NDA (N-term), NEIAA (C), NEIAA (Y), NEIAA:2H(5) (C), NEIAA:2H(5) (Y), NEM:2H(5) (C), NEM:2H(5)+H2O (C), NEMsulfur (C), NEMsulfurWater (C), Nethylmaleimide (C), Nethylmaleimide+water (C), Nethylmaleimide+water (K), NeuAc (N), NeuAc (S), NeuAc (T), NeuGc (N), NeuGc (S), NeuGc (T), NHS-fluorescein (K), NHS-LC-Biotin (K), NHS-LC-Biotin (N-term), NIC (K), NIC (N-term), NIPCAM (C), Nitrene (Y), Nitro (F), Nitro (W), Nitro (Y), Nitrosyl (C), Nitrosyl (Y), Nmethylmaleimide (C), Nmethylmaleimide (K), Nmethylmaleimide+water (C), NO_SMX_SEMD (C), NO_SMX_SIMD (C), NP40 (N-term), NQIGG (K), NQTGG (K), O-Dimethylphosphate (S), O-Dimethylphosphate (T), O-Dimethylphosphate (Y), O-Et-N-diMePhospho (S), O-Isopropylmethylphosphonate (S), O-Isopropylmethylphosphonate (T), O-Isopropylmethylphosphonate (Y), O-Methylphosphate (S), O-Methylphosphate (T), O-Methylphosphate (Y), O-pinacolylmethylphosphonate (H), O-pinacolylmethylphosphonate (K), O-pinacolylmethylphosphonate (S), O-pinacolylmethylphosphonate (T), O-pinacolylmethylphosphonate (Y), Octanoyl (C), Octanoyl (S), Octanoyl (T), OxArgBiotin (R), OxArgBiotinRed (R), Oxidation (C), Oxidation (C-term G), Oxidation (D), Oxidation (E), Oxidation (F), Oxidation (H), Oxidation (I), Oxidation (K), Oxidation (L), Oxidation (M), Oxidation (N), Oxidation (P), Oxidation (Q), Oxidation (R), Oxidation (S), Oxidation (T), Oxidation (U), Oxidation (V), Oxidation (W), Oxidation (Y), Oxidation+NEM (C), OxLysBiotin (K), OxLysBiotinRed (K), OxProBiotin (P), OxProBiotinRed (P), Palmitoleyl (C), Palmitoleyl (S), Palmitoleyl (T), Palmitoyl (C), Palmitoyl (K), Palmitoyl (Protein N-term), Palmitoyl (S), Palmitoyl (T), PEITC (C), PEITC (K), PEITC (N-term), Pent(1)HexNAc(1) (S), Pent(1)HexNAc(1) (T), Pent(2) (S), Pent(2) (T), Pentanoyl (K), Pentose (S), Pentose (T), Pentylamine (Q), PEO-Iodoacetyl-LC-Biotin (C), PET (S), PET (T), Phe->Ala (F), Phe->Arg (F), Phe->Asn (F), Phe->Asp (F), Phe->CamCys (F), Phe->Cys (F), Phe->Gln (F), Phe->Glu (F), Phe->Gly (F), Phe->His (F), Phe->Lys (F), Phe->Met (F), Phe->Pro (F), Phe->Ser (F), Phe->Thr (F), Phe->Trp (F), Phe->Tyr (F), Phe->Val (F), Phe->Xle (F), phenyl-phosphate (K), phenyl-phosphate (S), phenyl-phosphate (T), phenyl-phosphate (Y), Phenylisocyanate (N-term), Phenylisocyanate:2H(5) (N-term), phenylsulfonylethyl (C), Phospho (C), Phospho (D), Phospho (E), Phospho (H), Phospho (K), Phospho (R), Phospho (S), Phospho (T), Phospho (Y), Phosphoadenosine (H), Phosphoadenosine (K), Phosphoadenosine (S), Phosphoadenosine (T), Phosphoadenosine (Y), PhosphoCytidine (S), PhosphoCytidine (T), PhosphoCytidine (Y), PhosphoDecoy (A), PhosphoDecoy (G), PhosphoDecoy (L), Phosphogluconoylation (K), Phosphogluconoylation (N-term), Phosphoguanosine (H), Phosphoguanosine (K), PhosphoHex (S), PhosphoHex (T), PhosphoHex(2) (N), PhosphoHex(2) (S), PhosphoHex(2) (T), PhosphoHexNAc (S), PhosphoHexNAc (T), Phosphopantetheine (S), Phosphopropargyl (S), Phosphopropargyl (T), Phosphopropargyl (Y), phosphoRibosyl (D), phosphoRibosyl (E), phosphoRibosyl (R), PhosphoribosyldephosphoCoA (S), PhosphoUridine (H), PhosphoUridine (Y), Phycocyanobilin (C), Phycoerythrobilin (C), Phytochromobilin (C), Piperidine (K), Piperidine (N-term), pRBS-ID_4-thiouridine (F), pRBS-ID_6-thioguanosine (W), Pro+O(2) (H), Pro->Ala (P), Pro->Arg (P), Pro->Asn (P), Pro->Asp (P), Pro->Cys (P), Pro->Gln (P), Pro->Glu (P), Pro->Gly (P), Pro->HAVA (P), Pro->His (P), Pro->Lys (P), Pro->Met (P), Pro->Phe (P), Pro->pyro-Glu (P), Pro->Pyrrolidinone (P), Pro->Pyrrolidone (P), Pro->Ser (P), Pro->Thr (P), Pro->Trp (P), Pro->Tyr (P), Pro->Val (P), Pro->Xle (P), probiotinhydrazide (P), Propargylamine (C-term), Propargylamine (D), Propargylamine (E), Propionamide (C), Propionamide (K), Propionamide (N-term), Propionamide:2H(3) (C), Propionyl (K), Propionyl (N-term), Propionyl (Protein N-term), Propionyl (S), Propionyl (T), Propionyl:13C(3) (K), Propionyl:13C(3) (N-term), Propiophenone (C), Propiophenone (H), Propiophenone (K), Propiophenone (R), Propiophenone (S), Propiophenone (T), Propiophenone (W), Propyl (C-term), Propyl (D), Propyl (E), Propyl (K), Propyl (N-term), Propyl (Protein C-term), Propyl:2H(6) (K), Propyl:2H(6) (N-term), PropylNAGthiazoline (C), PS_Hapten (C), PS_Hapten (H), PS_Hapten (K), pupylation (K), Puromycin (C-term), PyMIC (N-term), PyridoxalPhosphate (K), PyridoxalPhosphateH2 (K), Pyridylacetyl (K), Pyridylacetyl (N-term), Pyridylethyl (C), Pyro-carbamidomethyl (N-term C), Pyro-QQTGG (K), pyrophospho (S), pyrophospho (T), PyruvicAcidIminyl (K), PyruvicAcidIminyl (Protein N-term C), PyruvicAcidIminyl (Protein N-term V), Pyruvoyl (K), QAT (C), QAT:2H(3) (C), QEQTGG (K), QQQTGG (K), QQTGG (K), QTGG (K), Quinone (W), Quinone (Y), RBS-ID_Uridine (Y), Retinylidene (K), RNPXL (N-term K), RNPXL (N-term R), RNPXlink1 (C), s-GlcNAc (S), s-GlcNAc (T), Saligenin (H), Saligenin (K), Ser->Ala (S), Ser->Arg (S), Ser->Asn (S), Ser->Asp (S), Ser->Cys (S), Ser->Gln (S), Ser->Glu (S), Ser->Gly (S), Ser->His (S), Ser->LacticAcid (Protein N-term S), Ser->Lys (S), Ser->Met (S), Ser->Phe (S), Ser->Pro (S), Ser->Thr (S), Ser->Trp (S), Ser->Tyr (S), Ser->Val (S), Ser->Xle (S), Ser/Thr-KDO (S), Ser/Thr-KDO (T), serotonylation (Q), shTMT (K), shTMT (N-term), shTMT (Protein N-term), shTMTpro (K), shTMTpro (N-term), shTMTpro (Protein N-term), SMA (K), SMA (N-term), spermidine (Q), spermine (Q), SPITC (K), SPITC (N-term), SPITC:13C(6) (K), SPITC:13C(6) (N-term), Succinyl (K), Succinyl (N-term), Succinyl (Protein N-term), Succinyl:13C(4) (K), Succinyl:13C(4) (N-term), Succinyl:2H(4) (K), Succinyl:2H(4) (N-term), SulfanilicAcid (C-term), SulfanilicAcid (D), SulfanilicAcid (E), SulfanilicAcid:13C(6) (C-term), SulfanilicAcid:13C(6) (D), SulfanilicAcid:13C(6) (E), Sulfide (C), Sulfide (D), Sulfide (W), Sulfo (C), Sulfo (S), Sulfo (T), Sulfo (Y), sulfo+amino (Y), Sulfo-NHS-LC-LC-Biotin (K), Sulfo-NHS-LC-LC-Biotin (N-term), SulfoGMBS (C), SulfurDioxide (C), SUMO2135 (K), SUMO3549 (K), TAMRA-FP (S), TAMRA-FP (Y), Thiadiazole (C), Thiazolidine (C), Thiazolidine (F), Thiazolidine (H), Thiazolidine (K), Thiazolidine (Protein N-term), Thiazolidine (R), Thiazolidine (W), Thiazolidine (Y), thioacylPA (K), Thiophos-S-S-biotin (S), Thiophos-S-S-biotin (T), Thiophos-S-S-biotin (Y), Thiophospho (S), Thiophospho (T), Thiophospho (Y), Thr->Ala (T), Thr->Arg (T), Thr->Asn (T), Thr->Asp (T), Thr->Cys (T), Thr->Gln (T), Thr->Glu (T), Thr->Gly (T), Thr->His (T), Thr->Lys (T), Thr->Met (T), Thr->Phe (T), Thr->Pro (T), Thr->Ser (T), Thr->Trp (T), Thr->Tyr (T), Thr->Val (T), Thr->Xle (T), Thrbiotinhydrazide (T), Thyroxine (Y), Tiglyl (K), TMAB (K), TMAB (N-term), TMAB:2H(9) (K), TMAB:2H(9) (N-term), TMPP-Ac (K), TMPP-Ac (N-term), TMPP-Ac (Y), TMPP-Ac:13C(9) (K), TMPP-Ac:13C(9) (N-term), TMPP-Ac:13C(9) (Y), TMT (H), TMT (K), TMT (N-term), TMT (Protein N-term), TMT (S), TMT (T), TMT2plex (H), TMT2plex (K), TMT2plex (N-term), TMT2plex (Protein N-term), TMT2plex (S), TMT2plex (T), TMT6plex (H), TMT6plex (K), TMT6plex (N-term), TMT6plex (Protein N-term), TMT6plex (S), TMT6plex (T), TMTpro (H), TMTpro (K), TMTpro (N-term), TMTpro (Protein N-term), TMTpro (S), TMTpro (T), TMTpro_zero (H), TMTpro_zero (K), TMTpro_zero (N-term), TMTpro_zero (Protein N-term), TMTpro_zero (S), TMTpro_zero (T), TNBS (K), TNBS (N-term), trifluoro (L), Triiodo (Y), Triiodothyronine (Y), Trimethyl (K), Trimethyl (Protein N-term A), Trimethyl (R), Trimethyl:13C(3)2H(9) (K), Trimethyl:13C(3)2H(9) (R), Trimethyl:2H(9) (K), Trimethyl:2H(9) (R), Trioxidation (C), Trioxidation (F), Trioxidation (W), Trioxidation (Y), Tripalmitate (Protein N-term C), Tris (N), Triton (C-term), Triton (N-term), Trp->Ala (W), Trp->Arg (W), Trp->Asn (W), Trp->Asp (W), Trp->Cys (W), Trp->Gln (W), Trp->Glu (W), Trp->Gly (W), Trp->His (W), Trp->Hydroxykynurenin (W), Trp->Kynurenin (W), Trp->Lys (W), Trp->Met (W), Trp->Oxolactone (W), Trp->Phe (W), Trp->Pro (W), Trp->Ser (W), Trp->Thr (W), Trp->Tyr (W), Trp->Val (W), Trp->Xle (W), Tween20 (N-term), Tween80 (C-term), Tyr->Ala (Y), Tyr->Arg (Y), Tyr->Asn (Y), Tyr->Asp (Y), Tyr->Cys (Y), Tyr->Dha (Y), Tyr->Gln (Y), Tyr->Glu (Y), Tyr->Gly (Y), Tyr->His (Y), Tyr->Lys (Y), Tyr->Met (Y), Tyr->Phe (Y), Tyr->Pro (Y), Tyr->Ser (Y), Tyr->Thr (Y), Tyr->Trp (Y), Tyr->Val (Y), Tyr->Xle (Y), Ub-Br2 (C), Ub-fluorescein (C), Ub-VME (C), UgiJoullie (D), UgiJoullie (E), UgiJoullieProGly (D), UgiJoullieProGly (E), UgiJoullieProGlyProGly (D), UgiJoullieProGlyProGly (E), Unknown:162 (C-term), Unknown:162 (D), Unknown:162 (E), Unknown:162 (N-term), Unknown:177 (C-term), Unknown:177 (D), Unknown:177 (E), Unknown:177 (N-term), Unknown:210 (C-term), Unknown:210 (D), Unknown:210 (E), Unknown:210 (N-term), Unknown:216 (C-term), Unknown:216 (D), Unknown:216 (E), Unknown:216 (N-term), Unknown:234 (C-term), Unknown:234 (D), Unknown:234 (E), Unknown:234 (N-term), Unknown:248 (C-term), Unknown:248 (D), Unknown:248 (E), Unknown:248 (N-term), Unknown:250 (C-term), Unknown:250 (D), Unknown:250 (E), Unknown:250 (N-term), Unknown:302 (C-term), Unknown:302 (D), Unknown:302 (E), Unknown:302 (N-term), Unknown:306 (C-term), Unknown:306 (D), Unknown:306 (E), Unknown:306 (N-term), Unknown:420 (C-term), Unknown:420 (N-term), Val->Ala (V), Val->Arg (V), Val->Asn (V), Val->Asp (V), Val->Cys (V), Val->Gln (V), Val->Glu (V), Val->Gly (V), Val->His (V), Val->Lys (V), Val->Met (V), Val->Phe (V), Val->Pro (V), Val->Ser (V), Val->Thr (V), Val->Trp (V), Val->Tyr (V), Val->Xle (V), ValGly (K), VFQQQTGG (K), VIEVYQEQTGG (K), Withaferin (C), Xle->Ala (I), Xle->Ala (L), Xle->Arg (I), Xle->Arg (L), Xle->Asn (I), Xle->Asn (L), Xle->Asp (I), Xle->Asp (L), Xle->Cys (I), Xle->Cys (L), Xle->Gln (I), Xle->Gln (L), Xle->Glu (I), Xle->Glu (L), Xle->Gly (I), Xle->Gly (L), Xle->His (I), Xle->His (L), Xle->Lys (I), Xle->Lys (L), Xle->Met (I), Xle->Met (L), Xle->Phe (I), Xle->Phe (L), Xle->Pro (I), Xle->Pro (L), Xle->Ser (I), Xle->Ser (L), Xle->Thr (I), Xle->Thr (L), Xle->Trp (I), Xle->Trp (L), Xle->Tyr (I), Xle->Tyr (L), Xle->Val (I), Xle->Val (L), Xlink:B10621 (C), Xlink:BMOE (C), Xlink:BS2G[113] (K), Xlink:BS2G[113] (Protein N-term), Xlink:BS2G[114] (K), Xlink:BS2G[114] (Protein N-term), Xlink:BS2G[217] (K), Xlink:BS2G[217] (Protein N-term), Xlink:BS2G[96] (K), Xlink:BS2G[96] (Protein N-term), Xlink:BuUrBu[111] (K), Xlink:BuUrBu[111] (Protein N-term), Xlink:BuUrBu[111] (S), Xlink:BuUrBu[111] (T), Xlink:BuUrBu[111] (Y), Xlink:BuUrBu[196] (K), Xlink:BuUrBu[196] (Protein N-term), Xlink:BuUrBu[196] (S), Xlink:BuUrBu[196] (T), Xlink:BuUrBu[196] (Y), Xlink:BuUrBu[213] (K), Xlink:BuUrBu[213] (Protein N-term), Xlink:BuUrBu[213] (S), Xlink:BuUrBu[213] (T), Xlink:BuUrBu[213] (Y), Xlink:BuUrBu[214] (K), Xlink:BuUrBu[214] (Protein N-term), Xlink:BuUrBu[214] (S), Xlink:BuUrBu[214] (T), Xlink:BuUrBu[214] (Y), Xlink:BuUrBu[317] (K), Xlink:BuUrBu[317] (Protein N-term), Xlink:BuUrBu[317] (S), Xlink:BuUrBu[317] (T), Xlink:BuUrBu[317] (Y), Xlink:BuUrBu[85] (K), Xlink:BuUrBu[85] (Protein N-term), Xlink:BuUrBu[85] (S), Xlink:BuUrBu[85] (T), Xlink:BuUrBu[85] (Y), Xlink:DFDNB (K), Xlink:DFDNB (N), Xlink:DFDNB (Q), Xlink:DFDNB (R), Xlink:DMP[122] (K), Xlink:DMP[122] (Protein N-term), Xlink:DMP[139] (K), Xlink:DMP[139] (Protein N-term), Xlink:DMP[140] (K), Xlink:DMP[140] (Protein N-term), Xlink:DMP[154] (K), Xlink:DMP[154] (Protein N-term), Xlink:DSPP[210] (K), Xlink:DSPP[210] (Protein N-term), Xlink:DSPP[226] (K), Xlink:DSPP[226] (Protein N-term), Xlink:DSPP[228] (K), Xlink:DSPP[228] (Protein N-term), Xlink:DSPP[331] (K), Xlink:DSPP[331] (Protein N-term), Xlink:DSS[138] (K), Xlink:DSS[138] (Protein N-term), Xlink:DSS[155] (K), Xlink:DSS[155] (Protein N-term), Xlink:DSS[156] (K), Xlink:DSS[156] (Protein N-term), Xlink:DSS[259] (K), Xlink:DSS[259] (Protein N-term), Xlink:DSSO[104] (K), Xlink:DSSO[104] (Protein N-term), Xlink:DSSO[158] (K), Xlink:DSSO[158] (Protein N-term), Xlink:DSSO[175] (K), Xlink:DSSO[175] (Protein N-term), Xlink:DSSO[176] (K), Xlink:DSSO[176] (Protein N-term), Xlink:DSSO[279] (K), Xlink:DSSO[279] (Protein N-term), Xlink:DSSO[54] (K), Xlink:DSSO[54] (Protein N-term), Xlink:DSSO[86] (K), Xlink:DSSO[86] (Protein N-term), Xlink:DST[114] (K), Xlink:DST[114] (Protein N-term), Xlink:DST[132] (K), Xlink:DST[132] (Protein N-term), Xlink:DST[56] (K), Xlink:DST[56] (Protein N-term), Xlink:DTBP[172] (K), Xlink:DTBP[172] (Protein N-term), Xlink:DTBP[87] (K), Xlink:DTBP[87] (Protein N-term), Xlink:DTSSP[174] (K), Xlink:DTSSP[174] (Protein N-term), Xlink:DTSSP[192] (K), Xlink:DTSSP[192] (Protein N-term), Xlink:DTSSP[88] (K), Xlink:DTSSP[88] (Protein N-term), Xlink:EGS[115] (K), Xlink:EGS[115] (Protein N-term), Xlink:EGS[226] (K), Xlink:EGS[226] (Protein N-term), Xlink:EGS[244] (K), Xlink:EGS[244] (Protein N-term), Xlink:SMCC[219] (C), Xlink:SMCC[219] (K), Xlink:SMCC[219] (Protein N-term), Xlink:SMCC[237] (C), Xlink:SMCC[237] (K), Xlink:SMCC[237] (Protein N-term), Xlink:SMCC[321] (C), ZGB (K), ZGB (N-term), ZQG (K)

variable[Oxidation (M), Acetyl (Protein N-term)] Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'. A terminus and a residue carry one modification each: a variable terminal modification (e.g. 'Acetyl (Protein N-term)', 'Gln->pyro-Glu (N-term Q)') is not searched where a fixed one sits on that terminus (e.g. 'TMT6plex (N-term)'), and a variable residue modification (e.g. 'Glutathione (C)') is not searched where a fixed one sits on that residue (e.g. 'Carbamidomethyl (C)').15N-oxobutanoic (N-term C), 15N-oxobutanoic (Protein N-term S), 15N-oxobutanoic (Protein N-term T), 2-dimethylsuccinyl (C), 2-methylbutyryl (K), 2-monomethylsuccinyl (C), 2-nitrobenzyl (Y), 2-succinyl (C), 2HPG (R), 2PCA-triazole-ethanethiol (N-term), 3-deoxyglucosone (R), 3-hydroxy-3-methylglutaryl (K), 3-hydroxybenzyl-phosphate (K), 3-hydroxybenzyl-phosphate (S), 3-hydroxybenzyl-phosphate (T), 3-hydroxybenzyl-phosphate (Y), 3-methylglutaconyl (K), 3-methylglutaryl (K), 3-phosphoglyceryl (K), 3sulfo (N-term), 4-ONE (C), 4-ONE (H), 4-ONE (K), 4-ONE+Delta:H(-2)O(-1) (C), 4-ONE+Delta:H(-2)O(-1) (H), 4-ONE+Delta:H(-2)O(-1) (K), 4AcAllylGal (C), 6C-CysPAT (C), 6C-CysPAT (D), 6C-CysPAT (E), 6C-CysPAT (H), 6C-CysPAT (K), 6C-CysPAT (N-term), 6C-CysPAT (S), 6C-CysPAT (T), 6C-CysPAT (Y), a-type-ion (C-term), AccQTag (K), AccQTag (N-term), Acetoacetyl (K), Acetyl (C), Acetyl (H), Acetyl (K), Acetyl (N-term), Acetyl (Protein N-term), Acetyl (R), Acetyl (S), Acetyl (T), Acetyl (Y), Acetyl:13C(2) (K), Acetyl:13C(2) (Protein N-term), Acetyl:2H(3) (H), Acetyl:2H(3) (K), Acetyl:2H(3) (N-term), Acetyl:2H(3) (Protein N-term), Acetyl:2H(3) (S), Acetyl:2H(3) (T), Acetyl:2H(3) (Y), Acetyldeoxyhypusine (K), Acetylhypusine (K), ADP-Ribosyl (C), ADP-Ribosyl (D), ADP-Ribosyl (E), ADP-Ribosyl (K), ADP-Ribosyl (N), ADP-Ribosyl (R), ADP-Ribosyl (S), ADP-Ribosyl (T), AEBS (H), AEBS (K), AEBS (Protein N-term), AEBS (S), AEBS (Y), AEC-MAEC (S), AEC-MAEC (T), AEC-MAEC:2H(4) (S), AEC-MAEC:2H(4) (T), AFB1_Dialdehyde (K), AHA-Alkyne (M), AHA-Alkyne-KDDDD (M), AHA-SS (M), AHA-SS_CAM (M), Ahx2+Hsl (C-term), Ala->Arg (A), Ala->Asn (A), Ala->Asp (A), Ala->Cys (A), Ala->Gln (A), Ala->Glu (A), Ala->Gly (A), Ala->His (A), Ala->Lys (A), Ala->Met (A), Ala->Phe (A), Ala->Pro (A), Ala->Ser (A), Ala->Thr (A), Ala->Trp (A), Ala->Tyr (A), Ala->Val (A), Ala->Xle (A), Amidated (C-term), Amidated (Protein C-term), Amidine (K), Amidine (N-term), Amidino (C), Amino (Y), Ammonia-loss (N), Ammonia-loss (N-term C), Ammonia-loss (Protein N-term S), Ammonia-loss (Protein N-term T), Ammonium (C-term), Ammonium (D), Ammonium (E), AMTzHexNAc2 (N), AMTzHexNAc2 (S), AMTzHexNAc2 (T), Andro-H2O (C), Archaeol (C), Arg (N-term), Arg->Ala (R), Arg->Asn (R), Arg->Asp (R), Arg->Cys (R), Arg->Gln (R), Arg->Glu (R), Arg->GluSA (R), Arg->Gly (R), Arg->His (R), Arg->Lys (R), Arg->Met (R), Arg->Npo (R), Arg->Orn (R), Arg->Phe (R), Arg->Pro (R), Arg->Ser (R), Arg->Thr (R), Arg->Trp (R), Arg->Tyr (R), Arg->Val (R), Arg->Xle (R), Arg-loss (C-term R), Arg2PG (R), Argbiotinhydrazide (R), AROD (C), Asn->Ala (N), Asn->Arg (N), Asn->Asp (N), Asn->Cys (N), Asn->Gln (N), Asn->Glu (N), Asn->Gly (N), Asn->His (N), Asn->Lys (N), Asn->Met (N), Asn->Phe (N), Asn->Pro (N), Asn->Ser (N), Asn->Thr (N), Asn->Trp (N), Asn->Tyr (N), Asn->Val (N), Asn->Xle (N), Asp->Ala (D), Asp->Arg (D), Asp->Asn (D), Asp->Cys (D), Asp->Gln (D), Asp->Glu (D), Asp->Gly (D), Asp->His (D), Asp->Lys (D), Asp->Met (D), Asp->Phe (D), Asp->Pro (D), Asp->Ser (D), Asp->Thr (D), Asp->Trp (D), Asp->Tyr (D), Asp->Val (D), Asp->Xle (D), Aspartylurea (H), Atto495Maleimide (C), AzidoF (F), azole (C), azole (S), Bacillosamine (N), BADGE (C), BDMAPP (H), BDMAPP (K), BDMAPP (Protein N-term), BDMAPP (W), BDMAPP (Y), BEMAD_C (C), BEMAD_C:2H(6) (C), BEMAD_ST (S), BEMAD_ST (T), BEMAD_ST:2H(6) (S), BEMAD_ST:2H(6) (T), Benzoyl (K), Benzoyl (N-term), benzylguanidine (K), betaFNA (C), betaFNA (K), BHT (C), BHT (H), BHT (K), BHTOH (C), BHTOH (H), BHTOH (K), Biotin (K), Biotin (N-term), Biotin-HPDP (C), Biotin-PEG-PRA (M), Biotin-PEO-Amine (D), Biotin-PEO-Amine (E), Biotin-PEO-Amine (Protein C-term), Biotin-phenacyl (C), Biotin-phenacyl (H), Biotin-phenacyl (S), Biotin-tyramide (C), Biotin-tyramide (W), Biotin-tyramide (Y), Biotin:Aha-DADPS (M), Biotin:Aha-PC (M), Biotin:Cayman-10013 (C), Biotin:Cayman-10141 (C), Biotin:Invitrogen-M1602 (C), Biotin:Sigma-B1267 (C), Biotin:Thermo-21325 (K), Biotin:Thermo-21328 (K), Biotin:Thermo-21328 (N-term), Biotin:Thermo-21330 (K), Biotin:Thermo-21330 (N-term), Biotin:Thermo-21345 (Q), Biotin:Thermo-21360 (X), Biotin:Thermo-21901+2H2O (C), Biotin:Thermo-21901+H2O (C), Biotin:Thermo-21911 (C), Biotin:Thermo-33033 (X), Biotin:Thermo-33033-H (X), Biotin:Thermo-88310 (K), Biotin:Thermo-88317 (S), Biotin:Thermo-88317 (Y), biotinAcrolein298 (C), biotinAcrolein298 (H), biotinAcrolein298 (K), biotinAcrolein298 (Protein N-term), BisANS (K), bisANS-sulfonates (K), bisANS-sulfonates (S), bisANS-sulfonates (T), BITC (C), BITC (K), BITC (N-term), BMP-piperidinol (C), BMP-piperidinol (M), Brij35 (N-term), Brij58 (N-term), Bromo (F), Bromo (H), Bromo (W), Bromo (Y), Bromobimane (C), Butyryl (K), C8-QAT (K), C8-QAT (N-term), CAF (N-term), CAMthiopropanoyl (K), CAMthiopropanoyl (Protein N-term), Can-FP-biotin (S), Can-FP-biotin (T), Can-FP-biotin (Y), Carbamidomethyl (C), Carbamidomethyl (D), Carbamidomethyl (E), Carbamidomethyl (H), Carbamidomethyl (K), Carbamidomethyl (M), Carbamidomethyl (N-term), Carbamidomethyl (S), Carbamidomethyl (T), Carbamidomethyl (U), Carbamidomethyl (Y), CarbamidomethylDTT (C), Carbamyl (C), Carbamyl (K), Carbamyl (M), Carbamyl (N-term), Carbamyl (Protein N-term), Carbamyl (R), Carbamyl (S), Carbamyl (T), Carbamyl (Y), Carbofuran (S), Carbonyl (A), Carbonyl (E), Carbonyl (I), Carbonyl (L), Carbonyl (Q), Carbonyl (R), Carbonyl (S), Carbonyl (V), Carboxy (D), Carboxy (E), Carboxy (K), Carboxy (Protein N-term M), Carboxy (W), Carboxy->Thiocarboxy (Protein C-term G), Carboxyethyl (H), Carboxyethyl (K), Carboxyethylpyrrole (K), Carboxymethyl (C), Carboxymethyl (K), Carboxymethyl (N-term), Carboxymethyl (U), Carboxymethyl (W), Carboxymethyl:13C(2) (C), CarboxymethylDMAP (N-term), CarboxymethylDTT (C), Cation:Ag (C-term), Cation:Ag (D), Cation:Ag (E), Cation:Al[III] (C-term), Cation:Al[III] (D), Cation:Al[III] (E), Cation:Ca[II] (C-term), Cation:Ca[II] (D), Cation:Ca[II] (E), Cation:Cu[I] (C-term), Cation:Cu[I] (D), Cation:Cu[I] (E), Cation:Cu[I] (H), Cation:Fe[II] (C-term), Cation:Fe[II] (D), Cation:Fe[II] (E), Cation:Fe[III] (C-term), Cation:Fe[III] (D), Cation:Fe[III] (E), Cation:K (C-term), Cation:K (D), Cation:K (E), Cation:Li (C-term), Cation:Li (D), Cation:Li (E), Cation:Mg[II] (C-term), Cation:Mg[II] (D), Cation:Mg[II] (E), Cation:Na (C-term), Cation:Na (D), Cation:Na (E), Cation:Ni[II] (C-term), Cation:Ni[II] (D), Cation:Ni[II] (E), Cation:Zn[II] (C-term), Cation:Zn[II] (D), Cation:Zn[II] (E), Cation:Zn[II] (H), cGMP (C), cGMP (S), cGMP+RMP-loss (C), cGMP+RMP-loss (S), CHDH (D), Chlorination (W), Chlorination (Y), Cholesterol (Protein C-term), CIGG (K), CLIP_TRAQ_2 (K), CLIP_TRAQ_2 (N-term), CLIP_TRAQ_2 (Y), CLIP_TRAQ_3 (K), CLIP_TRAQ_3 (N-term), CLIP_TRAQ_3 (Y), CLIP_TRAQ_4 (K), CLIP_TRAQ_4 (N-term), CLIP_TRAQ_4 (Y), CoenzymeA (C), Cresylphosphate (H), Cresylphosphate (K), Cresylphosphate (R), Cresylphosphate (S), Cresylphosphate (T), Cresylphosphate (Y), CresylSaligeninPhosphate (H), CresylSaligeninPhosphate (K), CresylSaligeninPhosphate (R), CresylSaligeninPhosphate (S), CresylSaligeninPhosphate (T), CresylSaligeninPhosphate (Y), Crotonaldehyde (C), Crotonaldehyde (H), Crotonaldehyde (K), Crotonyl (K), CuSMo (C), CUSTOM0 (A), CUSTOM0 (C), CUSTOM0 (C-term), CUSTOM0 (D), CUSTOM0 (E), CUSTOM0 (F), CUSTOM0 (G), CUSTOM0 (H), CUSTOM0 (I), CUSTOM0 (K), CUSTOM0 (L), CUSTOM0 (M), CUSTOM0 (N), CUSTOM0 (N-term), CUSTOM0 (P), CUSTOM0 (Q), CUSTOM0 (R), CUSTOM0 (S), CUSTOM0 (T), CUSTOM0 (V), CUSTOM0 (W), CUSTOM0 (Y), CUSTOM1 (A), CUSTOM1 (C), CUSTOM1 (C-term), CUSTOM1 (D), CUSTOM1 (E), CUSTOM1 (F), CUSTOM1 (G), CUSTOM1 (H), CUSTOM1 (I), CUSTOM1 (K), CUSTOM1 (L), CUSTOM1 (M), CUSTOM1 (N), CUSTOM1 (N-term), CUSTOM1 (P), CUSTOM1 (Q), CUSTOM1 (R), CUSTOM1 (S), CUSTOM1 (T), CUSTOM1 (V), CUSTOM1 (W), CUSTOM1 (Y), CUSTOM2 (A), CUSTOM2 (C), CUSTOM2 (C-term), CUSTOM2 (D), CUSTOM2 (E), CUSTOM2 (F), CUSTOM2 (G), CUSTOM2 (H), CUSTOM2 (I), CUSTOM2 (K), CUSTOM2 (L), CUSTOM2 (M), CUSTOM2 (N), CUSTOM2 (N-term), CUSTOM2 (P), CUSTOM2 (Q), CUSTOM2 (R), CUSTOM2 (S), CUSTOM2 (T), CUSTOM2 (V), CUSTOM2 (W), CUSTOM2 (Y), CUSTOM3 (A), CUSTOM3 (C), CUSTOM3 (C-term), CUSTOM3 (D), CUSTOM3 (E), CUSTOM3 (F), CUSTOM3 (G), CUSTOM3 (H), CUSTOM3 (I), CUSTOM3 (K), CUSTOM3 (L), CUSTOM3 (M), CUSTOM3 (N), CUSTOM3 (N-term), CUSTOM3 (P), CUSTOM3 (Q), CUSTOM3 (R), CUSTOM3 (S), CUSTOM3 (T), CUSTOM3 (V), CUSTOM3 (W), CUSTOM3 (Y), CUSTOM4 (A), CUSTOM4 (C), CUSTOM4 (C-term), CUSTOM4 (D), CUSTOM4 (E), CUSTOM4 (F), CUSTOM4 (G), CUSTOM4 (H), CUSTOM4 (I), CUSTOM4 (K), CUSTOM4 (L), CUSTOM4 (M), CUSTOM4 (N), CUSTOM4 (N-term), CUSTOM4 (P), CUSTOM4 (Q), CUSTOM4 (R), CUSTOM4 (S), CUSTOM4 (T), CUSTOM4 (V), CUSTOM4 (W), CUSTOM4 (Y), CUSTOM5 (A), CUSTOM5 (C), CUSTOM5 (C-term), CUSTOM5 (D), CUSTOM5 (E), CUSTOM5 (F), CUSTOM5 (G), CUSTOM5 (H), CUSTOM5 (I), CUSTOM5 (K), CUSTOM5 (L), CUSTOM5 (M), CUSTOM5 (N), CUSTOM5 (N-term), CUSTOM5 (P), CUSTOM5 (Q), CUSTOM5 (R), CUSTOM5 (S), CUSTOM5 (T), CUSTOM5 (V), CUSTOM5 (W), CUSTOM5 (Y), CUSTOM6 (A), CUSTOM6 (C), CUSTOM6 (C-term), CUSTOM6 (D), CUSTOM6 (E), CUSTOM6 (F), CUSTOM6 (G), CUSTOM6 (H), CUSTOM6 (I), CUSTOM6 (K), CUSTOM6 (L), CUSTOM6 (M), CUSTOM6 (N), CUSTOM6 (N-term), CUSTOM6 (P), CUSTOM6 (Q), CUSTOM6 (R), CUSTOM6 (S), CUSTOM6 (T), CUSTOM6 (V), CUSTOM6 (W), CUSTOM6 (Y), CUSTOM7 (A), CUSTOM7 (C), CUSTOM7 (C-term), CUSTOM7 (D), CUSTOM7 (E), CUSTOM7 (F), CUSTOM7 (G), CUSTOM7 (H), CUSTOM7 (I), CUSTOM7 (K), CUSTOM7 (L), CUSTOM7 (M), CUSTOM7 (N), CUSTOM7 (N-term), CUSTOM7 (P), CUSTOM7 (Q), CUSTOM7 (R), CUSTOM7 (S), CUSTOM7 (T), CUSTOM7 (V), CUSTOM7 (W), CUSTOM7 (Y), CUSTOM8 (A), CUSTOM8 (C), CUSTOM8 (C-term), CUSTOM8 (D), CUSTOM8 (E), CUSTOM8 (F), CUSTOM8 (G), CUSTOM8 (H), CUSTOM8 (I), CUSTOM8 (K), CUSTOM8 (L), CUSTOM8 (M), CUSTOM8 (N), CUSTOM8 (N-term), CUSTOM8 (P), CUSTOM8 (Q), CUSTOM8 (R), CUSTOM8 (S), CUSTOM8 (T), CUSTOM8 (V), CUSTOM8 (W), CUSTOM8 (Y), CUSTOM9 (A), CUSTOM9 (C), CUSTOM9 (C-term), CUSTOM9 (D), CUSTOM9 (E), CUSTOM9 (F), CUSTOM9 (G), CUSTOM9 (H), CUSTOM9 (I), CUSTOM9 (K), CUSTOM9 (L), CUSTOM9 (M), CUSTOM9 (N), CUSTOM9 (N-term), CUSTOM9 (P), CUSTOM9 (Q), CUSTOM9 (R), CUSTOM9 (S), CUSTOM9 (T), CUSTOM9 (V), CUSTOM9 (W), CUSTOM9 (Y), Cy3-maleimide (C), Cy3b-maleimide (C), Cyano (C), CyDye-Cy3 (C), CyDye-Cy5 (C), Cys->Ala (C), Cys->Arg (C), Cys->Asn (C), Cys->Asp (C), Cys->CamSec (C), Cys->Dha (C), Cys->ethylaminoAla (C), Cys->Gln (C), Cys->Glu (C), Cys->Gly (C), Cys->His (C), Cys->Lys (C), Cys->Met (C), Cys->methylaminoAla (C), Cys->Oxoalanine (C), Cys->Phe (C), Cys->Pro (C), Cys->PyruvicAcid (Protein N-term C), Cys->SecNEM (C), Cys->SecNEM:2H(5) (C), Cys->Ser (C), Cys->Thr (C), Cys->Trp (C), Cys->Tyr (C), Cys->Val (C), Cys->Xle (C), Cysteinyl (C), cysTMT (C), cysTMT6plex (C), Cytopiloyne (C), Cytopiloyne (K), Cytopiloyne (N-term), Cytopiloyne (P), Cytopiloyne (R), Cytopiloyne (S), Cytopiloyne (Y), Cytopiloyne+water (C), Cytopiloyne+water (K), Cytopiloyne+water (N-term), Cytopiloyne+water (R), Cytopiloyne+water (S), Cytopiloyne+water (T), Cytopiloyne+water (Y), DABCYL-C2-maleimide (C), DABCYL-C2-maleimide (K), DAET (S), DAET (T), Dansyl (K), Dansyl (N-term), Dap-DSP (A), Dap-DSP (E), Dap-DSP (K), DBIA (C), DCP (C), Deamidated (N), Deamidated (Protein N-term F), Deamidated (Q), Deamidated (R), Deamidated:18O(1) (N), Deamidated:18O(1) (Q), Decanoyl (S), Decanoyl (T), Decarboxylation (D), Decarboxylation (E), DEDGFLYMVYASQETFG (K), Dehydrated (D), Dehydrated (N-term C), Dehydrated (Protein C-term N), Dehydrated (Protein C-term Q), Dehydrated (S), Dehydrated (T), Dehydrated (Y), Dehydro (C), Delta:H(-1)N(-1)18O(1) (N), Delta:H(-4)O(2) (W), Delta:H(-4)O(3) (W), Delta:H(10)C(8)O(1) (K), Delta:H(2)C(2) (H), Delta:H(2)C(2) (K), Delta:H(2)C(2) (N-term), Delta:H(2)C(2) (Protein N-term), Delta:H(2)C(3) (K), Delta:H(2)C(3)O(1) (K), Delta:H(2)C(3)O(1) (R), Delta:H(2)C(5) (K), Delta:H(4)C(2) (H), Delta:H(4)C(2) (K), Delta:H(4)C(2) (N-term), Delta:H(4)C(2)O(-1)S(1) (S), Delta:H(4)C(3) (H), Delta:H(4)C(3) (K), Delta:H(4)C(3) (Protein N-term), Delta:H(4)C(3)O(1) (C), Delta:H(4)C(3)O(1) (H), Delta:H(4)C(3)O(1) (K), Delta:H(4)C(3)O(1) (R), Delta:H(4)C(3)O(2) (K), Delta:H(4)C(5)O(1) (R), Delta:H(4)C(6) (K), Delta:H(5)C(2) (P), Delta:H(6)C(3)O(1) (C), Delta:H(6)C(3)O(1) (H), Delta:H(6)C(3)O(1) (K), Delta:H(6)C(3)O(1) (Protein N-term), Delta:H(6)C(6)O(1) (K), Delta:H(6)C(7)O(4) (R), Delta:H(8)C(6)O(1) (K), Delta:H(8)C(6)O(1) (Protein N-term), Delta:H(8)C(6)O(2) (K), Delta:Hg(1) (C), Delta:O(4) (W), Delta:S(-1)Se(1) (C), Delta:S(-1)Se(1) (M), Delta:Se(1) (C), Deoxy (D), Deoxy (S), Deoxy (T), Deoxyhypusine (K), Deoxyhypusine (Q), DeStreak (C), Dethiomethyl (M), dHex (N), dHex (S), dHex (T), dHex(1)Hex(1) (S), dHex(1)Hex(1) (T), dHex(1)Hex(1)HexA(1)HexNAc(3) (S), dHex(1)Hex(1)HexA(1)HexNAc(3) (T), dHex(1)Hex(1)HexNAc(1)Kdn(1) (S), dHex(1)Hex(1)HexNAc(1)Kdn(1) (T), dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S), dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T), dHex(1)Hex(1)HexNAc(2)Kdn(1) (S), dHex(1)Hex(1)HexNAc(2)Kdn(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T), dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S), dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T), dHex(1)Hex(1)HexNAc(2)Sulf(1) (S), dHex(1)Hex(1)HexNAc(2)Sulf(1) (T), dHex(1)Hex(1)HexNAc(3) (S), dHex(1)Hex(1)HexNAc(3) (T), dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S), dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T), dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S), dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T), dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S), dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T), dHex(1)Hex(1)HexNAc(3)Sulf(1) (S), dHex(1)Hex(1)HexNAc(3)Sulf(1) (T), dHex(1)Hex(1)HexNAc(4) (S), dHex(1)Hex(1)HexNAc(4) (T), dHex(1)Hex(2) (S), dHex(1)Hex(2) (T), dHex(1)Hex(2)HexA(1) (S), dHex(1)Hex(2)HexA(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(1) (S), dHex(1)Hex(2)HexA(1)HexNAc(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S), dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T), dHex(1)Hex(2)HexA(1)HexNAc(2) (S), dHex(1)Hex(2)HexA(1)HexNAc(2) (T), dHex(1)Hex(2)HexNAc(1) (S), dHex(1)Hex(2)HexNAc(1) (T), dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S), dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T), dHex(1)Hex(2)HexNAc(1)Sulf(1) (S), dHex(1)Hex(2)HexNAc(1)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T), dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S), dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S), dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T), 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dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S), dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T), dHex(1)Hex(3)HexA(1)HexNAc(2) (S), dHex(1)Hex(3)HexA(1)HexNAc(2) (T), dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S), dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T), dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S), dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T), dHex(1)Hex(3)HexA(2)HexNAc(2) (S), dHex(1)Hex(3)HexA(2)HexNAc(2) (T), dHex(1)Hex(3)HexNAc(1) (S), dHex(1)Hex(3)HexNAc(1) (T), dHex(1)Hex(3)HexNAc(1)Sulf(1) (S), dHex(1)Hex(3)HexNAc(1)Sulf(1) (T), dHex(1)Hex(3)HexNAc(2) (N), dHex(1)Hex(3)HexNAc(2) (S), dHex(1)Hex(3)HexNAc(2) (T), dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S), dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T), dHex(1)Hex(3)HexNAc(2)Pent(1) (N), dHex(1)Hex(3)HexNAc(2)Sulf(1) (N), dHex(1)Hex(3)HexNAc(2)Sulf(1) (S), dHex(1)Hex(3)HexNAc(2)Sulf(1) (T), dHex(1)Hex(3)HexNAc(3) (N), dHex(1)Hex(3)HexNAc(3) (S), dHex(1)Hex(3)HexNAc(3) (T), dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S), dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T), dHex(1)Hex(3)HexNAc(3)Pent(1) 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dHex(2)Hex(3)HexNAc(5) (T), dHex(2)Hex(3)HexNAc(6) (N), dHex(2)Hex(4) (S), dHex(2)Hex(4) (T), dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S), dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T), dHex(2)Hex(4)HexNAc(1) (S), dHex(2)Hex(4)HexNAc(1) (T), dHex(2)Hex(4)HexNAc(2) (N), dHex(2)Hex(4)HexNAc(2) (S), dHex(2)Hex(4)HexNAc(2) (T), dHex(2)Hex(4)HexNAc(3) (N), dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N), dHex(2)Hex(4)HexNAc(3)Pent(1) (N), dHex(2)Hex(4)HexNAc(4) (N), dHex(2)Hex(4)HexNAc(4) (S), dHex(2)Hex(4)HexNAc(4) (T), dHex(2)Hex(4)HexNAc(4)Pent(1) (N), dHex(2)Hex(4)HexNAc(4)Sulf(1) (N), dHex(2)Hex(4)HexNAc(5) (N), dHex(2)Hex(4)HexNAc(5) (S), dHex(2)Hex(4)HexNAc(5) (T), dHex(2)Hex(5)HexNAc(2)Me(1) (S), dHex(2)Hex(5)HexNAc(2)Me(1) (T), dHex(2)Hex(5)HexNAc(3)Pent(1) (N), dHex(2)Hex(5)HexNAc(4) (N), dHex(2)HexNAc(2)Kdn(1) (S), dHex(2)HexNAc(2)Kdn(1) (T), dHex(2)HexNAc(5) (S), dHex(2)HexNAc(5) (T), dHex(2)HexNAc(7) (S), dHex(2)HexNAc(7) (T), dHex(3)Hex(1)HexNAc(2)Kdn(1) (S), dHex(3)Hex(1)HexNAc(2)Kdn(1) (T), dHex(3)Hex(1)HexNAc(3)Kdn(1) (S), dHex(3)Hex(1)HexNAc(3)Kdn(1) (T), dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S), dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T), dHex(3)Hex(2)HexNAc(2) (S), dHex(3)Hex(2)HexNAc(2) (T), dHex(3)Hex(2)HexNAc(2)Kdn(1) (S), dHex(3)Hex(2)HexNAc(2)Kdn(1) (T), dHex(3)Hex(2)HexNAc(3) (S), dHex(3)Hex(2)HexNAc(3) (T), dHex(3)Hex(2)HexNAc(3)Kdn(1) (S), dHex(3)Hex(2)HexNAc(3)Kdn(1) (T), dHex(3)Hex(2)HexNAc(4) (S), dHex(3)Hex(2)HexNAc(4) (T), dHex(3)Hex(2)HexNAc(4)Sulf(2) (S), dHex(3)Hex(2)HexNAc(4)Sulf(2) (T), dHex(3)Hex(3)HexNAc(1) (S), dHex(3)Hex(3)HexNAc(1) (T), dHex(3)Hex(3)HexNAc(2) (S), dHex(3)Hex(3)HexNAc(2) (T), dHex(3)Hex(3)HexNAc(3) (S), dHex(3)Hex(3)HexNAc(3) (T), dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S), dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T), dHex(3)Hex(3)HexNAc(3)Pent(1) (N), dHex(3)Hex(3)HexNAc(4) (N), dHex(3)Hex(3)HexNAc(4)Pent(1) (N), dHex(3)Hex(4)HexNAc(4) (N), dHex(3)Hex(4)HexNAc(4) (S), dHex(3)Hex(4)HexNAc(4) (T), dHex(3)Hex(4)HexNAc(4)Sulf(1) (N), dHex(3)HexNAc(3)Kdn(1) (S), dHex(3)HexNAc(3)Kdn(1) (T), dHex(4)Hex(1)HexNAc(1)Kdn(2) (S), dHex(4)Hex(1)HexNAc(1)Kdn(2) (T), dHex(4)Hex(1)HexNAc(2)Kdn(1) (S), dHex(4)Hex(1)HexNAc(2)Kdn(1) (T), dHex(4)Hex(1)HexNAc(3)Kdn(1) (S), dHex(4)Hex(1)HexNAc(3)Kdn(1) (T), dHex(4)Hex(2)HexNAc(2)Kdn(1) (S), dHex(4)Hex(2)HexNAc(2)Kdn(1) (T), dHex(4)Hex(2)HexNAc(3) (S), dHex(4)Hex(2)HexNAc(3) (T), dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S), dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T), dHex(4)Hex(3)HexNAc(3) (S), dHex(4)Hex(3)HexNAc(3) (T), dHex(4)HexNAc(3)Kdn(1) (S), dHex(4)HexNAc(3)Kdn(1) (T), DHP (C), Di_L-Gln_Ngamma-propargyl-L-Gln_desthiobiotin (D), Di_L-Gln_Ngamma-propargyl-L-Gln_desthiobiotin (E), Di_L-Glu_Ngamma-propargyl-L-Gln_desthiobiotin (D), Di_L-Glu_Ngamma-propargyl-L-Gln_desthiobiotin (E), Diacylglycerol (C), DiART6plex (K), DiART6plex (N-term), DiART6plex (Protein N-term), DiART6plex (Y), DiART6plex115 (K), DiART6plex115 (N-term), DiART6plex115 (Protein N-term), DiART6plex115 (Y), DiART6plex116/119 (K), DiART6plex116/119 (N-term), DiART6plex116/119 (Protein N-term), DiART6plex116/119 (Y), DiART6plex117 (K), DiART6plex117 (N-term), DiART6plex117 (Protein N-term), DiART6plex117 (Y), DiART6plex118 (K), DiART6plex118 (N-term), DiART6plex118 (Protein N-term), DiART6plex118 (Y), Dibromo (Y), Dicarbamidomethyl (C), Dicarbamidomethyl (H), Dicarbamidomethyl (K), Dicarbamidomethyl (N-term), Dicarbamidomethyl (R), dichlorination (C), dichlorination (Y), Didehydro (C-term K), Didehydro (S), Didehydro (T), Didehydro (Y), Didehydroretinylidene (K), Diethyl (K), Diethyl (N-term), Diethylphosphate (C), Diethylphosphate (H), Diethylphosphate (K), Diethylphosphate (N-term), Diethylphosphate (S), Diethylphosphate (T), Diethylphosphate (Y), Diethylphosphothione (C), Diethylphosphothione (H), Diethylphosphothione (K), Diethylphosphothione (S), Diethylphosphothione (T), Diethylphosphothione (Y), Difuran (Y), Dihydroxyimidazolidine (R), Diiodo (H), Diiodo (Y), Diironsubcluster (C), Diisopropylphosphate (K), Diisopropylphosphate (N-term), Diisopropylphosphate (S), Diisopropylphosphate (T), Diisopropylphosphate (Y), DiLeu4plex (K), DiLeu4plex (N-term), DiLeu4plex (Y), DiLeu4plex115 (K), DiLeu4plex115 (N-term), DiLeu4plex115 (Y), DiLeu4plex117 (K), DiLeu4plex117 (N-term), DiLeu4plex117 (Y), DiLeu4plex118 (K), DiLeu4plex118 (N-term), DiLeu4plex118 (Y), Dimethyl (K), Dimethyl (N), Dimethyl (N-term), Dimethyl (Protein N-term P), Dimethyl (Protein N-term), Dimethyl (R), Dimethyl:2H(2)13C (K), Dimethyl:2H(2)13C (N), Dimethyl:2H(2)13C (N-term), Dimethyl:2H(2)13C (Protein N-term P), Dimethyl:2H(2)13C (R), Dimethyl:2H(4) (K), Dimethyl:2H(4) (N-term), Dimethyl:2H(4) (Protein N-term), Dimethyl:2H(4) (R), Dimethyl:2H(4)13C(2) (K), Dimethyl:2H(4)13C(2) (N-term), Dimethyl:2H(4)13C(2) (Protein N-term), Dimethyl:2H(4)13C(2) (R), Dimethyl:2H(6) (K), Dimethyl:2H(6) (N-term), Dimethyl:2H(6) (R), Dimethyl:2H(6)13C(2) (K), Dimethyl:2H(6)13C(2) (N-term), Dimethyl:2H(6)13C(2) (Protein N-term), Dimethyl:2H(6)13C(2) (R), DimethylamineGMBS (C), Dimethylaminoethyl (C), DimethylArsino (C), Dimethylphosphothione (C), Dimethylphosphothione (H), Dimethylphosphothione (K), Dimethylphosphothione (S), Dimethylphosphothione (T), Dimethylphosphothione (Y), DimethylpyrroleAdduct (K), Dioxidation (C), Dioxidation (E), Dioxidation (F), Dioxidation (I), Dioxidation (K), Dioxidation (L), Dioxidation (M), Dioxidation (P), Dioxidation (R), Dioxidation (U), Dioxidation (V), Dioxidation (W), Dioxidation (Y), Diphthamide (H), Dipyridyl (C), Dipyrrolylmethanemethyl (C), DMPO (C), DMPO (H), DMPO (Y), DNCB_hapten (C), DNCB_hapten (H), DNCB_hapten (K), DNCB_hapten (Y), dNIC (K), dNIC (N-term), DNPS (C), DNPS (W), DPIA (C), DTT (C), DVFQQQTGG (K), DyLight-maleimide (C), DYn-2 (C), EDEDTIDVFQQQTGG (K), EDT-iodoacetyl-PEO-biotin (S), EDT-iodoacetyl-PEO-biotin (T), EDT-maleimide-PEO-biotin (S), EDT-maleimide-PEO-biotin (T), EEEDVIEVYQEQTGG (K), EGCG1 (C), EGCG2 (C), EHD-diphenylpentanone (C), EHD-diphenylpentanone (M), EQAT (C), EQAT:2H(5) (C), EQIGG (K), ESP (K), ESP (N-term), ESP:2H(10) (K), ESP:2H(10) (N-term), Ethanedithiol (S), Ethanedithiol (T), Ethanolamine (C), Ethanolamine (C-term), Ethanolamine (D), Ethanolamine (E), Ethanolyl (C), Ethanolyl (K), Ethanolyl (R), Ethyl (C-term), Ethyl (D), Ethyl (E), Ethyl (K), Ethyl (N-term), Ethyl (Protein N-term), Ethyl+Deamidated (N), Ethyl+Deamidated (Q), ethylamino (S), ethylamino (T), Ethylphosphate (K), Ethylphosphate (N-term), Ethylphosphate (S), Ethylphosphate (T), Ethylphosphate (Y), ethylsulfonylethyl (C), ethylsulfonylethyl (H), ethylsulfonylethyl (K), Ethynyl (C), ExacTagAmine (K), ExacTagThiol (C), FAD (C), FAD (H), FAD (Y), Farnesyl (C), Fluorescein (C), Fluorescein-tyramine (Y), Fluoro (A), Fluoro (F), Fluoro (W), Fluoro (Y), FMN (S), FMN (T), FMNC (C), FMNH (C), FMNH (H), FNEM (C), Formyl (K), Formyl (N-term), Formyl (Protein N-term), Formyl (S), Formyl (T), Formylasparagine (H), FormylMet (Protein N-term), FP-Biotin (K), FP-Biotin (S), FP-Biotin (T), FP-Biotin (Y), FTC (C), FTC (K), FTC (P), FTC (R), FTC (S), Furan (Y), G-H1 (R), Galactosyl (K), Galactosyl (N-term), GEE (Q), GeranylGeranyl (C), GG (C), GG (K), GG (Protein N-term), GG (S), GG (T), GGQ (K), GIST-Quat (K), GIST-Quat (N-term), GIST-Quat:2H(3) (K), GIST-Quat:2H(3) (N-term), GIST-Quat:2H(6) (K), GIST-Quat:2H(6) (N-term), GIST-Quat:2H(9) (K), GIST-Quat:2H(9) (N-term), Gln->Ala (Q), Gln->Arg (Q), Gln->Asn (Q), Gln->Asp (Q), Gln->Cys (Q), Gln->Glu (Q), Gln->Gly (Q), Gln->His (Q), Gln->Lys (Q), Gln->Met (Q), Gln->Phe (Q), Gln->Pro (Q), Gln->pyro-Glu (N-term Q), Gln->Ser (Q), Gln->Thr (Q), Gln->Trp (Q), Gln->Tyr (Q), Gln->Val (Q), Gln->Xle (Q), Glu (E), Glu (Protein C-term), Glu+O(2) (H), Glu->Ala (E), Glu->Arg (E), Glu->Asn (E), Glu->Asp (E), Glu->Cys (E), Glu->Gln (E), Glu->Gly (E), Glu->His (E), Glu->Lys (E), Glu->Met (E), Glu->Phe (E), Glu->Pro (E), Glu->pyro-Glu (N-term E), Glu->pyro-Glu+Methyl (N-term E), Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E), Glu->Ser (E), Glu->Thr (E), Glu->Trp (E), Glu->Tyr (E), Glu->Val (E), Glu->Xle (E), glucosone (R), Glucosylgalactosyl (K), Glucuronyl (Protein N-term), Glucuronyl (S), Glucuronyl (T), GluGlu (E), GluGlu (Protein C-term), GluGluGlu (E), GluGluGlu (Protein C-term), GluGluGluGlu (E), GluGluGluGlu (Protein C-term), Gluratylation (K), Glutathione (C), Gly (K), Gly (S), Gly (T), Gly+O(2) (H), Gly->Ala (G), Gly->Arg (G), Gly->Asn (G), Gly->Asp (G), Gly->Cys (G), Gly->Gln (G), Gly->Glu (G), Gly->His (G), Gly->Lys (G), Gly->Met (G), Gly->Phe (G), Gly->Pro (G), Gly->Ser (G), Gly->Thr (G), Gly->Trp (G), Gly->Tyr (G), Gly->Val (G), Gly->Xle (G), Gly-loss+Amide (C-term G), Glycerophospho (S), Glyceroyl (K), Glyceroyl (Protein N-term), GlycerylPE (E), glycidamide (K), glycidamide (N-term), Glycosyl (P), glyoxalAGE (R), Glyoxylyl (K), GNLLFLACYCIGG (K), GPIanchor (Protein C-term), Guanidinyl (K), Guanidinyl (N-term), Haloxon (C), Haloxon (H), Haloxon (K), Haloxon (S), Haloxon (T), Haloxon (Y), HCysteinyl (C), HCysThiolactone (K), Heme (C), Heme (H), Hep (K), Hep (N), Hep (Q), Hep (R), Hep (S), Hep (T), Hex (C), Hex (K), Hex (N), Hex (N-term), Hex (R), Hex (S), Hex (T), Hex (W), Hex (Y), Hex(1)HexA(1) (S), Hex(1)HexA(1) (T), Hex(1)HexA(1)HexNAc(1) (S), Hex(1)HexA(1)HexNAc(1) (T), Hex(1)HexA(1)HexNAc(2) (S), Hex(1)HexA(1)HexNAc(2) (T), Hex(1)HexNAc(1) (N), Hex(1)HexNAc(1) (S), Hex(1)HexNAc(1) (T), Hex(1)HexNAc(1)dHex(1) (N), Hex(1)HexNAc(1)dHex(1) (S), Hex(1)HexNAc(1)dHex(1) (T), Hex(1)HexNAc(1)dHex(1)Me(1) (S), Hex(1)HexNAc(1)dHex(1)Me(1) (T), Hex(1)HexNAc(1)dHex(1)Me(2) (S), Hex(1)HexNAc(1)dHex(1)Me(2) (T), Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S), Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T), Hex(1)HexNAc(1)NeuAc(1) (N), Hex(1)HexNAc(1)NeuAc(1) (S), Hex(1)HexNAc(1)NeuAc(1) (T), Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S), Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T), Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S), Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T), Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S), Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T), Hex(1)HexNAc(1)NeuAc(2) (N), Hex(1)HexNAc(1)NeuAc(2) (S), Hex(1)HexNAc(1)NeuAc(2) (T), Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S), Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T), Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S), Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T), Hex(1)HexNAc(1)NeuAc(3) (S), Hex(1)HexNAc(1)NeuAc(3) (T), Hex(1)HexNAc(1)NeuGc(1) (S), Hex(1)HexNAc(1)NeuGc(1) (T), Hex(1)HexNAc(1)NeuGc(2) (S), Hex(1)HexNAc(1)NeuGc(2) (T), Hex(1)HexNAc(1)NeuGc(3) (S), Hex(1)HexNAc(1)NeuGc(3) (T), Hex(1)HexNAc(1)NeuGc(4) (S), Hex(1)HexNAc(1)NeuGc(4) (T), Hex(1)HexNAc(1)NeuGc(5) (S), Hex(1)HexNAc(1)NeuGc(5) (T), Hex(1)HexNAc(1)Phos(1) (S), Hex(1)HexNAc(1)Phos(1) (T), Hex(1)HexNAc(1)Sulf(1) (S), Hex(1)HexNAc(1)Sulf(1) (T), Hex(1)HexNAc(2) (N), Hex(1)HexNAc(2) (S), Hex(1)HexNAc(2) (T), Hex(1)HexNAc(2)dHex(1) (N), Hex(1)HexNAc(2)dHex(1) (S), Hex(1)HexNAc(2)dHex(1) (T), Hex(1)HexNAc(2)dHex(1)Pent(1) (N), Hex(1)HexNAc(2)dHex(2) (N), Hex(1)HexNAc(2)dHex(2) (S), Hex(1)HexNAc(2)dHex(2) (T), Hex(1)HexNAc(2)dHex(2)Sulf(1) (S), Hex(1)HexNAc(2)dHex(2)Sulf(1) (T), Hex(1)HexNAc(2)NeuAc(1) (S), Hex(1)HexNAc(2)NeuAc(1) (T), Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S), Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T), Hex(1)HexNAc(2)NeuAc(2) (S), Hex(1)HexNAc(2)NeuAc(2) (T), Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S), Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T), Hex(1)HexNAc(2)NeuGc(1) (S), Hex(1)HexNAc(2)NeuGc(1) (T), Hex(1)HexNAc(2)Pent(1) (N), Hex(1)HexNAc(2)Sulf(1) (S), Hex(1)HexNAc(2)Sulf(1) (T), Hex(1)HexNAc(3) (S), Hex(1)HexNAc(3) (T), Hex(1)HexNAc(3)NeuAc(1) (S), Hex(1)HexNAc(3)NeuAc(1) (T), Hex(1)HexNAc(3)NeuAc(2) (S), Hex(1)HexNAc(3)NeuAc(2) (T), Hex(1)HexNAc(3)NeuGc(1) (S), Hex(1)HexNAc(3)NeuGc(1) (T), Hex(1)HexNAc(3)Sulf(1) (S), Hex(1)HexNAc(3)Sulf(1) (T), Hex(1)HexNAc(4)dHex(1)Sulf(1) (S), Hex(1)HexNAc(4)dHex(1)Sulf(1) (T), Hex(1)NeuAc(1) (S), Hex(1)NeuAc(1) (T), Hex(1)NeuAc(1)Pent(1) (S), Hex(1)NeuAc(1)Pent(1) (T), Hex(1)NeuGc(1) (S), Hex(1)NeuGc(1) (T), Hex(1)Pent(1) (S), Hex(1)Pent(1) (T), Hex(1)Pent(2) (S), Hex(1)Pent(2) (T), Hex(1)Pent(2)Me(1) (S), Hex(1)Pent(2)Me(1) (T), Hex(1)Pent(3) (S), Hex(1)Pent(3) (T), Hex(1)Pent(3)Me(1) (S), Hex(1)Pent(3)Me(1) (T), Hex(10)HexNAc(1) (N), Hex(10)Phos(3) (S), Hex(10)Phos(3) (T), Hex(2) (K), Hex(2) (R), Hex(2) (S), Hex(2) (T), Hex(2)HexA(1)HexNAc(1)Sulf(1) (S), Hex(2)HexA(1)HexNAc(1)Sulf(1) (T), Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S), Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T), Hex(2)HexA(1)Pent(1)Sulf(1) (S), Hex(2)HexA(1)Pent(1)Sulf(1) (T), Hex(2)HexNAc(1) (N), Hex(2)HexNAc(1) (S), Hex(2)HexNAc(1) (T), Hex(2)HexNAc(1)Me(1) (S), Hex(2)HexNAc(1)Me(1) (T), Hex(2)HexNAc(1)NeuGc(1) (S), Hex(2)HexNAc(1)NeuGc(1) (T), Hex(2)HexNAc(1)NeuGc(2) (S), Hex(2)HexNAc(1)NeuGc(2) (T), Hex(2)HexNAc(1)NeuGc(3) (S), Hex(2)HexNAc(1)NeuGc(3) (T), Hex(2)HexNAc(1)NeuGc(4) (S), Hex(2)HexNAc(1)NeuGc(4) (T), Hex(2)HexNAc(1)Pent(1)HexA(1) (S), Hex(2)HexNAc(1)Pent(1)HexA(1) (T), Hex(2)HexNAc(1)Sulf(1) (S), Hex(2)HexNAc(1)Sulf(1) (T), Hex(2)HexNAc(2) (N), Hex(2)HexNAc(2) (S), Hex(2)HexNAc(2) (T), Hex(2)HexNAc(2)dHex(1) (N), Hex(2)HexNAc(2)dHex(1) (S), Hex(2)HexNAc(2)dHex(1) (T), Hex(2)HexNAc(2)NeuAc(1) (N), Hex(2)HexNAc(2)NeuAc(1) (S), Hex(2)HexNAc(2)NeuAc(1) (T), Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S), Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T), Hex(2)HexNAc(2)NeuAc(2) (S), Hex(2)HexNAc(2)NeuAc(2) (T), Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S), Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T), Hex(2)HexNAc(2)NeuGc(1) (S), Hex(2)HexNAc(2)NeuGc(1) (T), Hex(2)HexNAc(2)Pent(1) (N), Hex(2)HexNAc(2)Sulf(1) (S), Hex(2)HexNAc(2)Sulf(1) (T), Hex(2)HexNAc(3) (N), Hex(2)HexNAc(3) (S), Hex(2)HexNAc(3) (T), Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S), Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T), Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S), Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T), Hex(2)HexNAc(3)NeuAc(2) (S), Hex(2)HexNAc(3)NeuAc(2) (T), Hex(2)HexNAc(3)NeuAc(3) (S), Hex(2)HexNAc(3)NeuAc(3) (T), Hex(2)HexNAc(3)NeuGc(1) (S), Hex(2)HexNAc(3)NeuGc(1) (T), Hex(2)HexNAc(3)NeuGc(2) (S), Hex(2)HexNAc(3)NeuGc(2) (T), Hex(2)HexNAc(3)NeuGc(3) (S), Hex(2)HexNAc(3)NeuGc(3) (T), Hex(2)HexNAc(3)Sulf(1) (S), Hex(2)HexNAc(3)Sulf(1) (T), Hex(2)HexNAc(4) (N), Hex(2)HexNAc(4) (S), Hex(2)HexNAc(4) (T), Hex(2)HexNAc(4)NeuAc(1) (S), Hex(2)HexNAc(4)NeuAc(1) (T), Hex(2)HexNAc(5) (S), Hex(2)HexNAc(5) (T), Hex(2)NeuAc(1) (S), Hex(2)NeuAc(1) (T), Hex(2)Pent(2) (S), Hex(2)Pent(2) (T), Hex(2)Pent(2)Me(1) (S), Hex(2)Pent(2)Me(1) (T), Hex(2)Sulf(1) (S), Hex(2)Sulf(1) (T), Hex(3) (N), Hex(3) (S), Hex(3) (T), Hex(3)HexNAc(1) (N), Hex(3)HexNAc(1) (S), Hex(3)HexNAc(1) (T), Hex(3)HexNAc(1)HexA(1) (S), Hex(3)HexNAc(1)HexA(1) (T), Hex(3)HexNAc(1)Me(1) (S), Hex(3)HexNAc(1)Me(1) (T), Hex(3)HexNAc(1)Pent(1) (N), Hex(3)HexNAc(2) (N), Hex(3)HexNAc(2) (S), Hex(3)HexNAc(2) (T), Hex(3)HexNAc(2)NeuAc(1) (N), Hex(3)HexNAc(2)NeuAc(2) (S), Hex(3)HexNAc(2)NeuAc(2) (T), Hex(3)HexNAc(2)Pent(1) (N), Hex(3)HexNAc(2)Phos(1) (N), Hex(3)HexNAc(3) (N), Hex(3)HexNAc(3) (S), Hex(3)HexNAc(3) (T), Hex(3)HexNAc(3)NeuAc(1) (S), Hex(3)HexNAc(3)NeuAc(1) (T), Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S), Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T), Hex(3)HexNAc(3)NeuAc(2) (S), Hex(3)HexNAc(3)NeuAc(2) (T), Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S), Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T), Hex(3)HexNAc(3)NeuAc(3) (S), Hex(3)HexNAc(3)NeuAc(3) (T), Hex(3)HexNAc(3)NeuGc(1) (S), Hex(3)HexNAc(3)NeuGc(1) (T), Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S), Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T), Hex(3)HexNAc(3)Pent(1) (N), Hex(3)HexNAc(3)Sulf(1) (N), Hex(3)HexNAc(3)Sulf(1) (S), Hex(3)HexNAc(3)Sulf(1) (T), Hex(3)HexNAc(4) (N), Hex(3)HexNAc(4) (S), Hex(3)HexNAc(4) (T), Hex(3)HexNAc(4)NeuAc(1) (N), Hex(3)HexNAc(4)NeuAc(2) (N), Hex(3)HexNAc(4)Pent(1) (N), Hex(3)HexNAc(4)Sulf(1) (N), Hex(3)HexNAc(5) (N), Hex(3)HexNAc(5) (S), Hex(3)HexNAc(5) (T), Hex(3)HexNAc(5)NeuAc(1) (N), Hex(3)HexNAc(5)Sulf(1) (N), Hex(3)HexNAc(6) (N), Hex(3)HexNAc(6) (S), Hex(3)HexNAc(6) (T), Hex(3)HexNAc(6)NeuAc(1) (N), Hex(3)HexNAc(6)Sulf(1) (N), Hex(3)HexNAc(6)Sulf(2) (N), Hex(3)HexNAc(7) (N), Hex(3)HexNAc(7)Sulf(1) (N), Hex(4) (S), Hex(4) (T), Hex(4)HexA(1) (S), Hex(4)HexA(1) (T), Hex(4)HexA(1)HexNAc(1) (S), Hex(4)HexA(1)HexNAc(1) (T), Hex(4)HexNAc(1) (N), Hex(4)HexNAc(1) (S), Hex(4)HexNAc(1) (T), Hex(4)HexNAc(2) (N), Hex(4)HexNAc(2)NeuAc(1) (N), Hex(4)HexNAc(2)NeuAc(1) (S), Hex(4)HexNAc(2)NeuAc(1) (T), Hex(4)HexNAc(2)Pent(1) (N), Hex(4)HexNAc(3) (N), Hex(4)HexNAc(3) (S), Hex(4)HexNAc(3) (T), Hex(4)HexNAc(3)NeuAc(1) (N), Hex(4)HexNAc(3)NeuAc(1) (S), Hex(4)HexNAc(3)NeuAc(1) (T), Hex(4)HexNAc(3)NeuAc(2) (N), Hex(4)HexNAc(3)NeuGc(1) (N), Hex(4)HexNAc(3)Pent(1) (N), Hex(4)HexNAc(4) (N), Hex(4)HexNAc(4) (S), Hex(4)HexNAc(4) (T), Hex(4)HexNAc(4)Me(2)Pent(1) (N), Hex(4)HexNAc(4)NeuAc(1) (N), Hex(4)HexNAc(4)NeuAc(1) (S), Hex(4)HexNAc(4)NeuAc(1) (T), Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S), Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T), Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S), Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T), Hex(4)HexNAc(4)NeuGc(1) (N), Hex(4)HexNAc(4)NeuGc(1) (S), Hex(4)HexNAc(4)NeuGc(1) (T), Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S), Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T), Hex(4)HexNAc(4)Pent(1) (N), Hex(4)HexNAc(4)Sulf(1) (N), Hex(4)HexNAc(4)Sulf(2) (S), Hex(4)HexNAc(4)Sulf(2) (T), Hex(4)HexNAc(5) (N), Hex(4)HexNAc(5)NeuAc(1) (N), Hex(4)HexNAc(5)Sulf(1) (N), Hex(4)HexNAc(6) (N), Hex(4)Phos(1) (S), Hex(4)Phos(1) (T), Hex(5) (S), Hex(5) (T), Hex(5)HexA(1) (S), Hex(5)HexA(1) (T), Hex(5)HexNAc(1) (N), Hex(5)HexNAc(1) (S), Hex(5)HexNAc(1) (T), Hex(5)HexNAc(2) (N), Hex(5)HexNAc(2)Phos(1) (N), Hex(5)HexNAc(3) (N), Hex(5)HexNAc(3)Pent(1) (N), Hex(5)HexNAc(4) (N), Hex(5)HexNAc(4) (S), Hex(5)HexNAc(4) (T), Hex(5)HexNAc(4)Me(2)Pent(1) (N), Hex(5)HexNAc(4)NeuAc(1) (N), Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N), Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N), Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N), Hex(5)HexNAc(4)NeuAc(2) (N), Hex(5)HexNAc(4)NeuGc(1) (N), Hex(5)HexNAc(4)Sulf(1) (N), Hex(5)HexNAc(5) (N), Hex(5)HexNAc(5) (S), Hex(5)HexNAc(5) (T), Hex(5)Phos(1) (S), Hex(5)Phos(1) (T), Hex(5)Phos(3) (S), Hex(5)Phos(3) (T), Hex(6)HexNAc(1) (N), Hex(6)HexNAc(2) (N), Hex(6)HexNAc(2)Phos(1) (N), Hex(6)HexNAc(3) (N), Hex(6)HexNAc(3)Phos(1) (N), Hex(6)HexNAc(4) (N), Hex(6)HexNAc(4) (S), Hex(6)HexNAc(4) (T), Hex(6)HexNAc(4)Me(3) (N), Hex(6)HexNAc(4)Me(3)Pent(1) (N), Hex(6)HexNAc(5) (N), Hex(6)HexNAc(5)NeuAc(3) (N), Hex(6)Phos(1) (S), Hex(6)Phos(1) (T), Hex(6)Phos(3) (S), Hex(6)Phos(3) (T), Hex(7)HexNAc(1) (N), Hex(7)HexNAc(2) (N), Hex(7)HexNAc(2)Phos(1) (N), Hex(7)HexNAc(2)Phos(2) (N), Hex(7)HexNAc(3) (N), Hex(7)HexNAc(3)Phos(1) (N), Hex(7)HexNAc(4) (N), Hex(7)HexNAc(6) (N), Hex(7)HexNAc(6) (S), Hex(7)HexNAc(6) (T), Hex(7)Phos(3) (S), Hex(7)Phos(3) (T), Hex(8)HexNAc(1) (N), Hex(8)HexNAc(2) (N), Hex(8)Phos(3) (S), Hex(8)Phos(3) (T), Hex(9) (N), Hex(9)HexNAc(1) (N), Hex(9)HexNAc(2) (N), Hex(9)Phos(3) (S), Hex(9)Phos(3) (T), HexA(2)HexNAc(3) (S), HexA(2)HexNAc(3) (T), Hexanoyl (K), HexN (K), HexN (N), HexN (S), HexN (T), HexN (W), HexNAc (C), HexNAc (N), HexNAc (S), HexNAc (T), HexNAc(1)dHex(1) (N), HexNAc(1)dHex(1) (S), HexNAc(1)dHex(1) (T), HexNAc(1)dHex(2) (N), HexNAc(1)Kdn(2) (S), HexNAc(1)Kdn(2) (T), HexNAc(1)NeuAc(1) (S), HexNAc(1)NeuAc(1) (T), HexNAc(1)NeuGc(1) (S), HexNAc(1)NeuGc(1) (T), HexNAc(1)NeuGc(2) (S), HexNAc(1)NeuGc(2) (T), HexNAc(2) (N), HexNAc(2) (S), HexNAc(2) (T), HexNAc(2)dHex(1) (N), HexNAc(2)dHex(2) (N), HexNAc(2)NeuAc(1) (S), HexNAc(2)NeuAc(1) (T), HexNAc(2)NeuAc(1)Sulf(1) (S), HexNAc(2)NeuAc(1)Sulf(1) (T), HexNAc(2)NeuGc(1) (S), HexNAc(2)NeuGc(1) (T), HexNAc(2)Sulf(1) (S), HexNAc(2)Sulf(1) (T), HexNAc(3) (S), HexNAc(3) (T), HexNAc(3)Sulf(1) (S), HexNAc(3)Sulf(1) (T), HexNAc(4) (S), HexNAc(4) (T), HexNAc(5) (S), HexNAc(5) (T), His+O(2) (H), His->Ala (H), His->Arg (H), His->Asn (H), His->Asp (H), His->Cys (H), His->Gln (H), His->Glu (H), His->Gly (H), His->Lys (H), His->Met (H), His->Phe (H), His->Pro (H), His->Ser (H), His->Thr (H), His->Trp (H), His->Tyr (H), His->Val (H), His->Xle (H), HMVK (C), HN2_mustard (C), HN2_mustard (H), HN2_mustard (K), HN3_mustard (C), HN3_mustard (H), HN3_mustard (K), HNE (A), HNE (C), HNE (H), HNE (K), HNE (L), HNE (R), HNE+Delta:H(2) (C), HNE+Delta:H(2) (H), HNE+Delta:H(2) (K), HNE-BAHAH (C), HNE-BAHAH (H), HNE-BAHAH (K), HNE-Delta:H(2)O (C), HNE-Delta:H(2)O (H), HNE-Delta:H(2)O (K), Homocysteic_acid (M), HPG (R), Hydroxamic_acid (D), Hydroxamic_acid (E), Hydroxycinnamyl (C), Hydroxyfarnesyl (C), Hydroxyheme (E), hydroxyisobutyryl (K), Hydroxymethyl (N), HydroxymethylOP (K), Hydroxytrimethyl (K), Hypusine (K), IASD (C), IBTP (C), ICAT-C (C), ICAT-C:13C(9) (C), ICAT-D (C), ICAT-D:2H(8) (C), ICAT-G (C), ICAT-G:2H(8) (C), ICAT-H (C), ICAT-H:13C(6) (C), ICDID (C), ICDID:2H(6) (C), ICPL (K), ICPL (N-term), ICPL (Protein N-term), ICPL:13C(6) (K), ICPL:13C(6) (N-term), ICPL:13C(6) (Protein N-term), ICPL:13C(6)2H(4) (K), ICPL:13C(6)2H(4) (N-term), ICPL:13C(6)2H(4) (Protein N-term), ICPL:2H(4) (K), ICPL:2H(4) (N-term), ICPL:2H(4) (Protein N-term), IDEnT (C), IED-Biotin (C), IGBP (C), IGBP:13C(2) (C), IMEHex(2)NeuAc(1) (K), IMID (K), IMID:2H(4) (K), Iminobiotin (K), Iminobiotin (N-term), Iodo (H), Iodo (Y), Iodoacetanilide (C), Iodoacetanilide (K), Iodoacetanilide (N-term), Iodoacetanilide:13C(6) (C), Iodoacetanilide:13C(6) (K), Iodoacetanilide:13C(6) (N-term), iodoTMT (C), iodoTMT (D), iodoTMT (E), iodoTMT (H), iodoTMT (K), iodoTMT6plex (C), iodoTMT6plex (D), iodoTMT6plex (E), iodoTMT6plex (H), iodoTMT6plex (K), IodoU-AMP (F), IodoU-AMP (W), IodoU-AMP (Y), ISD_z+2_ion (N-term), Isopropylphospho (S), Isopropylphospho (T), Isopropylphospho (Y), Isovaleryl (K), iST-NHS specific cysteine modification (C), Itaconatyl (C), Itaconyl (K), iTRAQ4plex (C), iTRAQ4plex (H), iTRAQ4plex (K), iTRAQ4plex (N-term), iTRAQ4plex (Protein N-term), iTRAQ4plex (S), iTRAQ4plex (T), iTRAQ4plex (Y), iTRAQ4plex114 (C), iTRAQ4plex114 (K), iTRAQ4plex114 (N-term), iTRAQ4plex114 (Y), iTRAQ4plex115 (C), iTRAQ4plex115 (K), iTRAQ4plex115 (N-term), iTRAQ4plex115 (Y), iTRAQ8plex (C), iTRAQ8plex (H), iTRAQ8plex (K), iTRAQ8plex (N-term), iTRAQ8plex (Protein N-term), iTRAQ8plex (S), iTRAQ8plex (T), iTRAQ8plex (Y), iTRAQ8plex:13C(6)15N(2) (C), iTRAQ8plex:13C(6)15N(2) (K), iTRAQ8plex:13C(6)15N(2) (N-term), iTRAQ8plex:13C(6)15N(2) (Y), L-Gln (D), L-Gln (E), Label:13C(1)2H(3) (M), Label:13C(1)2H(3)+Oxidation (M), Label:13C(2)15N(1) (G), Label:13C(2)15N(2) (K), Label:13C(3) (A), Label:13C(3)15N(1) (A), Label:13C(3)15N(1) (S), Label:13C(4) (M), Label:13C(4)+Oxidation (M), Label:13C(4)15N(1) (D), Label:13C(4)15N(2)+GG (K), Label:13C(5) (P), Label:13C(5)15N(1) (E), Label:13C(5)15N(1) (M), Label:13C(5)15N(1) (P), Label:13C(5)15N(1) (V), Label:13C(6) (I), Label:13C(6) (K), Label:13C(6) (L), Label:13C(6) (R), Label:13C(6)+Acetyl (K), Label:13C(6)+Dimethyl (K), Label:13C(6)+GG (K), Label:13C(6)15N(1) (I), Label:13C(6)15N(1) (L), Label:13C(6)15N(2) (K), Label:13C(6)15N(2)+Acetyl (K), Label:13C(6)15N(2)+Dimethyl (K), Label:13C(6)15N(2)+GG (K), Label:13C(6)15N(2)+TMT6plex (K), Label:13C(6)15N(2)+TMTpro (K), Label:13C(6)15N(4) (R), Label:13C(6)15N(4)+Dimethyl (R), Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R), Label:13C(6)15N(4)+Methyl (R), Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R), Label:13C(9) (F), Label:13C(9) (Y), Label:13C(9)+Phospho (Y), Label:13C(9)15N(1) (F), Label:15N(1) (A), Label:15N(1) (C), Label:15N(1) (D), Label:15N(1) (E), Label:15N(1) (F), Label:15N(1) (G), Label:15N(1) (I), Label:15N(1) (L), Label:15N(1) (M), Label:15N(1) (P), Label:15N(1) (S), Label:15N(1) (T), Label:15N(1) (V), Label:15N(1) (Y), Label:15N(2) (K), Label:15N(2) (N), Label:15N(2) (Q), Label:15N(2) (W), Label:15N(2)2H(9) (K), Label:15N(3) (H), Label:15N(4) (R), Label:18O(1) (C-term), Label:18O(1) (S), Label:18O(1) (T), Label:18O(1) (Y), Label:18O(2) (C-term), Label:2H(10) (L), Label:2H(3) (L), Label:2H(3) (M), Label:2H(3)+Oxidation (M), Label:2H(4) (A), Label:2H(4) (F), Label:2H(4) (K), Label:2H(4) (U), Label:2H(4) (Y), Label:2H(4)+Acetyl (K), Label:2H(4)+GG (K), Label:2H(4)13C(1) (R), Label:2H(6)15N(1) (P), Label:2H(7)15N(4) (R), Label:2H(9)13C(6)15N(2) (K), Lactylation (K), lapachenole (C), Leu->MetOx (L), LG-anhydrolactam (K), LG-anhydrolactam (N-term), LG-anhyropyrrole (K), LG-anhyropyrrole (N-term), LG-Hlactam-K (K), LG-Hlactam-K (Protein N-term), LG-Hlactam-R (R), LG-lactam-K (K), LG-lactam-K (Protein N-term), LG-lactam-R (R), LG-pyrrole (C), LG-pyrrole (K), LG-pyrrole (N-term), Lipoyl (K), LRGG (K), LRGG+dimethyl (K), LRGG+methyl (K), LTX+Lophotoxin (Y), Lys (N-term), Lys+O(2) (H), Lys->Ala (K), Lys->Allysine (K), Lys->AminoadipicAcid (K), Lys->Arg (K), Lys->Asn (K), Lys->Asp (K), Lys->CamCys (K), Lys->Cys (K), Lys->Gln (K), Lys->Glu (K), Lys->Gly (K), Lys->His (K), Lys->Met (K), Lys->MetOx (K), Lys->Phe (K), Lys->Pro (K), Lys->Ser (K), Lys->Thr (K), Lys->Trp (K), Lys->Tyr (K), Lys->Val (K), Lys->Xle (K), Lys-loss (K), Lys-loss (Protein C-term K), Lysbiotinhydrazide (K), maleimide (C), maleimide (K), Maleimide-PEO2-Biotin (C), maleimide3 (C), maleimide3 (K), maleimide5 (C), maleimide5 (K), Malonyl (C), Malonyl (K), Malonyl (S), MBS+peptide (C), MDCC (C), MeMePhosphorothioate (S), Menadione (C), Menadione (K), Menadione-HQ (C), Menadione-HQ (K), MercaptoEthanol (S), MercaptoEthanol (T), MesitylOxide (H), MesitylOxide (K), MesitylOxide (Protein N-term), Met+O(2) (H), Met->Aha (M), Met->Ala (M), Met->Arg (M), Met->Asn (M), Met->Asp (M), Met->AspSA (M), Met->Cys (M), Met->Gln (M), Met->Glu (M), Met->Gly (M), Met->His (M), Met->Hpg (M), Met->Hse (C-term M), Met->Hsl (C-term M), Met->Lys (M), Met->Phe (M), Met->Pro (M), Met->Ser (M), Met->Thr (M), Met->Trp (M), Met->Tyr (M), Met->Val (M), Met->Xle (M), Met-loss (Protein N-term M), Met-loss+Acetyl (Protein N-term M), Methamidophos-O (C), Methamidophos-O (H), Methamidophos-O (K), Methamidophos-O (S), Methamidophos-O (T), Methamidophos-O (Y), Methamidophos-S (C), Methamidophos-S (H), Methamidophos-S (K), Methamidophos-S (S), Methamidophos-S (T), Methamidophos-S (Y), Methyl (C), Methyl (C-term), Methyl (D), Methyl (E), Methyl (H), Methyl (I), Methyl (K), Methyl (L), Methyl (N), Methyl (N-term), Methyl (Protein N-term), Methyl (Q), Methyl (R), Methyl (S), Methyl (T), Methyl+Acetyl:2H(3) (K), Methyl+Deamidated (N), Methyl+Deamidated (Q), Methyl-PEO12-Maleimide (C), Methyl:2H(2) (K), Methyl:2H(2) (N-term), Methyl:2H(2)13C (C), Methyl:2H(2)13C (C-term), Methyl:2H(2)13C (D), Methyl:2H(2)13C (E), Methyl:2H(2)13C (H), Methyl:2H(2)13C (I), Methyl:2H(2)13C (K), Methyl:2H(2)13C (L), Methyl:2H(2)13C (N), Methyl:2H(2)13C (N-term), Methyl:2H(2)13C (Protein N-term), Methyl:2H(2)13C (Q), Methyl:2H(2)13C (R), Methyl:2H(2)13C (S), Methyl:2H(2)13C (T), Methyl:2H(3) (D), Methyl:2H(3) (E), Methyl:2H(3) (K), Methyl:2H(3) (R), Methyl:2H(3) (X), Methyl:2H(3)+Acetyl:2H(3) (K), Methyl:2H(3)13C(1) (K), Methyl:2H(3)13C(1) (N-term), Methyl:2H(3)13C(1) (R), Methylamine (S), Methylamine (T), Methylmalonylation (S), methylol (K), methylol (W), methylol (Y), Methylphosphonate (S), Methylphosphonate (T), Methylphosphonate (Y), Methylpyrroline (K), methylsulfonylethyl (C), methylsulfonylethyl (H), methylsulfonylethyl (K), Methylthio (C), Methylthio (D), Methylthio (K), Methylthio (N), Methylthio (N-term), MG-H1 (R), Microcin (Protein C-term), MicrocinC7 (Protein C-term), MM-diphenylpentanone (C), Molybdopterin (C), MolybdopterinGD (C), MolybdopterinGD (D), MolybdopterinGD (U), MolybdopterinGD+Delta:S(-1)Se(1) (C), Mono_Ngamma-propargyl-L-Gln_desthiobiotin (C), monomethylphosphothione (C), monomethylphosphothione (H), monomethylphosphothione (K), monomethylphosphothione (S), monomethylphosphothione (T), monomethylphosphothione (Y), mTRAQ (H), mTRAQ (K), mTRAQ (N-term), mTRAQ (S), mTRAQ (T), mTRAQ (Y), mTRAQ:13C(3)15N(1) (H), mTRAQ:13C(3)15N(1) (K), mTRAQ:13C(3)15N(1) (N-term), mTRAQ:13C(3)15N(1) (S), mTRAQ:13C(3)15N(1) (T), mTRAQ:13C(3)15N(1) (Y), mTRAQ:13C(6)15N(2) (H), mTRAQ:13C(6)15N(2) (K), mTRAQ:13C(6)15N(2) (N-term), mTRAQ:13C(6)15N(2) (S), mTRAQ:13C(6)15N(2) (T), mTRAQ:13C(6)15N(2) (Y), MTSL (C), MurNAc (A), Myristoleyl (Protein N-term G), Myristoyl (C), Myristoyl (K), Myristoyl (N-term G), Myristoyl+Delta:H(-4) (Protein N-term G), N-dimethylphosphate (S), N6pAMP (S), N6pAMP (T), N6pAMP (Y), NA-LNO2 (C), NA-LNO2 (H), NA-OA-NO2 (C), NA-OA-NO2 (H), NBF (C), NBF (K), NBF (R), NBS (W), NBS:13C(6) (W), NDA (K), NDA (N-term), NEIAA (C), NEIAA (Y), NEIAA:2H(5) (C), NEIAA:2H(5) (Y), NEM:2H(5) (C), NEM:2H(5)+H2O (C), NEMsulfur (C), NEMsulfurWater (C), Nethylmaleimide (C), Nethylmaleimide+water (C), Nethylmaleimide+water (K), NeuAc (N), NeuAc (S), NeuAc (T), NeuGc (N), NeuGc (S), NeuGc (T), NHS-fluorescein (K), NHS-LC-Biotin (K), NHS-LC-Biotin (N-term), NIC (K), NIC (N-term), NIPCAM (C), Nitrene (Y), Nitro (F), Nitro (W), Nitro (Y), Nitrosyl (C), Nitrosyl (Y), Nmethylmaleimide (C), Nmethylmaleimide (K), Nmethylmaleimide+water (C), NO_SMX_SEMD (C), NO_SMX_SIMD (C), NP40 (N-term), NQIGG (K), NQTGG (K), O-Dimethylphosphate (S), O-Dimethylphosphate (T), O-Dimethylphosphate (Y), O-Et-N-diMePhospho (S), O-Isopropylmethylphosphonate (S), O-Isopropylmethylphosphonate (T), O-Isopropylmethylphosphonate (Y), O-Methylphosphate (S), O-Methylphosphate (T), O-Methylphosphate (Y), O-pinacolylmethylphosphonate (H), O-pinacolylmethylphosphonate (K), O-pinacolylmethylphosphonate (S), O-pinacolylmethylphosphonate (T), O-pinacolylmethylphosphonate (Y), Octanoyl (C), Octanoyl (S), Octanoyl (T), OxArgBiotin (R), OxArgBiotinRed (R), Oxidation (C), Oxidation (C-term G), Oxidation (D), Oxidation (E), Oxidation (F), Oxidation (H), Oxidation (I), Oxidation (K), Oxidation (L), Oxidation (M), Oxidation (N), Oxidation (P), Oxidation (Q), Oxidation (R), Oxidation (S), Oxidation (T), Oxidation (U), Oxidation (V), Oxidation (W), Oxidation (Y), Oxidation+NEM (C), OxLysBiotin (K), OxLysBiotinRed (K), OxProBiotin (P), OxProBiotinRed (P), Palmitoleyl (C), Palmitoleyl (S), Palmitoleyl (T), Palmitoyl (C), Palmitoyl (K), Palmitoyl (Protein N-term), Palmitoyl (S), Palmitoyl (T), PEITC (C), PEITC (K), PEITC (N-term), Pent(1)HexNAc(1) (S), Pent(1)HexNAc(1) (T), Pent(2) (S), Pent(2) (T), Pentanoyl (K), Pentose (S), Pentose (T), Pentylamine (Q), PEO-Iodoacetyl-LC-Biotin (C), PET (S), PET (T), Phe->Ala (F), Phe->Arg (F), Phe->Asn (F), Phe->Asp (F), Phe->CamCys (F), Phe->Cys (F), Phe->Gln (F), Phe->Glu (F), Phe->Gly (F), Phe->His (F), Phe->Lys (F), Phe->Met (F), Phe->Pro (F), Phe->Ser (F), Phe->Thr (F), Phe->Trp (F), Phe->Tyr (F), Phe->Val (F), Phe->Xle (F), phenyl-phosphate (K), phenyl-phosphate (S), phenyl-phosphate (T), phenyl-phosphate (Y), Phenylisocyanate (N-term), Phenylisocyanate:2H(5) (N-term), phenylsulfonylethyl (C), Phospho (C), Phospho (D), Phospho (E), Phospho (H), Phospho (K), Phospho (R), Phospho (S), Phospho (T), Phospho (Y), Phosphoadenosine (H), Phosphoadenosine (K), Phosphoadenosine (S), Phosphoadenosine (T), Phosphoadenosine (Y), PhosphoCytidine (S), PhosphoCytidine (T), PhosphoCytidine (Y), PhosphoDecoy (A), PhosphoDecoy (G), PhosphoDecoy (L), Phosphogluconoylation (K), Phosphogluconoylation (N-term), Phosphoguanosine (H), Phosphoguanosine (K), PhosphoHex (S), PhosphoHex (T), PhosphoHex(2) (N), PhosphoHex(2) (S), PhosphoHex(2) (T), PhosphoHexNAc (S), PhosphoHexNAc (T), Phosphopantetheine (S), Phosphopropargyl (S), Phosphopropargyl (T), Phosphopropargyl (Y), phosphoRibosyl (D), phosphoRibosyl (E), phosphoRibosyl (R), PhosphoribosyldephosphoCoA (S), PhosphoUridine (H), PhosphoUridine (Y), Phycocyanobilin (C), Phycoerythrobilin (C), Phytochromobilin (C), Piperidine (K), Piperidine (N-term), pRBS-ID_4-thiouridine (F), pRBS-ID_6-thioguanosine (W), Pro+O(2) (H), Pro->Ala (P), Pro->Arg (P), Pro->Asn (P), Pro->Asp (P), Pro->Cys (P), Pro->Gln (P), Pro->Glu (P), Pro->Gly (P), Pro->HAVA (P), Pro->His (P), Pro->Lys (P), Pro->Met (P), Pro->Phe (P), Pro->pyro-Glu (P), Pro->Pyrrolidinone (P), Pro->Pyrrolidone (P), Pro->Ser (P), Pro->Thr (P), Pro->Trp (P), Pro->Tyr (P), Pro->Val (P), Pro->Xle (P), probiotinhydrazide (P), Propargylamine (C-term), Propargylamine (D), Propargylamine (E), Propionamide (C), Propionamide (K), Propionamide (N-term), Propionamide:2H(3) (C), Propionyl (K), Propionyl (N-term), Propionyl (Protein N-term), Propionyl (S), Propionyl (T), Propionyl:13C(3) (K), Propionyl:13C(3) (N-term), Propiophenone (C), Propiophenone (H), Propiophenone (K), Propiophenone (R), Propiophenone (S), Propiophenone (T), Propiophenone (W), Propyl (C-term), Propyl (D), Propyl (E), Propyl (K), Propyl (N-term), Propyl (Protein C-term), Propyl:2H(6) (K), Propyl:2H(6) (N-term), PropylNAGthiazoline (C), PS_Hapten (C), PS_Hapten (H), PS_Hapten (K), pupylation (K), Puromycin (C-term), PyMIC (N-term), PyridoxalPhosphate (K), PyridoxalPhosphateH2 (K), Pyridylacetyl (K), Pyridylacetyl (N-term), Pyridylethyl (C), Pyro-carbamidomethyl (N-term C), Pyro-QQTGG (K), pyrophospho (S), pyrophospho (T), PyruvicAcidIminyl (K), PyruvicAcidIminyl (Protein N-term C), PyruvicAcidIminyl (Protein N-term V), Pyruvoyl (K), QAT (C), QAT:2H(3) (C), QEQTGG (K), QQQTGG (K), QQTGG (K), QTGG (K), Quinone (W), Quinone (Y), RBS-ID_Uridine (Y), Retinylidene (K), RNPXL (N-term K), RNPXL (N-term R), RNPXlink1 (C), s-GlcNAc (S), s-GlcNAc (T), Saligenin (H), Saligenin (K), Ser->Ala (S), Ser->Arg (S), Ser->Asn (S), Ser->Asp (S), Ser->Cys (S), Ser->Gln (S), Ser->Glu (S), Ser->Gly (S), Ser->His (S), Ser->LacticAcid (Protein N-term S), Ser->Lys (S), Ser->Met (S), Ser->Phe (S), Ser->Pro (S), Ser->Thr (S), Ser->Trp (S), Ser->Tyr (S), Ser->Val (S), Ser->Xle (S), Ser/Thr-KDO (S), Ser/Thr-KDO (T), serotonylation (Q), shTMT (K), shTMT (N-term), shTMT (Protein N-term), shTMTpro (K), shTMTpro (N-term), shTMTpro (Protein N-term), SMA (K), SMA (N-term), spermidine (Q), spermine (Q), SPITC (K), SPITC (N-term), SPITC:13C(6) (K), SPITC:13C(6) (N-term), Succinyl (K), Succinyl (N-term), Succinyl (Protein N-term), Succinyl:13C(4) (K), Succinyl:13C(4) (N-term), Succinyl:2H(4) (K), Succinyl:2H(4) (N-term), SulfanilicAcid (C-term), SulfanilicAcid (D), SulfanilicAcid (E), SulfanilicAcid:13C(6) (C-term), SulfanilicAcid:13C(6) (D), SulfanilicAcid:13C(6) (E), Sulfide (C), Sulfide (D), Sulfide (W), Sulfo (C), Sulfo (S), Sulfo (T), Sulfo (Y), sulfo+amino (Y), Sulfo-NHS-LC-LC-Biotin (K), Sulfo-NHS-LC-LC-Biotin (N-term), SulfoGMBS (C), SulfurDioxide (C), SUMO2135 (K), SUMO3549 (K), TAMRA-FP (S), TAMRA-FP (Y), Thiadiazole (C), Thiazolidine (C), Thiazolidine (F), Thiazolidine (H), Thiazolidine (K), Thiazolidine (Protein N-term), Thiazolidine (R), Thiazolidine (W), Thiazolidine (Y), thioacylPA (K), Thiophos-S-S-biotin (S), Thiophos-S-S-biotin (T), Thiophos-S-S-biotin (Y), Thiophospho (S), Thiophospho (T), Thiophospho (Y), Thr->Ala (T), Thr->Arg (T), Thr->Asn (T), Thr->Asp (T), Thr->Cys (T), Thr->Gln (T), Thr->Glu (T), Thr->Gly (T), Thr->His (T), Thr->Lys (T), Thr->Met (T), Thr->Phe (T), Thr->Pro (T), Thr->Ser (T), Thr->Trp (T), Thr->Tyr (T), Thr->Val (T), Thr->Xle (T), Thrbiotinhydrazide (T), Thyroxine (Y), Tiglyl (K), TMAB (K), TMAB (N-term), TMAB:2H(9) (K), TMAB:2H(9) (N-term), TMPP-Ac (K), TMPP-Ac (N-term), TMPP-Ac (Y), TMPP-Ac:13C(9) (K), TMPP-Ac:13C(9) (N-term), TMPP-Ac:13C(9) (Y), TMT (H), TMT (K), TMT (N-term), TMT (Protein N-term), TMT (S), TMT (T), TMT2plex (H), TMT2plex (K), TMT2plex (N-term), TMT2plex (Protein N-term), TMT2plex (S), TMT2plex (T), TMT6plex (H), TMT6plex (K), TMT6plex (N-term), TMT6plex (Protein N-term), TMT6plex (S), TMT6plex (T), TMTpro (H), TMTpro (K), TMTpro (N-term), TMTpro (Protein N-term), TMTpro (S), TMTpro (T), TMTpro_zero (H), TMTpro_zero (K), TMTpro_zero (N-term), TMTpro_zero (Protein N-term), TMTpro_zero (S), TMTpro_zero (T), TNBS (K), TNBS (N-term), trifluoro (L), Triiodo (Y), Triiodothyronine (Y), Trimethyl (K), Trimethyl (Protein N-term A), Trimethyl (R), Trimethyl:13C(3)2H(9) (K), Trimethyl:13C(3)2H(9) (R), Trimethyl:2H(9) (K), Trimethyl:2H(9) (R), Trioxidation (C), Trioxidation (F), Trioxidation (W), Trioxidation (Y), Tripalmitate (Protein N-term C), Tris (N), Triton (C-term), Triton (N-term), Trp->Ala (W), Trp->Arg (W), Trp->Asn (W), Trp->Asp (W), Trp->Cys (W), Trp->Gln (W), Trp->Glu (W), Trp->Gly (W), Trp->His (W), Trp->Hydroxykynurenin (W), Trp->Kynurenin (W), Trp->Lys (W), Trp->Met (W), Trp->Oxolactone (W), Trp->Phe (W), Trp->Pro (W), Trp->Ser (W), Trp->Thr (W), Trp->Tyr (W), Trp->Val (W), Trp->Xle (W), Tween20 (N-term), Tween80 (C-term), Tyr->Ala (Y), Tyr->Arg (Y), Tyr->Asn (Y), Tyr->Asp (Y), Tyr->Cys (Y), Tyr->Dha (Y), Tyr->Gln (Y), Tyr->Glu (Y), Tyr->Gly (Y), Tyr->His (Y), Tyr->Lys (Y), Tyr->Met (Y), Tyr->Phe (Y), Tyr->Pro (Y), Tyr->Ser (Y), Tyr->Thr (Y), Tyr->Trp (Y), Tyr->Val (Y), Tyr->Xle (Y), Ub-Br2 (C), Ub-fluorescein (C), Ub-VME (C), UgiJoullie (D), UgiJoullie (E), UgiJoullieProGly (D), UgiJoullieProGly (E), UgiJoullieProGlyProGly (D), UgiJoullieProGlyProGly (E), Unknown:162 (C-term), Unknown:162 (D), Unknown:162 (E), Unknown:162 (N-term), Unknown:177 (C-term), Unknown:177 (D), Unknown:177 (E), Unknown:177 (N-term), Unknown:210 (C-term), Unknown:210 (D), Unknown:210 (E), Unknown:210 (N-term), Unknown:216 (C-term), Unknown:216 (D), Unknown:216 (E), Unknown:216 (N-term), Unknown:234 (C-term), Unknown:234 (D), Unknown:234 (E), Unknown:234 (N-term), Unknown:248 (C-term), Unknown:248 (D), Unknown:248 (E), Unknown:248 (N-term), Unknown:250 (C-term), Unknown:250 (D), Unknown:250 (E), Unknown:250 (N-term), Unknown:302 (C-term), Unknown:302 (D), Unknown:302 (E), Unknown:302 (N-term), Unknown:306 (C-term), Unknown:306 (D), Unknown:306 (E), Unknown:306 (N-term), Unknown:420 (C-term), Unknown:420 (N-term), Val->Ala (V), Val->Arg (V), Val->Asn (V), Val->Asp (V), Val->Cys (V), Val->Gln (V), Val->Glu (V), Val->Gly (V), Val->His (V), Val->Lys (V), Val->Met (V), Val->Phe (V), Val->Pro (V), Val->Ser (V), Val->Thr (V), Val->Trp (V), Val->Tyr (V), Val->Xle (V), ValGly (K), VFQQQTGG (K), VIEVYQEQTGG (K), Withaferin (C), Xle->Ala (I), Xle->Ala (L), Xle->Arg (I), Xle->Arg (L), Xle->Asn (I), Xle->Asn (L), Xle->Asp (I), Xle->Asp (L), Xle->Cys (I), Xle->Cys (L), Xle->Gln (I), Xle->Gln (L), Xle->Glu (I), Xle->Glu (L), Xle->Gly (I), Xle->Gly (L), Xle->His (I), Xle->His (L), Xle->Lys (I), Xle->Lys (L), Xle->Met (I), Xle->Met (L), Xle->Phe (I), Xle->Phe (L), Xle->Pro (I), Xle->Pro (L), Xle->Ser (I), Xle->Ser (L), Xle->Thr (I), Xle->Thr (L), Xle->Trp (I), Xle->Trp (L), Xle->Tyr (I), Xle->Tyr (L), Xle->Val (I), Xle->Val (L), Xlink:B10621 (C), Xlink:BMOE (C), Xlink:BS2G[113] (K), Xlink:BS2G[113] (Protein N-term), Xlink:BS2G[114] (K), Xlink:BS2G[114] (Protein N-term), Xlink:BS2G[217] (K), Xlink:BS2G[217] (Protein N-term), Xlink:BS2G[96] (K), Xlink:BS2G[96] (Protein N-term), Xlink:BuUrBu[111] (K), Xlink:BuUrBu[111] (Protein N-term), Xlink:BuUrBu[111] (S), Xlink:BuUrBu[111] (T), Xlink:BuUrBu[111] (Y), Xlink:BuUrBu[196] (K), Xlink:BuUrBu[196] (Protein N-term), Xlink:BuUrBu[196] (S), Xlink:BuUrBu[196] (T), Xlink:BuUrBu[196] (Y), Xlink:BuUrBu[213] (K), Xlink:BuUrBu[213] (Protein N-term), Xlink:BuUrBu[213] (S), Xlink:BuUrBu[213] (T), Xlink:BuUrBu[213] (Y), Xlink:BuUrBu[214] (K), Xlink:BuUrBu[214] (Protein N-term), Xlink:BuUrBu[214] (S), Xlink:BuUrBu[214] (T), Xlink:BuUrBu[214] (Y), Xlink:BuUrBu[317] (K), Xlink:BuUrBu[317] (Protein N-term), Xlink:BuUrBu[317] (S), Xlink:BuUrBu[317] (T), Xlink:BuUrBu[317] (Y), Xlink:BuUrBu[85] (K), Xlink:BuUrBu[85] (Protein N-term), Xlink:BuUrBu[85] (S), Xlink:BuUrBu[85] (T), Xlink:BuUrBu[85] (Y), Xlink:DFDNB (K), Xlink:DFDNB (N), Xlink:DFDNB (Q), Xlink:DFDNB (R), Xlink:DMP[122] (K), Xlink:DMP[122] (Protein N-term), Xlink:DMP[139] (K), Xlink:DMP[139] (Protein N-term), Xlink:DMP[140] (K), Xlink:DMP[140] (Protein N-term), Xlink:DMP[154] (K), Xlink:DMP[154] (Protein N-term), Xlink:DSPP[210] (K), Xlink:DSPP[210] (Protein N-term), Xlink:DSPP[226] (K), Xlink:DSPP[226] (Protein N-term), Xlink:DSPP[228] (K), Xlink:DSPP[228] (Protein N-term), Xlink:DSPP[331] (K), Xlink:DSPP[331] (Protein N-term), Xlink:DSS[138] (K), Xlink:DSS[138] (Protein N-term), Xlink:DSS[155] (K), Xlink:DSS[155] (Protein N-term), Xlink:DSS[156] (K), Xlink:DSS[156] (Protein N-term), Xlink:DSS[259] (K), Xlink:DSS[259] (Protein N-term), Xlink:DSSO[104] (K), Xlink:DSSO[104] (Protein N-term), Xlink:DSSO[158] (K), Xlink:DSSO[158] (Protein N-term), Xlink:DSSO[175] (K), Xlink:DSSO[175] (Protein N-term), Xlink:DSSO[176] (K), Xlink:DSSO[176] (Protein N-term), Xlink:DSSO[279] (K), Xlink:DSSO[279] (Protein N-term), Xlink:DSSO[54] (K), Xlink:DSSO[54] (Protein N-term), Xlink:DSSO[86] (K), Xlink:DSSO[86] (Protein N-term), Xlink:DST[114] (K), Xlink:DST[114] (Protein N-term), Xlink:DST[132] (K), Xlink:DST[132] (Protein N-term), Xlink:DST[56] (K), Xlink:DST[56] (Protein N-term), Xlink:DTBP[172] (K), Xlink:DTBP[172] (Protein N-term), Xlink:DTBP[87] (K), Xlink:DTBP[87] (Protein N-term), Xlink:DTSSP[174] (K), Xlink:DTSSP[174] (Protein N-term), Xlink:DTSSP[192] (K), Xlink:DTSSP[192] (Protein N-term), Xlink:DTSSP[88] (K), Xlink:DTSSP[88] (Protein N-term), Xlink:EGS[115] (K), Xlink:EGS[115] (Protein N-term), Xlink:EGS[226] (K), Xlink:EGS[226] (Protein N-term), Xlink:EGS[244] (K), Xlink:EGS[244] (Protein N-term), Xlink:SMCC[219] (C), Xlink:SMCC[219] (K), Xlink:SMCC[219] (Protein N-term), Xlink:SMCC[237] (C), Xlink:SMCC[237] (K), Xlink:SMCC[237] (Protein N-term), Xlink:SMCC[321] (C), ZGB (K), ZGB (N-term), ZQG (K)

variable_max_per_peptide2 Maximum number of residues carrying a variable modification per candidate peptide0:5

++++annotateAnnotation Options

PSM[ALL] Annotations added to each PSM.ALL, fragment_mz_error_median_ppm, precursor_mz_error_ppm, matched_prefix_ions_fraction, matched_suffix_ions_fraction, num_matched_peaks, matched_prefix_ions, matched_suffix_ions, longest_peptide_ion_sequence, matched_ion_current, fragment_annotation, hyperscore_zscore, ln_num_candidates, matched_ion_current_fraction, complementary_ions_fraction

self_trained_ion_priorstrue Learn per-run fragment ion likelihoods from the confident PSMs of each file and add the Percolator features of annotate:ion_prior_features to every hit. The spectra are split into two halves by scan parity. Each half trains a model on its rank-one target hits at target-decoy competition q <= annotate:ion_prior_train_fdr of the native score (their reversed sequences on the same spectra are the noise model), and every hit is scored by the model of the other half, so no PSM is scored by a model that saw its spectrum or its label. Needs annotate:ion_prior_min_psms training PSMs in each half, otherwise the features are 0. Not applied to target-only searches (decoys=ignore), which get no features. Native scores and candidate selection are unchanged. Independent of annotate:PSM.true, false

ion_prior_modelrich Contexts and outcomes of the ion priors. Both keep the ion series a/b, x/y, c and z apart (c and z ions are scored for electron-activated spectra, see ions:by_activation). 'rich': ion series, precursor charge, fragment charge, relative position, the residues at the cleavage site (bond before P, bond after D or E) and whether the complementary singly charged ion matched; outcome: intensity rank x mass error (|error| / tolerance below 0.25, below 0.5, up to 1). 'basic': ion series, precursor charge, fragment charge and relative position; outcome: intensity rank.rich, basic

ion_prior_peaksall Peaks the ion priors rank and match. 'all': every peak after deisotoping, before the peaks:window_top and peaks:keep_n filters, so weak fragment ions count as evidence for the model without entering HyperScore. 'scored': the peaks that are scored.all, scored

ion_prior_max_fragment_charge2 Highest fragment charge of the ions of the ion priors; capped at the precursor charge - 1 (at least 1).1:∞

ion_prior_train_fdr0.01 Target-decoy competition q-value threshold selecting the training PSMs of annotate:self_trained_ion_priors.0.0:1.0

ion_prior_min_psms100 Minimum number of training PSMs of annotate:self_trained_ion_priors in each half of the spectra; with fewer, the features are 0.1:∞

ion_prior_features[ion_prior_llr, ion_prior_explained] Features of annotate:self_trained_ion_priors written to every hit and listed for Percolator: ion_prior_llr (summed log-likelihood ratio of the ion outcomes, signal vs reversed noise), ion_prior_explained (share of the predicted ion presence that was observed), ion_prior_topk_observed (share of the 6 ions most likely present that were observed).ion_prior_llr, ion_prior_explained, ion_prior_topk_observed

local_fragment_evidencetrue Add chance_match_surprise and mass_competition_evidence annotations and Percolator features. Uses local peak density and alternative intact/neutral-loss fragment assignments. Retains an additional peak list before window/top-N filtering, increasing memory use. Does not change native scores or candidate selection. Independent of annotate:PSM.true, false

++++peptdeepPeptDeep (ONNX) prediction-based rescoring features

enablefalse Add PeptDeep prediction-based rescoring features (ms2_cosine, ms2_spectral_angle, ms2_pearson, ms2_frac_pred_found, rt_abs_error) to every PSM. Uses the models shipped in OpenMS' 'share/OpenMS/models' unless 'peptdeep:ms2_model'/'peptdeep:rt_model' name others. Requires an OpenMS built with ONNX support.true, false

ms2_modelmodels/peptdeep_ms2_dynamic.onnx PeptDeep MS2 fragment-intensity ONNX model, used when 'peptdeep:enable' is true. A relative name is resolved against OpenMS' shared-data directory; an absolute path is used as given.

rt_modelmodels/peptdeep_rt_dynamic.onnx PeptDeep retention-time ONNX model. See 'peptdeep:ms2_model'.

instrumentQE Instrument class passed to the PeptDeep MS2 model. An instrument that is not in this list is best approximated by the closest one that is.QE, Lumos, timsTOF, SciexTOF, ThermoTOF

nce-1.0 Normalised collision energy for the PeptDeep MS2 model. Negative selects it automatically from the collision energy recorded in the spectra, refined by scoring a small grid on confident PSMs.

rt_model_typeb_spline Model mapping predicted onto observed retention time.b_spline, lowess, linear

batch_size64 Peptides per ONNX inference call. The calls run side by side, one per thread: small ones keep the threads evenly busy and the memory low (on iPRG2015 with 16 threads, 64 took 40% less time than 500 and 1 GB less memory).1:∞

++++peptidePeptide Options

min_size7 Minimum size a peptide must have after digestion to be considered in the search.0:∞

max_size40 Maximum size a peptide must have after digestion to be considered in the search (0 = disabled).0:∞

missed_cleavages1 Number of missed cleavages.0:∞

clip_nterm_methioninetrue Also search protein N-terminal peptides after removal of their initial methionine. The retained-M form is still searched; length, mass and missed-cleavage limits apply to each form. Set false for the previous search space.true, false

deduplicatetrue Index each exact peptidoform once before candidate selection. Protein mappings still list every protein occurrence. Across database chunks, count each peptide/charge/isotope hypothesis once; retaining queried keys adds memory per spectrum. With low_memory, the repeated peptidoforms among the candidates of a spectrum are dropped instead. Set false for occurrence-based legacy candidates.true, false

protein_mappingindex How the hits are mapped to their proteins (peptide evidences, target_decoy, protein_references, protein hits). 'index': from the digest of the fragment index, which holds every protein occurrence of a candidate (with a protein-terminal modification: from a pass over the database for the hits' sequences); the result is that of PeptideIndexing, which runs instead wherever the index cannot reproduce it exactly (e.g. low_memory, a specificity other than full, a chunked database, symbols other than letters or long stretches of ambiguous residues in the database). 'PeptideIndexing': always search every hit in the whole database (Aho-Corasick), as before.index, PeptideIndexing

enzyme_specificityfull Enzyme cleavage specificity required for both peptide termini.
'full' : both termini must be enzyme-specific (canonical, e.g. tryptic).
'semi' : only one terminus needs to be enzyme-specific (semi-tryptic).
'none' : no enzyme constraint at either terminus; every substring of length
[min_size, max_size] is enumerated. Use this for immunopeptidomics
(e.g. HLA peptides 8..12mers). For very large search spaces consider
tightening 'peptide:min_size'/'peptide:max_size'.full, semi, none

motif If set, only peptides whose unmodified sequence (one-letter codes) contains a match of this regular expression are searched, target and decoy peptides alike, e.g. 'N[^P][ST]' for N-glycosylation sequons or 'C' for cysteine-containing peptides; '^' and '$' anchor it to the peptide termini.

min_mass100 Minimal peptide mass for database0:∞

max_mass9000 Maximal peptide mass for database0:∞

++++reportReporting Options

top_hits1 Maximum number of top scoring hits per spectrum that are reported. With 'rescore', only the best hit per spectrum is reported after the rescoring, and the hits that Percolator rescores are set by 'rescoring:top_hits' (report:top_hits then applies to a run that is not rescored and to -out_pin). FDR:PSM > 0 and the protein FDR (FDR:protein > 0) also keep the best hit of each spectrum only, so values above 1 apply with 'rescore' false, FDR:PSM 0 and FDR:protein 0.1:100

isotope_error_conventionobserved_minus_theoretical Sign of the precursor isotope error reported for each PSM (meta value 'isotope_error', in 13C spacings of 1.00336 Da). 'observed_minus_theoretical': +1 means the observed precursor lies one 13C spacing above the peptide (its first 13C isotope peak was selected), as in MS-GF+, pepXML and Sage; PercolatorInfile and PercolatorAdapter (-out_pin, -percolator_executable) remove the offset from the precursor mass difference with this sign. The search parameters of the result record it as 'isotope_error_convention'. 'theoretical_minus_observed': the opposite sign, as written by earlier ProSE versions (no record in the search parameters); with it the Percolator input doubles the offset in dm/absdm instead of removing it.observed_minus_theoretical, theoretical_minus_observed

++++percolatorPercolator rescoring ('rescore')

max_train_psms500000 With 'rescore': the most PSMs Percolator trains a model on (0: all). Every PSM is scored, also beyond the cap. For a run with more PSMs, Percolator samples the training PSMs by spectrum (see 'rescoring:subset_mode'); for the model of the files of a multi-file search too small for a model of their own (trained on the files rescored on their own), each of these files contributes at most this many divided by the number of input files (reproducible random spectra), so that none dominates. The run log says when the training PSMs were sampled. Searches below the cap are not affected. Until all files of such a search are searched, ProSE keeps their PSMs before the rescoring for that model: all PSMs of the files too small, and of the others only their share (with 0, all PSMs of every file, also with the ProSE tool's -out_pin).0:∞

++++rescoringOptions of the Percolator training of the rescoring (see 'rescore')

top_hits2 With 'rescore': the top scoring hits per spectrum (by the search engine score) that Percolator rescores: its training and scoring rows, of which its target-decoy competition keeps the best per spectrum, which is reported. 2 (default) gives Percolator the runner-up of each spectrum as well; more hits cost time and memory. 0 = 'report:top_hits' (as earlier ProSE versions, whose Percolator rescored the reported hits). The search keeps these hits for Percolator (with -out_pin also the reported ones): a run that Percolator does not rescore (fewer than 100 PSMs, no decoy PSM, a failure) reports at most rescoring:top_hits (if above 0) of its report:top_hits hits per spectrum; with decoys 'ignore' (no rescoring) report:top_hits.0:∞

subset_modeout_of_fold With a training cap ('percolator:max_train_psms' > 0) on a run above it (Percolator's parameter 'subset_mode'): 'out_of_fold' (default) assigns every spectrum to one of Percolator's three cross-validation folds first, draws the training sample (whole spectra, at random from the entire run, seeded), trains each fold's model on the sampled spectra of the other folds only, and scores every PSM with the model of its own fold, which never saw its spectrum. 'out_of_fold_avg': the same, but the PSMs of the spectra outside the sample (which no model saw) are scored by the average of the fold models. 'in_sample' = the percolator executable's --subset-max-train: cross-validation on the sample and all PSMs scored by the average of the fold models (the sampled PSMs by two models that trained on them). 'learning_curve' (also without a cap): out-of-fold training on nested samples of 'rescoring:curve_start', twice, four times ... as many PSMs, up to 'percolator:max_train_psms' (0: 1,000,000) or the whole run but the validation spectra (the end of the random order, at most 250,000 PSMs or 20 %); each fold's model stops at the first doubling that adds less than 'rescoring:curve_min_gain' or 2 standard errors of targets at 1 % among the validation spectra of the other folds (no label of its own fold is used), and is not trained further; every PSM is scored by its fold's model. The sizes and the curve are recorded as Percolator:subset_curve.out_of_fold, out_of_fold_avg, in_sample, learning_curve

curve_start100000 'rescoring:subset_mode' learning_curve: PSMs of the first sample.1:∞

curve_min_gain2.0e-03 'rescoring:subset_mode' learning_curve: a fold stops at the first doubling that adds less than this fraction of validation targets.0.0:∞

iterations10 Iterations of Percolator's cross-validation training (the percolator executable's --maxiter). Fewer are faster; the results differ.1:∞

tron_epsilon1.0e-07 Stopping tolerance of the SVM solver (TRON) of Percolator's training (Percolator: 1e-7). Larger values (e.g. 1e-3) train much faster on large runs; the results differ.1.0e-15:∞

warm_startfalse Each SVM training of an iteration starts from the weights of the previous iteration instead of 0 (faster; the results differ).true, false

single_cnegfalse Percolator trains with one Cneg (3 x the target/decoy ratio x Cpos) instead of selecting among three by cross-validation (faster; the results differ).true, false

use_pi0true Percolator's q-values and PEPs with its pi0 estimate (default) or with pi0 = 1, as the percolator executable computes them with target-decoy competition (-Y). 'false' gives slightly fewer PSMs and a lower measured false discovery proportion; the results differ. 'auto' decides as the executable (OpenMS develop's in-process default since #10721): with ProSE's target-decoy competition that is 'false'.true, false, auto

calc_mass_featurefalse Percolator's training uses the CalcMass column (the theoretical m/z) as a feature. 'false' (the default): as the percolator executable, which reads it as metadata (OpenMS develop since #10717); 'true': the behaviour before #10717. The results differ.true, false

fixed_enzyme_terminifalse A protein terminus counts as an enzymatic site for the enzN/enzC features of the rescoring and of '-out_pin' (Percolator's convention). Default 'false' keeps the former features, in which a peptide at a protein N-terminus has enzN = 0 and one at a protein C-terminus that does not end in a cleavage residue has enzC = 0; the results differ. The peptide after an initial Met (the Met-clipped protein N-terminal peptide of peptide:clip_nterm_methionine) counts as N-terminal too. Experimental: tested only with decoy_method 'keep_termini'; without the Met-clip rule, with the decoys of a database of reversed proteins (which rarely start with M) enzN = 0 was left almost only to Met-clipped peptides of targets and the FDR was no longer controlled (entrapment FDP 13-24 % at 1 % q).true, false

terminal_featurestrue Two more rescoring features: 'protein_nterm' (1 if the peptide occurs at a protein N-terminus) and 'met_clipped' (1 if it occurs only as the Met-clipped protein N-terminal peptide of peptide:clip_nterm_methionine). They let the rescoring learn the different rate of correct matches of these small peptide classes. Use them only with decoys that populate both classes like the targets (decoy_method 'keep_termini'): with decoys that rarely start with M (reversed proteins, reused with decoys 'auto') they would tell targets from decoys, so they are switched off with a warning. The results differ.true, false

stratum_q_valuestrue Also q-values per stratum (meta values 'stratum' and 'stratum_q_value'): the rescored PSMs of protein N-terminal peptides (incl. Met-clipped ones) and the others each get target-decoy competition of their own ((decoys + 1) / targets, as mokapot's grouped confidence). For a list of N-terminal peptides at an FDR, use the stratum q-value; the main score stays the pooled q-value. Needs decoys that populate the N-terminal classes like the targets (decoy_method 'keep_termini'; with reused decoys that rarely start with M it is switched off with a warning). With rescore_method 'reset' the values are computed on RESET's scores (both decoy sets count as decoys with reset:decoys 'two'), not as RESET's estimate.true, false

peptide_leveltrue Also Percolator's peptide-level q-values (default; 'false' leaves them out), as the percolator executable reports peptides (without -U): after the target-decoy competition of the spectra, the best PSM of each peptide (modified sequence) and label competes, and q-values and PEPs are estimated on these peptides. Every rescored hit gets the values of its peptide as meta values 'percolator_peptide_q_value' and 'percolator_peptide_pep'; a list of peptides at an FDR is the target peptides with percolator_peptide_q_value at most that FDR (the distinct peptides of the PSMs at an FDR are not FDR-controlled at the peptide level). The main score stays the PSM-level q-value. Default Percolator rescoring only (not with rescore_method 'reset', which reports RESET:peptide_q_value, nor with rescore_reuse models). Independent of this parameter, every rescored hit gets ProSE's peptide-level q-value 'peptide q-value' (the name FalseDiscoveryRate writes and EntrapmentEvaluator reads), with one peptide definition for each run and for the pooled runs of a multi-file search (the ProSE tool's -out_merged): FalseDiscoveryRate::applyBasicPeptideLevel() (a peptide is an unmodified sequence, whose best PSM competes with its label) on the PSMs' Percolator PEPs, also with rescore_reuse models; not with rescore_method 'reset'.true, false

++++resetPercolator-RESET options (rescore_method 'reset')

salt rescore_method 'reset': salt of the decoy coins (unsigned 64-bit integer); empty = random per run. The salt is recorded in the search parameters ('RESET:salt'). Never pick the best of several salts.

learnersvm rescore_method 'reset': 'svm' = linear SVM; 'mlp' = small MLP ensemble (experimental).svm, mlp

mlp_members8 rescore_method 'reset', learner 'mlp': networks per ensemble.1:∞

mlp_hidden16 rescore_method 'reset', learner 'mlp': units of each of the two hidden layers.1:∞

mlp_epochs30 rescore_method 'reset', learner 'mlp': training epochs of the first round.1:∞

mlp_warm_epochs3 rescore_method 'reset', learner 'mlp': > 0 = the networks continue from the previous round for this many epochs (warm starts); 0 = trained afresh (mlp_epochs) every round.0:∞

mlp_crossfittrue rescore_method 'reset', learner 'mlp': score each peptide by the networks that did not train on it (3 folds by sequence hash); 'false' = one final ensemble (memorizes its training decoys: fewer peptides).true, false

mlp_norm_min_decoys1000 rescore_method 'reset', learner 'mlp', cross-fitted: normalize the folds' scores (as Percolator) only if every fold has at least this many training decoys (0 = always).0:∞

representativemodel rescore_method 'reset': the PSM that represents a peptide (stem): 'model' (default) = after each training round, best score under the new model (+2 % peptides on DIA; the FDR then also assumes that null targets and decoys are exchangeable over their whole PSM collections, including their sizes); 'search' = best search engine score (the paper).search, model

iterations25 rescore_method 'reset': training rounds (the paper: 5; on DIA pseudo-spectra 5 rounds stop far from convergence: 82 % of the peptides of 20 rounds on HeLa).1:∞

auditfalse rescore_method 'reset': feature-symmetry audit before training (log).true, false

decoyssingle rescore_method 'reset': 'single' = one decoy database (default); 'two' = the two-decoy mode of Percolator-RESET: the database holds a second decoy set of the same construction (accessions starting with reset:second_decoy_prefix, also recognized as decoys by the decoy marker), the spectra are searched against targets and both decoy sets, and RESET estimates the FDR with the factors of two decoy databases (fewer peptides lost to the decoy split, less variation between salts; the search is larger).single, two

second_decoy_prefixDECOY_X_ rescore_method 'reset', reset:decoys 'two': accession prefix of the proteins of the second decoy set.

stem_table rescore_method 'reset': write the stems with their q-values (tab-separated) to this file, or, if it ends with '/' or is a directory, to /.reset_stems.tsv per run.

++++rescore_reusePercolator model reuse across the files of a search ('rescore')

modeper_file Which PSMs train the Percolator model of a run ('rescore'). 'per_file': the run itself, with Percolator's three-fold cross-validation. The other modes cross-fit: the spectra are split into two halves at random (by Percolator's seed), one model is trained per half on about 'rescore_reuse:max_train' PSMs, and every PSM is scored by the model of the other half, so that no PSM is scored by a model that was trained on it (5 % of the spectra of each half are not trained on: their decoys put the scores of their own half's model on one scale; they are scored by the other model). 'joint' (a multi-file search): the training PSMs are drawn from all files, the same number from each, and the files are rescored once all are searched (mokapot's joint model). 'static' (a multi-file search): they are drawn from the first 'rescore_reuse:static_files' files, and every later file is rescored with these models after its search, unless the features of its PSMs differ from those of the training PSMs by more than 'rescore_reuse:max_shift': then it is rescored as with 'per_file'. 'own': every file trains its two models on its own PSMs. In every mode the q-values and PEPs of a file come from its own target-decoy competition (Percolator's, as with 'per_file'). 'joint' and 'static' need an unchunked closed search of several files and keep all files' PSMs in memory until they are rescored; otherwise 'per_file' applies.per_file, joint, static, own

max_train250000 Training PSMs per model of 'rescore_reuse:mode' (0: all PSMs of the half but the calibration spectra). The spectra are drawn at random, all PSMs of a drawn spectrum together, so the number is met on average; the files share it equally (a file with fewer PSMs gives all).0:∞

static_files1 With 'rescore_reuse:mode' static: the number of (first) input files that train the models.1:∞

max_shift0.5 With 'rescore_reuse:mode' static: the largest domain shift for which a file is rescored with the static models. The shift is max |2 AUC - 1| over the features the models use, AUC comparing the file's PSMs with the training PSMs, targets and decoys alike (0: same distribution, 1: separated).0.0:1.0

++++FDRFalse Discovery Rate control (requires decoys)

PSM0.0 Filter PSMs based on q-value (e.g., 0.05 = 5% FDR; 0 disables the filter). Target and decoy PSMs are filtered alike by the threshold; decoys that pass are kept (no decoy-specific stripping here — decoys are removed only at protein-FDR finalization). With 'rescore' (the default), the threshold applies to the Percolator q-values, the main score of the rescored PSMs. Without rescoring ('rescore' false, or a run that Percolator did not rescore), 0 computes no q-values: every PSM keeps its search engine score ('ln(hyperscore)') as main score, e.g. as input for Percolator or a downstream FDR step. Above 0, the target-decoy q-value (see FDR:PSM_groups) replaces the main score (the search engine score is kept as meta value 'ln(hyperscore)_score') and only the best hit of each spectrum is kept. If no PSM matched a decoy, the q-value of the T PSMs is the conservative 1/T (target-decoy competition with +1), so a lower threshold reports no PSM instead of lifting the filter. Needs decoys ('decoys' auto or generate); with 'ignore', a threshold above 0 is skipped with a warning (the QPX run view of the ProSE tool's -qpx_extended records per input whether the filter was applied: 'psm_fdr_applied'). Afterwards, the proteins that no remaining PSM references are removed. The final PSM FDR with FDR:protein > 0 (e.g. 0.01), a loose evidence threshold of the intermediates with FDR:protein 0 (e.g. 0.1; see there).0.0:1.0

PSM_groupsscored_charges Target-decoy competitions of FDR:PSM. 'pooled' ranks all PSMs together. 'scored_charges' computes q-values separately for PSMs scored with different numbers of fragment charges (scoring:fragment_charges): HyperScore grows with the number of theoretical ions, so when multiply charged fragments are scored for precursors of charge 3 and above but not for charge 2, a pooled competition is dominated by the higher precursor charges. With singly charged fragments only (deisotoped, high-resolution spectra) there is one group, as with 'pooled'. With fragment:max_charge above 2, precursor charges of 4 and above form further groups, which accept few PSMs per run (tens), so their q-values (D/T, as FalseDiscoveryRate) are coarse. A group without decoy or without target PSMs falls back to 'pooled'.scored_charges, pooled

protein0.0 Picked-protein FDR threshold (e.g. 0.01 = 1 %), and the switch between the two modes of a search. Above 0, the search is the whole experiment: its proteins are inferred on the pooled PSMs of all its inputs, filtered at this protein FDR, and the PSMs filtered finally, so every output is the final result (the decoys removed, see the ProSE tool's -keep_decoys). With 0 (the default), the search is one part of a larger experiment, e.g. one shard of files searched on one compute node: every output is a per-run intermediate (PSM q-values and PEPs per run, FDR:PSM as a loose evidence threshold, decoys and the proteins the search indexed for the run's PSMs kept), to be finished downstream on all parts together (e.g. ProteomicsLFQ, or IDMerger, ProteinInference or Epifany, FalseDiscoveryRate and IDFilter). Uses the picked-protein approach (Savitski et al. 2015) which pairs target and decoy proteins by accession. The protein inference and the picked-protein FDR use the PSMs up to FDR:protein_inference_PSM, and a protein scores with the best posterior error probability of its PSMs (Percolator's, with 'rescore'; without it the best search engine score). The proteins and the protein groups (which have q-values of their own) are filtered at the threshold, and only the proteins of the groups that pass are kept. Proteins without a reported PSM (one that passes FDR:PSM) are removed afterwards, and so are the PSMs all of whose proteins failed the protein FDR. Needs decoys ('decoys' auto or generate).0.0:1.0

protein_inference_PSM0.1 q-value cutoff of the PSMs that protein inference and the protein FDR (FDR:protein > 0) use; FDR:PSM still filters the reported PSMs. Without the protein FDR it has no effect. The q-values are those FDR:PSM filters on (Percolator's with 'rescore', else see FDR:PSM_groups). A looser cutoff than FDR:PSM leaves more decoy proteins for the picked-protein FDR, as ProteomicsLFQ infers proteins on PSMs at a looser q-value than its PSM FDR. Values at or below FDR:PSM use the PSMs of FDR:PSM; with FDR:PSM 0 (no PSM filter) all PSMs are used.0.0:1.0

++++scoringSearch/Scoring Limits

max_candidates_per_spectrum50 The number of initial hits for which we calculate a score1:∞

fragment_chargesauto Fragment charges of the theoretical spectra that score each candidate. 'single' scores singly charged fragments only. 'multiple' adds charges up to min(precursor charge - 1, fragment:max_charge). 'auto' uses 'multiple' when the MS2 spectra are not deisotoped (fragment:deisotope=false, or a fragment tolerance above the deisotoper's limit of 0.1 Da / 100 ppm, as for ion-trap CID) and 'single' otherwise, because deisotoping converts fragments to charge 1.auto, single, multiple

methodauto Native score. 'hyperscore' is the X!Tandem HyperScore. 'mass_accuracy' weights each matched fragment's contribution to HyperScore's ion counts and intensity product by exp(-0.5 * (error / scoring:mass_error_sd)^2), with the error in ppm, so that matches near the theoretical m/z count fully and matches at the edge of the tolerance count little; exact matches score as HyperScore. The kernel is centred at 0 and suits high-resolution fragments only. 'auto' (default) uses 'mass_accuracy' for fragment tolerances in ppm within the high-resolution range (<= 100 ppm) and 'hyperscore' otherwise (Da tolerances, e.g. ion-trap CID). Matching tolerances, candidates and the unweighted match annotations are unchanged. The score type stays 'ln(hyperscore)'; the search parameters record scoring:method_resolved when the weighted score is used.hyperscore, mass_accuracy, auto

mass_error_sd7.0 Standard deviation in ppm of the Gaussian fragment mass-error kernel of scoring:method 'mass_accuracy'. Fixed (not fitted) and independent of the matching tolerance and of calibration.1.0e-06:∞

++++ionsTheoretical ion series toggles

add_y_ionstrue Add peaks of y-ions to the spectrumtrue, false

add_b_ionstrue Add peaks of b-ions to the spectrumtrue, false

add_a_ionsfalse Add peaks of a-ions to the spectrumtrue, false

add_c_ionsfalse Add peaks of c-ions to the spectrumtrue, false

add_x_ionsfalse Add peaks of x-ions to the spectrumtrue, false

add_z_ionsfalse Add peaks of z-ions (y - NH3) to the spectrum. These are not the z+1 ions of ETD-type spectra; see ions:by_activation and ions:add_zp1_ions.true, false

add_zp1_ionsfalse Add peaks of z+1 ions (z-dot, y - NH2) to the spectrum, the main C-terminal fragments of ETD, EThcD and ETciD spectra, for all spectra. ions:by_activation adds them (with c ions) for spectra recorded as electron-activated; set this, typically with ions:add_c_ions, for ETD-type data without activation information.true, false

by_activationtrue Score spectra whose precursor was activated by electrons (ETD, ECD, EThcD or ETciD, as recorded in the input file) with c and z+1 ions in addition to the ion series above. Other spectra, and spectra without activation information, use the ion series above.true, false

++++calibrationAutomatic mass tolerances (two-pass search). A fast first pass on the most intense spectra measures the offset and spread of the precursor and fragment mass errors of the run; the main search uses windows derived from them, never wider than the configured tolerances.

enabledtrue Measure the mass error of the run and search with windows derived from it: a fast calibration pass on the most intense spectra (calibration:subset_ratio), searched with at least 20 ppm (in Da: twice the configured window, up to 0.5 Da) precursor and fragment windows (the configured ones if wider) so the error is measured and not censored, takes the offset (median) and the spread (robust standard deviation, 1.4826 * MAD) of the signed mass errors of its confident PSMs; the main search then uses the fragment tolerance |median| + k sigma (calibration:sigma_factor k) within [calibration:min_fragment_tolerance, the configured tolerance], and the precursor window [median - k sigma, median + k sigma] only with calibration:precursor_sigma_factor k > 0 (by default the precursor errors are measured and reported, the configured window kept): the configured tolerances are the widest windows searched. The pass takes its spectra per tenth of the run; a window that covers less than 98 % of the calibration PSMs (precursor; heavy tails or a mass offset that changes over the run) or 95 % of their matched fragment peaks (fragment) is not trusted, and the configured tolerance is kept with a warning. The fragment index is not rebuilt, only the query-time tolerances change. With too few PSMs (calibration:min_psms) the configured tolerances are used. 'false' searches with the configured tolerances as given.true, false

subset_ratio0.1 Fraction of spectra (by TIC, highest first) used for the calibration pass (0.0-1.0).0.01:1.0

min_psms50 Minimum number of confident PSMs required for calibration. If fewer are found, calibration is skipped and the user-configured tolerances are used.1:∞

sigma_factor4.0 Half-width of the calibrated fragment tolerance in robust standard deviations (1.4826 * MAD) of the signed errors of the matched fragment peaks of the calibration PSMs: |median| + k sigma. 4 covers practically all correct matches of a normal error distribution.1.0:∞

precursor_sigma_factor0.0 Half-width of the calibrated precursor window in robust standard deviations of the precursor errors of the calibration PSMs, around their median (asymmetric about zero when the run has an offset). 0 keeps the configured precursor window and only measures and reports the errors: precursor yields are flat from 5 to 50 ppm, and a tightened precursor window cost identifications on every Orbitrap HCD set of the benchmark (heavy tails), while the fragment window gains. A value such as 4 tightens it, within calibration:min_precursor_tolerance and the configured window, when the window covers 98 % of the calibration PSMs.0.0:∞

min_precursor_tolerance0.0 Smallest calibrated precursor tolerance per side, in precursor:mass_tolerance_unit (0: 2.5 ppm or 0.005 Da). The calibrated window never exceeds the configured one.0.0:∞

min_fragment_tolerance0.0 Smallest calibrated fragment tolerance, in fragment:mass_tolerance_unit (0: 10 ppm or 0.02 Da; 5 ppm or 0.01 Da with calibration:recalibrate). The calibrated tolerance never exceeds the configured one.0.0:∞

recalibrateoffset Correct the m/z of the spectra by the mass errors the calibration pass measures, before the main search: 'offset' subtracts the median error, 'linear' a line in m/z fitted to the errors (precursor errors against the precursor m/z, fragment errors against the fragment m/z), each per retention-time chunk (calibration:recalibrate_rt_chunks) and interpolated between the chunks; a chunk of the precursor model whose calibration PSMs are mostly false matches (more than a quarter of them decoy hits) takes the model of its neighbours. The precursor m/z and the fragment peaks of the searched MS2 spectra are corrected in place (the candidate retrieval, the scoring and the PSMs' mass errors use the corrected values; a PeakMap passed to the library is corrected too); the PSMs report the observed precursor m/z and their fragment annotations the observed peak m/z. The windows are then derived from the residual errors, with a fragment floor of 5 ppm (0.01 Da) unless calibration:min_fragment_tolerance is set. The co-isolated precursors of a chimeric search, from the same survey scans, are corrected by the precursor model. 'none' measures only.none, offset, linear

recalibrate_rt_chunks10 Retention-time chunks of the recalibration models (calibration:recalibrate): the calibration PSMs are split in acquisition order into this many groups of equal size (fewer when a group would hold less than calibration:min_psms PSMs), one model each, interpolated between the groups' median retention times. 1: one model for the run; 10 follows an offset that changes over the run (the pass samples each tenth of it).1:∞

++++database

chunk_size0 Split the protein database into chunks of at most this many proteins for fragment index building. 0 = disabled (load entire database at once). Enable for very large databases (e.g. MHC-II immunopeptidomics with variants) that exceed available memory. Each chunk builds its own fragment index; results are merged across chunks before post-processing. Calibration (when enabled) runs on a strided, size-bounded sample of the full decoy-augmented database — sample size is tied to chunk_size so calibration memory respects the same budget as main-search chunks. In multi-file mode (-in a.mzML b.mzML), the chunk-major path builds each chunk's fragment index once and scores all files against it before moving to the next chunk. Note that chunk_size bounds only the fragment-index memory: the chunk-major schedule holds ALL input files' preprocessed MS2 spectra in memory for the whole search, so budget for their sum as well, or split very large cohorts across separate ProSE invocations.0:∞

++++chimericSearch of precursors co-isolated with the selected one (chimeric spectra).

enabledfalse Also identify precursors co-isolated with the selected one (after the andes chimeric cascade). The survey scan of each MS2 spectrum is searched for isotope envelopes in its isolation window that fit averagine (needs centroided MS1 spectra in the input and isolation windows on the precursors). After the search, the peaks the best hit of the spectrum explains are removed, and the rest is searched for each co-isolated precursor in turn, at its m/z and charge; the best hit of each removes the peaks it explains before the next is searched. The best hit's peptide is not a hit of a co-isolated precursor, and a co-isolated precursor whose best hit repeats a PSM of the spectrum (same peptide and charge) is dropped. These PSMs get the spectrum reference of their spectrum and the PSM meta value 'chimeric_rank' 2 (the others 1). Not with database:chunk_size > 0.true, false

max_coisolated4 At most this many co-isolated precursors per spectrum, the most intense first.1:∞

max_kl0.3 Largest Kullback-Leibler divergence of an isotope envelope in the survey scan from averagine (first four isotope peaks) to accept it as a co-isolated precursor.0.0:∞

top_hits3 At most this many hits of a co-isolated precursor are reported (and at most report:top_hits). Each takes about as much memory as a hit of a spectrum.1:∞

mz_tolerance10.0 Tolerance (ppm) for the m/z of the isotope peaks in the survey scan.0.0:∞