stty: 'standard input': Inappropriate ioctl for device OpenDIA -- High-level DIA workflow front-end built on the OpenSWATH/OpenMS stack. Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenDIA.html Version: 3.7.0-pre-feature-opendia-prediction-cache-storage-2026-10-09 Oct 9 2026, 10:56:36, Revision: cb99c9a To cite OpenMS: + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7. Usage: OpenDIA Options (mandatory options marked with '*'): -in * Input DIA files separated by blank. (valid formats: 'mzML', 'mzXML', 'sqMass', 'd', 'raw') -tr * Library input file, or FASTA database for predicted mode. (valid formats: 'traML', 'tsv', 'pqp', 'oswpq', 'fasta', 'fa', 'faa') -tr_type Library input file type -- default: determined from file extension or content. (valid: 'traML', 'tsv', 'pqp', 'oswpq', 'fasta') -out_dir Directory for final exported OpenDIA outputs. Workflow options.: -workflow:library_mode How to enter the workflow: auto-detect FASTA/predicted or transition-library preparation, force prepared peptide-query normalization, force transition-list assay/decoy preparation, or predict a library from FASTA. (default: 'auto') (valid: 'auto', 'prepared_pqp', 'transition_list', 'predicted') -workflow:working_format Internal workflow container used after extraction/scoring: 'sqlite' writes a .osw workflow, 'parquet' writes a .oswpq archive. (default: 'sqlite') (valid: 'sqlite', 'parquet') -workflow:keep_intermediate_files Whether to retain prepared_library.pqp and the single working workflow.osw (.sqlite workflow) or workflow.oswpq (.parquet archive workflow) after success. (default: 'false') (valid: 'true', 'false') -workflow:intermediate_dir Optional parent directory for intermediate workflow files. Preserved automatically on failure. When cleanup is enabled, OpenDIA creates a unique run-owned child beneath this directory and removes only that child after success. When left empty, OpenDIA uses a run-owned child beneath OpenDIA_intermediates under out_dir. Assay-generation parameters used when workflow:library_mode=transition_list.: -PeptideQueryParameters:AssayGenerator:min_transitions Minimal number of transitions. (default: '6') -PeptideQueryParameters:AssayGenerator:max_transitions Maximal number of transitions. (default: '6') -PeptideQueryParameters:AssayGenerator:allowed_fragment_types Allowed fragment types. (default: 'b,y') -PeptideQueryParameters:AssayGenerator:allowed_fragment_charges Allowed fragment charge states. (default: '1,2,3,4') -PeptideQueryParameters:AssayGenerator:enable_detection_specific_losses Allow specific neutral losses for detecting transitions. -PeptideQueryParameters:AssayGenerator:enable_detection_unspecific_losses Allow unspecific neutral losses for detecting transitions. -PeptideQueryParameters:AssayGenerator:precursor_mz_threshold Precursor m/z threshold in Thomson for precursor annotation. (default: '0.025') -PeptideQueryParameters:AssayGenerator:precursor_lower_mz_limit Lower precursor m/z limit. (default: '400.0') -PeptideQueryParameters:AssayGenerator:precursor_upper_mz_limit Upper precursor m/z limit. (default: '1200.0') -PeptideQueryParameters:AssayGenerator:product_mz_threshold Fragment m/z threshold in Thomson for annotation. (default: '0.025') -PeptideQueryParameters:AssayGenerator:product_lower_mz_limit Lower fragment m/z limit. (default: '350.0') -PeptideQueryParameters:AssayGenerator:product_upper_mz_limit Upper fragment m/z limit. (default: '2000.0') -PeptideQueryParameters:AssayGenerator:swath_windows_file Optional SWATH window file for exclusion of fragment ions in the precursor isolation window. (valid formats: 'txt') -PeptideQueryParameters:AssayGenerator:unimod_file Optional Unimod XML file used for IPF transition generation. (valid formats: 'xml') -PeptideQueryParameters:AssayGenerator:reuse_existing_modifications_db Explicitly reuse an already-initialized ModificationsDB for IPF. -PeptideQueryParameters:AssayGenerator:enable_ipf Generate identifying transitions for IPF during transition-list library preparation. -PeptideQueryParameters:AssayGenerator:max_num_alternative_localizations IPF: maximum number of site-localization permutations. (default: '10000') -PeptideQueryParameters:AssayGenerator:disable_identification_ms2_precursors IPF: disable MS2 precursor ions for identification transitions. -PeptideQueryParameters:AssayGenerator:disable_identification_specific_losses IPF: disable specific neutral losses for identification transitions. -PeptideQueryParameters:AssayGenerator:enable_identification_unspecific_losses IPF: allow unspecific neutral losses for identification transitions. -PeptideQueryParameters:AssayGenerator:enable_swath_specifity IPF: use precursor-isolation windows instead of precursor m/z-specific identification transitions. -PeptideQueryParameters:AssayGenerator:disable_decoy_transitions IPF: disable generation of decoy UIS transitions. -PeptideQueryParameters:AssayGenerator:ipf_decoy_seed IPF: random seed for decoy shuffle (-1 = time-based). (default: '-1') FASTA digestion and native PeptDeep prediction parameters used when workflow:library_mode=predicted.: -PeptideQueryParameters:LibraryPrediction:enzyme Protease used for in-silico FASTA digestion. (default: 'Trypsin') (valid: 'Arg-C/P', 'Asp-N', 'Asp-N/B', 'Asp-N_ambic', 'Chymotrypsin', 'Clostripain/P', 'elastase-trypsin-chymotrypsin', 'no cleavage', 'unspecific cleavage', 'Trypsin', 'Arg-C', 'Chymotrypsin/P', 'CNBr', 'Formic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA', 'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'leukocyte elastase', 'proline endopeptidase', 'glutamyl endopeptidase', 'Alpha-lytic protease', '2-iodobenzoate', 'iodosobenzoate', 'staphylococcal protease/D', 'proline-endopeptidase/HKR', 'Glu-C+P', 'PepsinA + P', 'cyanogen-bromide') -PeptideQueryParameters:LibraryPrediction:missed_cleavages Maximum number of missed cleavages. (default: '2') (min: '0') -PeptideQueryParameters:LibraryPrediction:min_peptide_length Minimum peptide length retained for prediction. (default: '7') (min: '2') -PeptideQueryParameters:LibraryPrediction:max_peptide_length Maximum peptide length retained for prediction. (default: '30') (min: '2') -PeptideQueryParameters:LibraryPrediction:precursor_charges Precursor charge states to predict. (default: '[2 3]') (min: '1') -PeptideQueryParameters:LibraryPrediction:fixed_modifications Fixed OpenMS/UniMod modification names applied before prediction. (default: '[Carbamidomethyl (C)]') -PeptideQueryParameters:LibraryPrediction:variable_modifications Variable OpenMS/UniMod modification names enumerated before prediction. -PeptideQueryParameters:LibraryPrediction:max_variable_modifications Maximum number of variable modifications per peptide. (default: '1') (min: '0') -PeptideQueryParameters:LibraryPrediction:clip_nterm_methionine Also digest the mature protein sequence after initiator-methionine removal. (default: 'true') (valid: 'true', 'false') -PeptideQueryParameters:LibraryPrediction:prediction_batch_size Number of precursors predicted per materialization batch. (default: '500') (min: '1') -PeptideQueryParameters:LibraryPrediction:inference_threads ONNX Runtime intra-op thread count for each PeptDeep predictor. (default: '4') (min: '1') -PeptideQueryParameters:LibraryPrediction:nce Normalized collision energy supplied to PeptDeep MS2 prediction. (default: '30.0') (min: '0.0' max: '100.0') -PeptideQueryParameters:LibraryPrediction:instrument_index PeptDeep instrument category (0=QE, 1=Lumos, 2=timsTOF, 3=SciexTOF, 4=ThermoTOF, 7=other/unknown). (default: '0') (min: '0' max: '7') -PeptideQueryParameters:LibraryPrediction:predict_ccs Predict CCS and store converted 1/K0 values in the materialized library. (default: 'true') (valid: 'true', 'false') -PeptideQueryParameters:LibraryPrediction:rt_model Optional explicit PeptDeep RT ONNX model. Empty uses the installed OpenMS model. -PeptideQueryParameters:LibraryPrediction:ccs_model Optional explicit PeptDeep CCS ONNX model. Empty uses the installed OpenMS model. -PeptideQueryParameters:LibraryPrediction:ms2_model Optional explicit PeptDeep MS2 ONNX model. Empty uses the installed OpenMS model. -PeptideQueryParameters:LibraryPrediction:out Optional reusable prepared target/decoy PQP generated from the FASTA input. (valid formats: 'pqp') Decoy-generation parameters used when workflow:library_mode=transition_list or predicted.: -PeptideQueryParameters:DecoyGenerator:method Decoy generation method. (default: 'shuffle') (valid: 'shuffle', 'pseudo-reverse', 'reverse', 'shift') -PeptideQueryParameters:DecoyGenerator:decoy_tag Decoy tag. (default: 'DECOY_') -PeptideQueryParameters:DecoyGenerator:min_decoy_fraction Minimum fraction of decoy / target peptides and proteins. (default: '0.8') -PeptideQueryParameters:DecoyGenerator:aim_decoy_fraction Requested fraction of decoys to generate. (default: '1.0') -PeptideQueryParameters:DecoyGenerator:shuffle_max_attempts Shuffle: maximum attempts to reduce target/decoy sequence identity. (default: '30') -PeptideQueryParameters:DecoyGenerator:shuffle_sequence_identity_threshold Shuffle: target-decoy amino-acid sequence identity threshold. (default: '0.5') -PeptideQueryParameters:DecoyGenerator:shift_precursor_mz_shift Shift: precursor ion m/z shift in Thomson. (default: '0.0') -PeptideQueryParameters:DecoyGenerator:shift_product_mz_shift Shift: fragment ion m/z shift in Thomson. (default: '20.0') -PeptideQueryParameters:DecoyGenerator:product_mz_threshold Fragment m/z threshold used during decoy annotation. (default: '0.025') -PeptideQueryParameters:DecoyGenerator:allowed_fragment_types Allowed fragment types. (default: 'b,y') -PeptideQueryParameters:DecoyGenerator:allowed_fragment_charges Allowed fragment charge states. (default: '1,2,3,4') -PeptideQueryParameters:DecoyGenerator:enable_detection_specific_losses Allow specific neutral losses for decoy generation. -PeptideQueryParameters:DecoyGenerator:enable_detection_unspecific_losses Allow unspecific neutral losses for decoy generation. -PeptideQueryParameters:DecoyGenerator:switchKR Whether to switch terminal K and R to achieve different precursor masses. (default: 'true') (valid: 'true', 'false') Targeted data extraction options.: -TargetedDataExtraction:swath_windows_file Optional tab-separated SWATH window file used during extraction. -TargetedDataExtraction:sort_swath_maps Sort input SWATH files when matching to SWATH windows from TargetedDataExtraction:swath_windows_file. -TargetedDataExtraction:enable_ms1 Extract precursor traces and use them for scoring if present. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:enable_ipf Enable extraction-time UIS/IPF scoring when identifying transitions are present. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:write_debug_files Automatically write per-run calibration/debug files into out_dir using .debug.* names when explicit debug output paths are not set. (default: 'false') (valid: 'true', 'false') -TargetedDataExtraction:write_chromatograms Automatically write per-run extracted chromatograms into out_dir using .chrom.sqMass for sqlite workflows or .chrom.xic for parquet workflows when TargetedDataExtraction:out_chrom is not set. (default: 'false') (valid: 'true', 'false') -TargetedDataExtraction:write_mobilograms Automatically write per-run extracted ion mobilograms into out_dir using .mobi.xim when TargetedDataExtraction:out_mobilogram is not set. (default: 'false') (valid: 'true', 'false') -TargetedDataExtraction:out_chrom Optional chromatogram output in mzML (chrom.mzML), sqMass, or xic (Parquet). If multiple runs are analyzed, explicit file names are expanded per run as _. (valid formats: 'mzML', 'sqMass', 'xic') -TargetedDataExtraction:out_mobilogram Optional extracted ion mobilogram output in Parquet (.xim). If multiple runs are analyzed, explicit file names are expanded per run as _. (valid formats: 'xim') -TargetedDataExtraction:min_upper_edge_dist Minimal distance to the upper edge of a SWATH window to still consider a precursor, in Thomson. (default: '0.0') -TargetedDataExtraction:pasef Treat the input as PASEF / diaPASEF data. -TargetedDataExtraction:ion_mobility_mode How to use the ion mobility dimension. 'auto' detects ion mobility SWATH windows and enables PASEF-style extraction/scoring automatically, filling negative IM extraction windows with 0.06 1/K0 defaults. 'disabled' disables ion mobility extraction, calibration, and scoring even if the input contains ion mobility. (default: 'auto') (valid: 'auto', 'disabled') -TargetedDataExtraction:rt_extraction_window Only extract RT around this value (-1 means extract the whole range; 600 means +/- 300 s around the expected elution). (default: '600.0') -TargetedDataExtraction:extra_rt_extraction_window Optional extra RT padding for the written chromatogram output. (default: '0.0') (min: '0.0') -TargetedDataExtraction:ion_mobility_window Extraction window in ion mobility dimension (full width; negative values extract the whole range unless detected diaPASEF/timsTOF data trigger automatic 0.06 1/K0 defaults). (default: '-1.0') -TargetedDataExtraction:mz_extraction_window MS2 extraction window in Thomson or ppm (see TargetedDataExtraction:mz_extraction_window_unit). (default: '50.0') (min: '0.0') -TargetedDataExtraction:mz_extraction_window_unit Unit for the MS2 m/z extraction window. (default: 'ppm') (valid: 'Th', 'ppm') -TargetedDataExtraction:mz_extraction_window_ms1 MS1 extraction window in Thomson or ppm (see TargetedDataExtraction:mz_extraction_window_ms1_unit). (default: '50.0') (min: '0.0') -TargetedDataExtraction:mz_extraction_window_ms1_unit Unit for the MS1 m/z extraction window. (default: 'ppm') (valid: 'ppm', 'Th') -TargetedDataExtraction:im_extraction_window_ms1 MS1 ion mobility extraction window. Negative values disable MS1 ion mobility extraction unless detected diaPASEF/timsTOF data trigger automatic 0.06 1/K0 defaults. (default: '-1.0') -TargetedDataExtraction:use_ms1_ion_mobility Also perform precursor extraction using the fragment-ion ion mobility window. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:matching_window_only Assume PRM-like overlapping DIA windows and extract each assay only from the best matching window. (default: 'false') (valid: 'true', 'false') -TargetedDataExtraction:irt_mz_extraction_window Extraction window used for iRT and m/z correction in Thomson or ppm (see TargetedDataExtraction:irt_mz_extraction_window_unit). (default: '50.0') (min: '0.0') -TargetedDataExtraction:irt_mz_extraction_window_unit Unit for the iRT m/z extraction window. (default: 'ppm') (valid: 'Th', 'ppm') -TargetedDataExtraction:irt_im_extraction_window Ion mobility extraction window used for iRT calibration (negative values disable IM calibration unless detected diaPASEF/timsTOF data trigger automatic 0.06 1/K0 defaults). (default: '-1.0') -TargetedDataExtraction:split_file_input Interpret the input files as one SWATH window per file. -TargetedDataExtraction:use_elution_model_score Turn on the CPU-intensive EMG elution model score. -TargetedDataExtraction:readOptions Whether to read directly, cache to disk first, or keep cached data in memory. (default: 'normal') (valid: 'normal', 'cache', 'cacheWorkingInMemory', 'workingInMemory') -TargetedDataExtraction:tempDirectory Temporary directory used for cached SWATH input files. When left empty, OpenDIA uses out_dir as the base directory and creates protected per-run temporary subdirectories there. -TargetedDataExtraction:keep_cached_files If set, do not remove cached input files created in TargetedDataExtraction:tempDirectory. -TargetedDataExtraction:extraction_function Extraction kernel used for signal extraction. (default: 'tophat') (valid: 'tophat', 'bartlett') -TargetedDataExtraction:batchSize Compound batch size for extraction/scoring scheduling. 0 enables automatic scheduling. (default: '0') (min: '0') -TargetedDataExtraction:innerBatchSize Inner scoring batch size for automatic scheduling (<=0 means auto). (default: '-1') (min: '-1') -TargetedDataExtraction:maxConcurrentSwaths Maximum concurrent non-MS1 SWATH maps kept in memory for automatic scheduling (-1 means auto). (default: '-1') (min: '-1') -TargetedDataExtraction:outer_loop_threads Legacy nested OpenMP outer-loop thread count. Leave -1 for automatic scheduling. (default: '-1') -TargetedDataExtraction:ms1_isotopes The number of MS1 isotopes used for extraction. (default: '3') (min: '0') -TargetedDataExtraction:irt_mzml Optional chromatogram mzML containing the iRT peptides. If multiple runs are analyzed, explicit file names are expanded per run as _. (valid formats: 'mzML') -TargetedDataExtraction:irt_trafo Optional transformation file for RT normalization. If multiple runs are analyzed, explicit file names are expanded per run as _. (valid formats: 'trafoXML') -TargetedDataExtraction:disable_features Debug-only feature toggles: no_IM_calibration, no_IM_windowing. (valid: 'no_IM_calibration', 'no_IM_windowing') In-process Percolator rescoring parameters.: -Rescoring:level One or more rescoring levels to run sequentially. Transition rescoring is appended automatically when peptidoform inference is enabled. (default: '[ms1ms2]') (valid: 'ms1', 'ms2', 'ms1ms2', 'transition') Peptidoform inference options.: -Inference:peptidoform:run Enable peptidoform inference. (default: 'false') (valid: 'true', 'false') -Inference:peptidoform:ipf_ms1_scoring Use MS1 precursor evidence for peptidoform inference. (default: 'false') (valid: 'true', 'false') -Inference:peptidoform:ipf_ms2_scoring Use MS2 precursor evidence for peptidoform inference. (default: 'false') (valid: 'true', 'false') -Inference:peptidoform:ipf_h0 Include the null hypothesis in IPF inference. (default: 'true') (valid: 'true', 'false') -Inference:peptidoform:ipf_grouped_fdr Compute model FDR separately per num_peptidoforms group. (default: 'false') (valid: 'true', 'false') -Inference:peptidoform:ipf_max_peakgroup_pep Maximum peakgroup PEP for entering precursor inference. (default: '0.7') -Inference:peptidoform:ipf_max_precursor_pep Maximum precursor-level evidence PEP. (default: '0.7') -Inference:peptidoform:ipf_max_precursor_peakgroup_pep Maximum precursor-peakgroup PEP retained for transition inference. (default: '0.4') -Inference:peptidoform:ipf_max_transition_pep Maximum transition evidence PEP retained for IPF. (default: '0.6') -Inference:peptidoform:propagate_signal_across_runs Propagate confident transition evidence across aligned runs. (default: 'false') (valid: 'true', 'false') -Inference:peptidoform:ipf_min_alignment_mapping_confidence Minimum mapping confidence retained for across-run propagation. (default: '0.5') -Inference:peptidoform:across_run_confidence_threshold Maximum transition PEP eligible for across-run propagation. (default: '0.5') Peptide inference options.: -Inference:peptide:global Enable peptide inference in the global context. (default: 'true') (valid: 'true', 'false') -Inference:peptide:experiment_wide Enable peptide inference in the experiment-wide context. (default: 'false') (valid: 'true', 'false') -Inference:peptide:run_specific Enable peptide inference in the run-specific context. (default: 'false') (valid: 'true', 'false') Protein inference options.: -Inference:protein:global Enable protein inference in the global context. (default: 'true') (valid: 'true', 'false') -Inference:protein:experiment_wide Enable protein inference in the experiment-wide context. (default: 'false') (valid: 'true', 'false') -Inference:protein:run_specific Enable protein inference in the run-specific context. (default: 'false') (valid: 'true', 'false') Gene inference options.: -Inference:gene:global Enable gene inference in the global context. (default: 'false') (valid: 'true', 'false') -Inference:gene:experiment_wide Enable gene inference in the experiment-wide context. (default: 'false') (valid: 'true', 'false') -Inference:gene:run_specific Enable gene inference in the run-specific context. (default: 'false') (valid: 'true', 'false') Context-level error estimation options.: -Inference:error_estimation:parametric Use parametric p-value estimation instead of empirical estimation. (default: 'false') (valid: 'true', 'false') -Inference:error_estimation:pfdr Use positive FDR in q-value and s-value calculations. (default: 'false') (valid: 'true', 'false') -Inference:error_estimation:pi0_lambda Lambda grid for pi0 estimation. (default: '[0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45]') -Inference:error_estimation:pi0_method Method for pi0 estimation. (default: 'bootstrap') (valid: 'bootstrap', 'smoother') -Inference:error_estimation:pi0_smooth_df Degrees of freedom for smoother-based pi0 estimation. (default: '3') (min: '1') -Inference:error_estimation:pi0_smooth_log_pi0 Smooth log(pi0) instead of pi0 directly. (default: 'false') (valid: 'true', 'false') -Inference:error_estimation:lfdr_truncate Truncate local FDR/PEP values to [0,1]. (default: 'true') (valid: 'true', 'false') -Inference:error_estimation:lfdr_monotone Enforce monotone local FDR/PEP estimates. (default: 'true') (valid: 'true', 'false') -Inference:error_estimation:lfdr_transformation Transformation used by local FDR estimation. (default: 'probit') (valid: 'probit', 'logit') -Inference:error_estimation:lfdr_adj Adjustment factor for local FDR estimation bandwidth. (default: '1.5') -Inference:error_estimation:lfdr_eps Epsilon used to clip p-values before local FDR estimation. (default: '1.0e-08') Options for scored feature parquet export.: -Export:parquet:run Whether to export scored feature parquet tables. (default: 'false') (valid: 'true', 'false') -Export:parquet:include_transition_data Whether to also export transition-level parquet tables. (default: 'true') (valid: 'true', 'false') -Export:parquet:exclude_decoys Whether to exclude decoys from parquet feature exports. (default: 'false') (valid: 'true', 'false') Options for user-facing filtered result export.: -Export:results:run Whether to export the filtered results table. (default: 'true') (valid: 'true', 'false') -Export:results:format Output format for the filtered results table. (default: 'tsv') (valid: 'tsv', 'parquet') -Export:results:ipf How IPF results should be represented when SCORE_IPF is present. (default: 'peptidoform') (valid: 'peptidoform', 'augmented', 'disable') -Export:results:transition_quantification Whether to aggregate transition-level quantification columns. (default: 'true') (valid: 'true', 'false') -Export:results:max_transition_pep Maximum transition PEP used for aggregated transition quantification. (default: '0.7') -Export:results:ipf_max_peptidoform_pep Maximum IPF PEP used for peptidoform export filtering. (default: '0.4') -Export:results:max_rs_peakgroup_qvalue Maximum run-specific peakgroup q-value retained. (default: '0.05') -Export:results:use_peptide_scores Whether to append peptide-level scores if SCORE_PEPTIDE is present and to require passing the peptide-level threshold. (default: 'true') (valid: 'true', 'false') -Export:results:max_global_peptide_qvalue Maximum global peptide-level q-value retained when peptide filtering is enabled. (default: '0.01') -Export:results:use_protein_scores Whether to append protein-level scores if SCORE_PROTEIN is present and to require passing the protein-level threshold. (default: 'true') (valid: 'true', 'false') -Export:results:max_global_protein_qvalue Maximum global protein-level q-value retained when protein filtering is enabled. (default: '0.01') -Export:results:use_gene_scores Whether to append gene-level scores if SCORE_GENE is present and to require passing the gene-level threshold. (default: 'false') (valid: 'true', 'false') -Export:results:max_global_gene_qvalue Maximum global gene-level q-value retained when gene filtering is enabled. (default: '0.01') -Export:results:use_alignment Whether to recover aligned features when legacy alignment tables are present. (default: 'false') (valid: 'true', 'false') -Export:results:max_alignment_pep Maximum alignment PEP retained when alignment recovery is enabled. (default: '0.7') -Export:results:exclude_decoys Whether to exclude decoys from the filtered results export. (default: 'true') (valid: 'true', 'false') Options for quantification matrix exports.: -Export:matrix:precursor Whether to export the precursor-level quantification matrix. (default: 'false') (valid: 'true', 'false') -Export:matrix:peptide Whether to export the peptide-level quantification matrix. (default: 'true') (valid: 'true', 'false') -Export:matrix:protein Whether to export the protein-level quantification matrix. (default: 'true') (valid: 'true', 'false') -Export:matrix:gene Whether to export the gene-level quantification matrix. (default: 'false') (valid: 'true', 'false') -Export:matrix:format Output format for quantification matrices. (default: 'tsv') (valid: 'tsv', 'parquet') -Export:matrix:ipf How IPF results should be represented when SCORE_IPF is present. (default: 'peptidoform') (valid: 'peptidoform', 'augmented', 'disable') -Export:matrix:transition_quantification Whether to aggregate transition-level quantification columns onto the filtered feature rows. (default: 'true') (valid: 'true', 'false') -Export:matrix:max_transition_pep Maximum transition PEP used for aggregated transition quantification. (default: '0.7') -Export:matrix:ipf_max_peptidoform_pep Maximum IPF PEP used for peptidoform export filtering. (default: '0.4') -Export:matrix:max_rs_peakgroup_qvalue Maximum run-specific peakgroup q-value retained. (default: '0.05') -Export:matrix:use_peptide_scores Whether peptide-level scores should be required when peptide filtering is enabled. (default: 'true') (valid: 'true', 'false') -Export:matrix:max_global_peptide_qvalue Maximum global peptide-level q-value retained when peptide filtering is enabled. (default: '0.01') -Export:matrix:use_protein_scores Whether protein-level scores should be required when protein filtering is enabled. (default: 'true') (valid: 'true', 'false') -Export:matrix:max_global_protein_qvalue Maximum global protein-level q-value retained when protein filtering is enabled. (default: '0.01') -Export:matrix:use_gene_scores Whether gene-level scores should be required when gene filtering is enabled. (default: 'false') (valid: 'true', 'false') -Export:matrix:max_global_gene_qvalue Maximum global gene-level q-value retained when gene filtering is enabled. (default: '0.01') -Export:matrix:use_alignment Whether to recover aligned features when legacy alignment tables are present. (default: 'false') (valid: 'true', 'false') -Export:matrix:max_alignment_pep Maximum alignment PEP retained when alignment recovery is enabled. (default: '0.7') -Export:matrix:exclude_decoys Whether to exclude decoys from the filtered matrix input rows. (default: 'true') (valid: 'true', 'false') -Export:matrix:top_n Number of top precursors / peptides retained during matrix summarization. (default: '3') -Export:matrix:consistent_top Whether to use the same top precursors / peptides across all runs. (default: 'true') (valid: 'true', 'false') -Export:matrix:normalization Normalization applied to matrix sample columns after summarization. (default: 'none') (valid: 'none', 'median', 'medianmedian') Common TOPP options: -ini Use the given TOPP INI file -log Name of log file (created only when specified) -debug Sets the debug level (default: '0') -threads Sets the number of threads allowed to be used by the TOPP tool (0 = all available cores) (default: '1') -write_ini Writes the default configuration file -write_ctd Writes the common tool description file(s) (Toolname(s).ctd) to -write_nested_cwl Writes the Common Workflow Language file(s) (Toolname(s).cwl) to -write_cwl Writes the Common Workflow Language file(s) (Toolname(s).cwl) to , but enforce a flat parameter hierarchy -write_nested_json Writes the default configuration file -write_json Writes the default configuration file, but compatible to the flat hierarchy -no_progress Disables progress logging to command line -force Overrides tool-specific checks -test Enables the test mode (needed for internal use only) --help Shows options --helphelp Shows all options (including advanced) Rescoring:transition: -Rescoring:transition:peakgroup_max_rank Transition scoring: maximum MS2 peak-group rank retained for transition rescoring. (default: '1') (min: '1') -Rescoring:transition:peakgroup_max_pep Transition scoring: maximum MS2 peak-group PEP retained for transition rescoring. (default: '0.7') (min: '0.0' max: '1.0') -Rescoring:transition:max_isotope_overlap Transition scoring: maximum transition isotope-overlap score retained for rescoring. (default: '0.5') (min: '0.0') -Rescoring:transition:min_log_sn Transition scoring: minimum log signal-to-noise score retained for rescoring. (default: '0.0') Rescoring:percolator: -Rescoring:percolator:c_pos Positive regularization constant (C+). (default: '0.1') (min: '0.0') -Rescoring:percolator:c_neg Negative regularization constant (C-). 0 = auto-select. (default: '0.0') (min: '0.0') -Rescoring:percolator:test_fdr Test FDR threshold for SVM direction selection. (default: '0.01') (min: '0.0' max: '1.0') -Rescoring:percolator:train_fdr Training FDR for SVM iterations. (default: '0.01') (min: '0.0' max: '1.0') -Rescoring:percolator:num_iterations Number of SVM training iterations. (default: '10') (min: '1') -Rescoring:percolator:initial_direction Feature name to use as the initial scoring direction. Prefix with '-' if LOWER values are more target-like (e.g. 'COMET:lnExpect' means higher is better; '-COMET:lnExpect' means lower is better). Leave empty (default) to let Percolator auto-select by testing every feature in both directions and picking the one that separates the most targets at train_fdr. -Rescoring:percolator:pep_method Posterior error probability estimator: 'logistic_regression' (target-decoy competition + isotonic fit; legacy name, not actually logistic regression), 'isotonic' (target-q → pep monotone regression), or 'nonparametric' (kernel smoothing). (default: 'logistic_regression') (valid: 'logistic_regression', 'isotonic', 'nonparametric') -Rescoring:percolator:seed Random seed for CV splitting. (default: '1') -Rescoring:percolator:target_decoy_metavalue Meta-value on PeptideHit indicating target/decoy ('target'/'decoy'). (default: 'target_decoy') -Rescoring:percolator:normalizer Feature normalizer: 'stdv' (zero-mean, unit-stdv, default), 'uni' (min/max), or 'none' (no normalization). (default: 'stdv') (valid: 'stdv', 'uni', 'none') -Rescoring:percolator:train_best_positive During TRAINING, use only the best PSM per spectrum as a positive example. Affects the SVM (weights change). Orthogonal to post_processing_tdc. Default is 'true' because typical OpenMS inputs are multi-hit-per-spectrum (Comet/MSGF+/Sage top-N, OSW peak groups). Inert on one-hit-per-spectrum inputs. Note: the upstream percolator binary defaults this to off — PercolatorAdapter preserves the CLI contract by mirroring its flag state when writing this param. (default: 'true') (valid: 'true', 'false') -Rescoring:percolator:post_processing_tdc AFTER training, before PEP/q-value calculation, apply Target-Decoy Competition: keep only the highest-scoring PSM per (scan, mass, charge) and drop the rest from the score set. Does NOT touch the SVM — only the score distribution used for FDR. Default is 'true' because without TDC on multi-hit input, q-values count every candidate as an independent 'chance' and drift optimistic. Inert on one-hit-per-spectrum inputs. Note: the upstream percolator binary defaults this to off — PercolatorAdapter preserves the CLI contract by mirroring its flag state when writing this param. (default: 'true') (valid: 'true', 'false') -Rescoring:percolator:nested_xval_bins Number of nested CV bins for grid search of Cpos/Cneg. Upstream default for cross validation is 3; 1 disables nested search. (default: '1') (min: '1') -Rescoring:percolator:subset_max_train Cap on the training set size (0 = use all). Default 100000 bounds training time on very large inputs (>1M PSMs) at negligible quality loss. Sampling is reservoir-based, keyed by (scan, exp_mass) so all PSMs sharing a spectrum travel together; the trained model is then applied to ALL input rows via a second scoring pass (matches upstream Caller.cpp behavior). Inert when the input size is at or below the cap. Note: upstream percolator binary defaults this to 0 — PercolatorAdapter preserves the CLI contract by passing its own int option (CLI default 0) through to this param. (default: '100000') (min: '0') -Rescoring:percolator:report_as_main_score Which Percolator output to stamp as the main PeptideHit score after rescoring. 'none' (default) leaves hit.getScore() and the PeptideIdentification score_type untouched — callers who want the original search score preserved (or who run their own post-processing like PercolatorAdapter) rely on this. 'q-value' sets main score to the PSM-level q-value and marks higher_score_better=false. 'pep' sets main score to the PEP and marks higher_score_better=false. 'svm' sets main score to the SVM discriminant and marks higher_score_better=true. All three Percolator outputs remain accessible as percolator_{score,q_value,pep} meta values regardless of this setting. (default: 'none') (valid: 'none', 'q-value', 'pep', 'svm') -Rescoring:percolator:num_threads Number of OpenMP threads for cross-validation (one per CV fold; max useful = 3). Matches upstream's default. (default: '3') (min: '1' max: '3') -Rescoring:percolator:use_pi0 Enable pi0 correction when computing q-values and PEPs (default). When true, pi0 is estimated per CV fold via bootstrap spline fit on the target score distribution using decoys as the null. When false, pi0 is fixed at 1.0 (pure target-decoy FDR, no bootstrap estimation). Affects both Scores::calcQvals and Scores::calcPep. Upstream percolator has no CLI flag for this; the in-library Scores(bool usePi0) constructor is the only toggle, matched here. (default: 'true') (valid: 'true', 'false') Parameters for calibrant iRT peptides for RT normalization and mass / ion mobility correction.: -TargetedDataExtraction:Calibration:tr_irt_priority_sampling Optional custom TSV transition file containing additional priority peptides for auto-iRT sampling. -TargetedDataExtraction:Calibration:rt_norm RT normalization file (if set, linear iRT files may be omitted). TargetedDataExtraction:Calibration:auto_irt: -TargetedDataExtraction:Calibration:auto_irt:enabled Whether to sample iRTs on‐the‐fly (true) from the input targeted transition file (instead of passing specific iRT files). This may be useful if standard iRTs (Biognosys iRT kit) were not spiked-in. If set to false, and no additional iRT files are provided, and no transformation is provided, then no calibration is performed. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Calibration:auto_irt:irt_bins Number of RT bins for linear iRT sampling (default: '100') (min: '1' max: '10000') -TargetedDataExtraction:Calibration:auto_irt:irt_peptides_per_bin Peptides sampled per bin for linear iRT (default: '5') (min: '1') -TargetedDataExtraction:Calibration:auto_irt:irt_seed RNG seed for reproducible sampling (0 = non-deterministic) (default: '5489') (min: '0') -TargetedDataExtraction:Calibration:auto_irt:irt_bins_nonlinear Number of RT bins for nonlinear iRT sampling (default: '2000') (min: '1' max: '10000') -TargetedDataExtraction:Calibration:auto_irt:irt_peptides_per_bin_nonlinear Peptides sampled per bin for nonlinear iRT (0 = skip nonlinear) (default: '50') (min: '0') -TargetedDataExtraction:Calibration:auto_irt:linear_top_fraction Top fraction of intense peptides to sample for linear iRT (default: '0.4') (min: '0.01' max: '1.0') -TargetedDataExtraction:Calibration:auto_irt:nonlinear_top_fraction Top fraction of intense peptides to sample for nonlinear iRT (default: '0.7') (min: '0.01' max: '1.0') -TargetedDataExtraction:Calibration:auto_irt:irt_nonlinear_rt_extraction_window Only extract RT around this value for non linear iRT calibration (set to -1 to use whole range) (default: '600.0') (min: '-1.0') TargetedDataExtraction:Calibration:auto_irt:prefilter: -TargetedDataExtraction:Calibration:auto_irt:prefilter:enabled Enable raw-data evidence prefiltering for sampled iRT peptides. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Calibration:auto_irt:prefilter:evidence_sources Evidence source for iRT prefiltering: use MS2 fragments only (more stringent than hybrid). (default: 'ms2') (valid: 'ms1', 'ms2', 'hybrid') -TargetedDataExtraction:Calibration:auto_irt:prefilter:ms1_top_peaks_per_spectrum Number of most intense MS1 peaks to keep per spectrum before precursor m/z matching. (default: '1000') (min: '1') -TargetedDataExtraction:Calibration:auto_irt:prefilter:ms2_top_peaks_per_spectrum Number of most intense MS2 peaks to keep per spectrum before fragment m/z matching. (default: '1000') (min: '1') -TargetedDataExtraction:Calibration:auto_irt:prefilter:ms2_top_transitions_per_precursor Number of highest library-intensity fragment transitions to index per precursor for MS2 evidence. (default: '6') (min: '1' max: '64') -TargetedDataExtraction:Calibration:auto_irt:prefilter:ms2_min_fragment_hits Minimum fragment hits for iRT prefiltering (higher threshold ensures robust iRT peptides). (default: '6') (min: '1' max: '64') -TargetedDataExtraction:Calibration:auto_irt:prefilter:min_supported_precursors Minimum number of supported precursors required when the prefilter is enabled. (default: '3') (min: '1') TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking: -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:enabled Run PeakPickerHiRes on spectra before top-N matching. This is intended for profile data and is disabled by default. -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:use_gauss Use Gaussian smoothing before PeakPickerHiRes. If false, use Savitzky-Golay smoothing. (default: 'true') (valid: 'true', 'false') TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes: -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:signal_to_noise Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!) (default: '0.0') (min: '0.0') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:spacing_difference_gap The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms. (default: '4.0') (min: '0.0') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:spacing_difference Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms. (default: '1.5') (min: '0.0') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:missing Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms. (default: '1') (min: '0') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:ms_levels List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes. (min: '1') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:report_FWHM Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak. -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:report_FWHM_unit Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms). (default: 'relative') (valid: 'relative', 'absolute') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:allow_missing_flank Allow peaks without flanking data points on both sides. This is useful for TimsTOF data where profile peaks may be missing the leading or trailing edge. TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise: -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:max_intensity Maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N. (default: '-1') (min: '-1') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:auto_max_stdev_factor Parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev (default: '3.0') (min: '0.0' max: '999.0') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:auto_max_percentile Parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile (default: '95') (min: '0' max: '100') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:auto_mode Method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method (default: '0') (min: '-1' max: '1') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:win_len Window length in Thomson (default: '200.0') (min: '1.0') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:bin_count Number of bins for intensity values (default: '30') (min: '3') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:min_required_elements Minimum number of elements required in a window (otherwise it is considered sparse) (default: '10') (min: '1') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:noise_for_empty_window Noise value used for sparse windows (default: '1.0e20') -TargetedDataExtraction:Calibration:auto_irt:prefilter:peak_picking:PeakPickerHiRes:SignalToNoise:write_log_messages Write out log messages in case of sparse windows or median in rightmost histogram bin (default: 'true') (valid: 'true', 'false') TargetedDataExtraction:Calibration:files: -TargetedDataExtraction:Calibration:files:linear_irt_file Path(s) to linear iRT transition file(s) (TraML, TSV, or PQP). Accepts a string of a single file path or multiple file paths (space-separated, 'run1_irt.pqp run2_irt.pqp ... runN_irt.pqp') for run-specific mapping (positional: nth entry -> nth run). -TargetedDataExtraction:Calibration:files:nonlinear_irt_file Path(s) to nonlinear iRT transition file(s) (TraML, TSV, or PQP). Accepts a string of a single file path or multiple file paths (space-separated, 'run1_irt.pqp run2_irt.pqp ... runN_irt.pqp') for run-specific mapping (positional: nth entry -> nth run). Entries may be empty to indicate no nonlinear iRT for that run. TargetedDataExtraction:Calibration:linear: -TargetedDataExtraction:Calibration:linear:outlier_detection Which outlier detection method to use for linear calibration (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none'). Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides). (default: 'iter_residual') (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none') TargetedDataExtraction:Calibration:nonlinear: -TargetedDataExtraction:Calibration:nonlinear:outlier_detection Which outlier detection method to use for nonlinear calibration (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none'). Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides). (default: 'iter_residual') (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none') TargetedDataExtraction:Calibration:windows: -TargetedDataExtraction:Calibration:windows:estimate_rt Estimate RT extraction windows from calibration (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Calibration:windows:estimate_mz Estimate m/z extraction windows from calibration (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Calibration:windows:estimate_im Estimate ion mobility extraction windows from calibration (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Calibration:windows:rt_percentile Percentile for RT window estimation (25.0-99.9) (default: '95.0') (min: '25.0' max: '99.900000000000006') -TargetedDataExtraction:Calibration:windows:rt_estimation_padding_factor A padding factor to multiply the estimated RT window by. For example, a factor of 1.3 will add a 30% padding to the estimated RT window, so if the estimated RT window is 144, then 43 will be added for a total estimated RT window of 187 seconds. A factor of 1.0 will not add any padding to the estimated window. (default: '1.3') (min: '1.0') -TargetedDataExtraction:Calibration:windows:min_rt_window Minimum RT extraction window in seconds to apply after RT-window estimation in OpenDIA. This guards against overconfident auto-estimated RT windows on broad or sparse-gradient data; set to 0 to disable the floor. (default: '30.0') (min: '0.0') -TargetedDataExtraction:Calibration:windows:max_rt_window Maximum RT extraction window in seconds to apply after RT-window estimation. Set to 0 to disable the ceiling and use the raw estimated RT window. (default: '600.0') (min: '0.0') TargetedDataExtraction:Calibration:qc: -TargetedDataExtraction:Calibration:qc:min_rsq Minimum R-squared required for RT peptides regression (default: '0.95') (min: '0.0' max: '1.0') -TargetedDataExtraction:Calibration:qc:min_coverage Minimum relative amount of RT peptides to keep (default: '0.6') (min: '0.0' max: '1.0') m/z and ion mobility calibration.: -TargetedDataExtraction:Calibration:MassIMCorrection:mz_extraction_window M/z extraction window width (default: '-1.0') -TargetedDataExtraction:Calibration:MassIMCorrection:mz_extraction_window_ppm Whether m/z extraction is in ppm -TargetedDataExtraction:Calibration:MassIMCorrection:ms1_im_calibration Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration) -TargetedDataExtraction:Calibration:MassIMCorrection:im_extraction_window Ion mobility extraction window width (default: '-1.0') -TargetedDataExtraction:Calibration:MassIMCorrection:mz_estimation_padding_factor A padding factor to multiply the estimated m/z window by. For example, a factor of 1.3 will add a 30% padding to the estimated m/z window, so if the estimated m/z window is 18, then 5.4 will be added for a total estimated m/z window of 23.4. A factor of 1.0 will not add any padding to the estimated window. (default: '1.3') (min: '1.0') -TargetedDataExtraction:Calibration:MassIMCorrection:im_estimation_padding_factor A padding factor to multiply the estimated ion_mobility window by. For example, a factor of 1.3 will add a 30% padding to the estimated ion_mobility window, so if the estimated ion_mobility window is 0.03, then 0.009 will be added for a total estimated ion_mobility window of 0.039. A factor of 1.0 will not add any padding to the estimated window. (default: '1.3') (min: '1.0') -TargetedDataExtraction:Calibration:MassIMCorrection:mz_estimation_percentile Percentile for m/z window estimation (25.0-99.9) (default: '99.0') (min: '25.0' max: '99.900000000000006') -TargetedDataExtraction:Calibration:MassIMCorrection:im_estimation_percentile Percentile for ion mobility window estimation (25.0-99.9) (default: '99.0') (min: '25.0' max: '99.900000000000006') -TargetedDataExtraction:Calibration:MassIMCorrection:mz_correction_function Type of normalization function for m/z calibration. (default: 'quadratic_regression_delta_ppm') (valid: 'none', 'regression_delta_ppm', 'unweighted_regression', 'weighted_regression', 'quadratic_regression', 'weighted_quadratic_regression', 'weighted_quadratic_regression_delta_ppm', 'quadratic_regression_delta_ppm') -TargetedDataExtraction:Calibration:MassIMCorrection:im_correction_function Type of normalization function for IM calibration. (default: 'linear') (valid: 'none', 'linear') -TargetedDataExtraction:Calibration:MassIMCorrection:debug_im_file Debug file for Ion Mobility calibration. -TargetedDataExtraction:Calibration:MassIMCorrection:debug_mz_file Debug file for m/z calibration. RT normalization model and outlier handling.: -TargetedDataExtraction:Calibration:RTNormalization:alignmentMethod How to perform the RT alignment. (default: 'linear') (valid: 'linear', 'interpolated', 'lowess', 'b_spline') -TargetedDataExtraction:Calibration:RTNormalization:useIterativeChauvenet Use Chauvenet's criterion in iterative outlier removal. -TargetedDataExtraction:Calibration:RTNormalization:RANSACMaxIterations Maximum iterations for RANSAC outlier detection. (default: '1000') -TargetedDataExtraction:Calibration:RTNormalization:RANSACMaxPercentRTThreshold Maximum RT threshold in percent of the total gradient for RANSAC. (default: '3') -TargetedDataExtraction:Calibration:RTNormalization:RANSACSamplingSize Sampling size per RANSAC iteration. (default: '10') -TargetedDataExtraction:Calibration:RTNormalization:estimateBestPeptides Whether to choose the best peptides based on peak shape for RT normalization. -TargetedDataExtraction:Calibration:RTNormalization:InitialQualityCutoff Initial overall quality cutoff for a peak to be scored. (default: '0.5') -TargetedDataExtraction:Calibration:RTNormalization:OverallQualityCutoff Overall quality cutoff for a peak to enter RT estimation. (default: '5.5') -TargetedDataExtraction:Calibration:RTNormalization:NrRTBins Number of RT bins to use to compute coverage. (default: '10') -TargetedDataExtraction:Calibration:RTNormalization:MinPeptidesPerBin Minimal number of peptides required for a bin to be counted as covered. (default: '1') -TargetedDataExtraction:Calibration:RTNormalization:MinBinsFilled Minimal number of bins required to be covered. (default: '8') TargetedDataExtraction:Calibration:RTNormalization:lowess: -TargetedDataExtraction:Calibration:RTNormalization:lowess:auto_span Automatically select LOWESS span by cross-validation. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Calibration:RTNormalization:lowess:span Span parameter for lowess. (default: '0.05') (min: '0.0' max: '1.0') -TargetedDataExtraction:Calibration:RTNormalization:lowess:auto_span_min Lower bound for auto-selected LOWESS span. (default: '0.15') (min: '1.0e-03') -TargetedDataExtraction:Calibration:RTNormalization:lowess:auto_span_max Upper bound for auto-selected LOWESS span. (default: '0.8') (max: '0.99') -TargetedDataExtraction:Calibration:RTNormalization:lowess:auto_span_grid Optional explicit grid of LOWESS span candidates. (default: '0.005,0.01,0.05,0.15,0.25,0.30,0.50,0.70,0.90') TargetedDataExtraction:Calibration:RTNormalization:b_spline: -TargetedDataExtraction:Calibration:RTNormalization:b_spline:num_nodes Number of nodes for b spline. (default: '5') (min: '0') Transition-library reader parameters section.: -TargetedDataExtraction:Library:retentionTimeInterpretation How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds) (default: 'iRT') (valid: 'iRT', 'seconds', 'minutes') -TargetedDataExtraction:Library:override_group_label_check Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing. -TargetedDataExtraction:Library:force_invalid_mods Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification) Parameters for mapping chromatograms to transitions in SRM/MRM data.: -TargetedDataExtraction:MRMMapping:precursor_tolerance Precursor tolerance when mapping (in Th). (default: '0.9') -TargetedDataExtraction:MRMMapping:product_tolerance Product tolerance when mapping (in Th). (default: '1.2') -TargetedDataExtraction:MRMMapping:irt_precursor_tolerance Precursor tolerance when mapping iRT transitions (in Th). (default: '1.5') -TargetedDataExtraction:MRMMapping:irt_product_tolerance Product tolerance when mapping iRT transitions (in Th). (default: '1.5') -TargetedDataExtraction:MRMMapping:map_multiple_assays Allow mapping multiple assays to chromatograms and duplicate the chromatograms in the output. -TargetedDataExtraction:MRMMapping:error_on_unmapped Treat remaining unmapped chromatograms as an error. Scoring parameters section.: -TargetedDataExtraction:Scoring:stop_report_after_feature Stop reporting after feature (ordered by quality; -1 means do not stop). (default: '5') -TargetedDataExtraction:Scoring:rt_normalization_factor The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100) (default: '100.0') -TargetedDataExtraction:Scoring:quantification_cutoff Cutoff in m/z below which peaks should not be used for quantification any more (default: '0.0') (min: '0.0') -TargetedDataExtraction:Scoring:write_convex_hull Whether to write out all points of all features into the featureXML -TargetedDataExtraction:Scoring:spectrum_addition_method For spectrum addition, either use simple concatenation or use peak resampling (default: 'simple') (valid: 'simple', 'resample') -TargetedDataExtraction:Scoring:spectrum_merge_method_type For spectrum addition, either use a fixed number of spectra or dynamically select the number of spectra to add around the peak apex based on the merge_spectra_by_peak_width_fraction. (default: 'fixed') (valid: 'fixed', 'dynamic') -TargetedDataExtraction:Scoring:add_up_spectra Add up spectra on the left and right around the retention time peak apex. (default: '1') (min: '1') -TargetedDataExtraction:Scoring:spacing_for_spectra_resampling If spectra are to be added, use this spacing to add them up (default: '5.0e-03') (min: '0.0') -TargetedDataExtraction:Scoring:merge_spectra_by_peak_width_fraction If spectra are to be added based on the peak width of peak, construct number of spectra to be added based on N percent of number of points of peak width. (default: '0.15') (min: '1.0e-04' max: '1.0') -TargetedDataExtraction:Scoring:uis_threshold_sn S/N threshold to consider identification transition (set to -1 to consider all) (default: '-1') -TargetedDataExtraction:Scoring:uis_threshold_peak_area Peak area threshold to consider identification transition (set to -1 to consider all) (default: '0') -TargetedDataExtraction:Scoring:scoring_model Scoring model to use (default: 'default') (valid: 'default', 'single_transition') -TargetedDataExtraction:Scoring:im_extra_drift Extra drift time to extract for IM scoring (as a fraction, e.g. 0.25 means 25% extra on each side) (default: '0.0') (min: '0.0') -TargetedDataExtraction:Scoring:strict Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:use_ms1_ion_mobility Performs ion mobility extraction in MS1. Set to false if MS1 spectra do not contain ion mobility (default: 'true') -TargetedDataExtraction:Scoring:apply_im_peak_picking Perform peak picking on the extracted ion mobilograms. This is useful for reducing intefering signals from co-eluting analytes in the ion mobility dimension. The peak picking will take the highest peak and discard the remaining peaks for ion mobility scoring. -TargetedDataExtraction:Scoring:enzyme Enzyme used for counting missed cleavages in peptide sequences (default: 'Trypsin') (valid: 'Arg-C/P', 'Asp-N', 'Asp-N/B', 'Asp-N_ambic', 'Chymotrypsin', 'Clostripain/P', 'elastase-trypsin-chymotrypsin', 'no cleavage', 'unspecific cleavage', 'Trypsin', 'Arg-C', 'Chymotrypsin/P', 'CNBr', 'Formic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA', 'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'leukocyte elastase', 'proline endopeptidase', 'glutamyl endopeptidase', 'Alpha-lytic protease', '2-iodobenzoate', 'iodosobenzoate', 'staphylococcal protease/D', 'proline-endopeptidase/HKR', 'Glu-C+P', 'PepsinA + P', 'cyanogen-bromide') -TargetedDataExtraction:Scoring:mz_extraction_window M/z extraction window (full width) to be used for matching/extraction. If -1, defaults in workflow will be used. (default: '-1.0') -TargetedDataExtraction:Scoring:mz_extraction_window_unit Unit for mz_extraction_window: 'Th' or 'ppm' (default: 'Th') (valid: 'Th', 'ppm') -TargetedDataExtraction:Scoring:mz_extraction_window_ms1 M/z extraction window for MS1 (full width). If -1, defaults in workflow will be used. (default: '-1.0') -TargetedDataExtraction:Scoring:mz_extraction_window_ms1_unit Unit for mz_extraction_window_ms1: 'Th' or 'ppm' (default: 'Th') (valid: 'Th', 'ppm') -TargetedDataExtraction:Scoring:irt_mz_extraction_window M/z extraction window (full width) to be used specifically for iRT matching/extraction. If -1, defaults in workflow will be used. (default: '-1.0') -TargetedDataExtraction:Scoring:irt_mz_extraction_window_unit Unit for irt_mz_extraction_window: 'Th' or 'ppm' (default: 'Th') (valid: 'Th', 'ppm') TargetedDataExtraction:Scoring:TransitionGroupPicker: -TargetedDataExtraction:Scoring:TransitionGroupPicker:stop_after_feature Stop finding after feature (ordered by intensity; -1 means do not stop). (default: '-1') -TargetedDataExtraction:Scoring:TransitionGroupPicker:min_peak_width Minimal peak width (s), discard all peaks below this value (-1 means no action). (default: '-1.0') -TargetedDataExtraction:Scoring:TransitionGroupPicker:peak_integration Calculate the peak area and height either the smoothed or the raw chromatogram data. (default: 'original') (valid: 'original', 'smoothed') -TargetedDataExtraction:Scoring:TransitionGroupPicker:background_subtraction Remove background from peak signal using estimated noise levels. The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation. (default: 'none') (valid: 'none', 'original', 'exact') -TargetedDataExtraction:Scoring:TransitionGroupPicker:recalculate_peaks Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if the variation within the picked peaks is too large. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:TransitionGroupPicker:use_precursors Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking) -TargetedDataExtraction:Scoring:TransitionGroupPicker:use_consensus Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition) (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:TransitionGroupPicker:recalculate_peaks_max_z Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0). (default: '0.75') -TargetedDataExtraction:Scoring:TransitionGroupPicker:minimal_quality Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold (default: '-1.5') -TargetedDataExtraction:Scoring:TransitionGroupPicker:resample_boundary For computing peak quality, how many extra seconds should be sample left and right of the actual peak (default: '15.0') -TargetedDataExtraction:Scoring:TransitionGroupPicker:compute_peak_quality Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad. -TargetedDataExtraction:Scoring:TransitionGroupPicker:compute_peak_shape_metrics Calculates various peak shape metrics (e.g., tailing) that can be used for downstream QC/QA. -TargetedDataExtraction:Scoring:TransitionGroupPicker:compute_total_mi Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring. -TargetedDataExtraction:Scoring:TransitionGroupPicker:boundary_selection_method Method to use when selecting the best boundaries for peaks. (default: 'largest') (valid: 'largest', 'widest') TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram: -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added. (default: '11') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:sgolay_polynomial_order Order of the polynomial that is fitted. (default: '3') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:gauss_width Gaussian width in seconds, estimated peak size. (default: '30.0') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:use_gauss Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter) (default: 'false') (valid: 'false', 'true') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:peak_width Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off. (default: '-1.0') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:signal_to_noise Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured. (default: '0.1') (min: '0.0') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:write_sn_log_messages Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:report_sn Also report the apex signal-to-noise ratio for each picked peak (as an additional 'SN' FloatDataArray on the picked chromatogram). Forces initialization of the S/N estimator even if 'signal_to_noise' is 0. -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:remove_overlapping_peaks Try to remove overlapping peaks during peak picking (default: 'true') (valid: 'false', 'true') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakPickerChromatogram:method Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram). (default: 'corrected') (valid: 'legacy', 'corrected', 'crawdad') TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakIntegrator: -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakIntegrator:integration_type The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration. (default: 'intensity_sum') (valid: 'intensity_sum', 'simpson', 'trapezoid') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type The baseline type to use in estimateBackground() based on the peak boundaries. A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base). (default: 'base_to_base') (valid: 'base_to_base', 'vertical_division', 'vertical_division_min', 'vertical_division_max') -TargetedDataExtraction:Scoring:TransitionGroupPicker:PeakIntegrator:fit_EMG Fit the chromatogram/spectrum to the EMG peak model. (default: 'false') (valid: 'false', 'true') TargetedDataExtraction:Scoring:DIAScoring: -TargetedDataExtraction:Scoring:DIAScoring:dia_extraction_window DIA extraction window in Th or ppm. (default: '0.05') (min: '0.0') -TargetedDataExtraction:Scoring:DIAScoring:dia_extraction_unit DIA extraction window unit (default: 'Th') (valid: 'Th', 'ppm') -TargetedDataExtraction:Scoring:DIAScoring:dia_centroided Use centroided DIA data. -TargetedDataExtraction:Scoring:DIAScoring:dia_byseries_intensity_min DIA b/y series minimum intensity to consider. (default: '300.0') (min: '0.0') -TargetedDataExtraction:Scoring:DIAScoring:dia_byseries_ppm_diff DIA b/y series minimal difference in ppm to consider. (default: '10.0') (min: '0.0') -TargetedDataExtraction:Scoring:DIAScoring:dia_nr_isotopes DIA number of isotopes to consider. (default: '4') (min: '0') -TargetedDataExtraction:Scoring:DIAScoring:dia_nr_charges DIA number of charges to consider. (default: '4') (min: '0') -TargetedDataExtraction:Scoring:DIAScoring:peak_before_mono_max_ppm_diff DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic. (default: '20.0') (min: '0.0') TargetedDataExtraction:Scoring:EMGScoring: -TargetedDataExtraction:Scoring:EMGScoring:max_iteration Maximum number of iterations using by Levenberg-Marquardt algorithm. (default: '10') -TargetedDataExtraction:Scoring:EMGScoring:init_mom Initialize parameters using method of moments estimators. TargetedDataExtraction:Scoring:Scores: -TargetedDataExtraction:Scoring:Scores:use_shape_score Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation) (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_coelution_score Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation) (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_rt_score Use the retention time score (this score measure the difference in retention time) (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_library_score Use the library score (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_intensity_score Use the intensity score (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_nr_peaks_score Use the number of peaks score (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_total_xic_score Use the total XIC score (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_total_mi_score Use the total MI score -TargetedDataExtraction:Scoring:Scores:use_sn_score Use the SN (signal to noise) score (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_mi_score Use the MI (mutual information) score (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_dia_scores Use the DIA (SWATH) scores. If turned off, will not use fragment ion spectra for scoring. (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_ms1_correlation Use the correlation scores with the MS1 elution profiles -TargetedDataExtraction:Scoring:Scores:use_ion_mobility_scores Use the scores for Ion Mobility scans (default: 'auto') (valid: 'true', 'false', 'auto') -TargetedDataExtraction:Scoring:Scores:use_ms1_fullscan Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern) -TargetedDataExtraction:Scoring:Scores:use_ms1_mi Use the MS1 MI score (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_uis_scores Use UIS scores for peptidoform identification -TargetedDataExtraction:Scoring:Scores:use_peak_shape_metrics Use peak shape metrics for scoring (default: 'false') -TargetedDataExtraction:Scoring:Scores:use_ionseries_scores Use MS2-level b/y ion-series scores for peptidoform identification (default: 'true') (valid: 'true', 'false') -TargetedDataExtraction:Scoring:Scores:use_ms2_isotope_scores Use MS2-level isotope scores (pearson & manhattan) across product transitions (based on ID if annotated or averagine) (default: 'true') (valid: 'true', 'false')