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OpenMS
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Matches tandem mass spectra to nucleic acid sequences.
Given a FASTA file containing RNA sequences (and optionally decoys) and an mzML file from a nucleic acid mass spec experiment:
Output is in the form of an mzTab-like text file containing the search results. Optionally, an idXML file suitable for visualizing search results in TOPPView (parameter id_out) and a "target coordinates" file for label-free quantification using FeatureFinderMetaboIdent (parameter lfq_out) can be generated.
Modified ribonucleotides can either be specified in the FASTA input file if they are expected at a specific site. As globally replacing the unmodified base (as fixed modifications), or set as variable modifications in the tool options. Information on available modifications is taken from the Modomics database (http://modomics.genesilico.pl/). In addition to these "standard" modifications, OpenMS defines "generic" and "ambiguous" ones:
A generic modification represents a group of modifications that cannot be distinguished by tandem mass spectrometry. For example, "mA" stands for any methyladenosine (could be "m1A", "m2A", "m6A" or "m8A"), "mmA" for any dimethyladenosine (with two methyl groups on the base), and "mAm" for any 2'-O-dimethyladenosine (with one methyl group each on base and ribose). There is no technical difference between searching for "mA" or e.g. "m1A", but the generic code better represents that no statement can be made about the position of the methyl group on the base.
In contrast, an ambiguous modification represents two isobaric modifications (or modification groups) with a methyl group on either the base or the ribose, that could in principle be distinguished based on a-B ions. For example, "mA?" stands for methyladenosine ("mA", see above) or 2'-O-methyladenosine ("Am"). When using ambiguous modifications in a search, NucleicAcidSearchEngine can optionally try to assign the alternative that generates better a-B ion matches in a spectrum (see parameter modifications:resolve_ambiguities).
Exact score ties at report:top_hits remain a complete group. Exported ties use the library's deterministic molecule, charge and adduct value order. A representative selected downstream is reproducible but does not establish unique modification localization. When using digest, search tolerances and modifications in the output describe the current run while database and digestion provenance remain from the cache. LFQ targets use a finite intensity-weighted retention time, falling back to the median of finite observations when no valid positive intensity weights exist.
The command line parameters of this tool are:
NucleicAcidSearchEngine -- Annotate nucleic acid identifications to MS/MS spectra.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_NucleicAcidSearchEngine.html
Version: 3.7.0-pre-nightly-2026-11-08 Nov 9 2026, 01:20:48, Revision: a335fa6
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:
NucleicAcidSearchEngine <options>
Options (mandatory options marked with '*'):
-in <file>* Input file: spectra (valid formats: 'mzML', 'd', 'raw')
-database <file> Input file: sequence database. Required unless 'digest' is
set. (valid formats: 'fasta', 'fa', 'faa')
-digest <file> Input file: pre-digested sequence database. Can be used instea
d of 'database'. Sets all 'oligo:...' parameters. (valid forma
ts: 'oms')
-out <file>* Output file: mzTab (valid formats: 'mzTab')
-id_out <file> Output file: idXML (for visualization in TOPPView) (valid form
ats: 'idXML')
-db_out <file> Output file: oms (SQLite database) (valid formats: 'oms')
-digest_out <file> Output file: sequence database digest. Ignored if 'digest'
input is used. (valid formats: 'oms')
-lfq_out <file> Output file: targets for label-free quantification using Featu
reFinderMetaboIdent ('id' input) (valid formats: 'tsv')
-bedrmod_out <file> Output file: bedRMod v2 RNA modification track (valid formats:
'bedrmod')
Reference metadata for bedRMod export:
-bedrmod:organism <value> Explicit reference organism for bedRMod export (NA when unknow
n) (default: 'NA')
-bedrmod:assembly <value> Explicit reference assembly for bedRMod export (NA when unknow
n) (default: 'NA')
-bedrmod:annotation_source <value> Explicit reference annotation_source for bedRMod export (NA
when unknown) (default: 'NA')
-bedrmod:annotation_version <value> Explicit reference annotation_version for bedRMod export (NA
when unknown) (default: 'NA')
Precursor (parent ion) options:
-precursor:mass_tolerance <tolerance> Precursor mass tolerance (+/- around uncharged precursor mass)
(default: '10.0')
-precursor:mass_tolerance_unit <unit> Unit of precursor mass tolerance (default: 'ppm') (valid: 'Da'
, 'ppm')
-precursor:min_charge <num> Minimum precursor charge to be considered (default: '-1')
-precursor:max_charge <num> Maximum precursor charge to be considered (default: '-20')
-precursor:include_unknown_charge Include MS2 spectra with unknown precursor charge - try to
match them in any possible charge between 'min_charge' and
'max_charge', at the risk of a higher error rate
-precursor:use_avg_mass Use average instead of monoisotopic precursor masses (appropri
ate for low-resolution instruments)
-precursor:use_adducts Consider possible salt adducts (see 'precursor:potential_adduc
ts') when matching precursor masses
-precursor:potential_adducts <list> Adducts considered to explain mass differences. Format: 'Eleme
nt:Charge(+/-)', i.e. the number of '+' or '-' indicates the
charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use
_adducts' is set. (default: '[Na:+]')
-precursor:isotopes <list> Correct for mono-isotopic peak misassignments. E.g.: 1 = precu
rsor may be misassigned to the first isotopic peak. Ignored
if 'use_avg_mass' is set. (default: '[0 1 2 3 4]')
-precursor:correct_with_flash Infer MS2 monoisotopic precursor m/z using precursor-directed
FLASH RNA on the complete parent MS1. Confident corrected or
monoisotopic scans search only additional isotope offset 0
around the corrected m/z. The configured 'precursor:isotopes'
list is used only for unresolved or ambiguous scans. Requires
monoisotopic masses and ppm precursor tolerance.
Fragment (Product Ion) Options:
-fragment:mass_tolerance <tolerance> Fragment mass tolerance (+/- around fragment m/z) (default:
'10.0')
-fragment:mass_tolerance_unit <unit> Unit of fragment mass tolerance (default: 'ppm') (valid: 'Da',
'ppm')
-fragment:ions <choice> Fragment ions to include in theoretical spectra (default: '[a-
B a b c d w x y z]') (valid: 'a-B', 'a', 'b', 'c', 'd', 'w',
'x', 'y', 'z')
Spectrum preprocessing options:
-preprocessing:remove_precursor_peak Remove the precursor peak (and isotopic peaks) from the MS2
spectrum
Scoring Options:
-scoring:method <method> Scoring method to use for spectrum matching (default: 'hypersc
ore') (valid: 'hyperscore', 'mvh')
Modification options:
-modifications:fixed <mods> Fixed modifications, specified using modomics (https://genesil
ico.pl/modomics/modifications) terms. (valid: 'io6A', 's2U',
'k2C', 'm2Gm', 'Ym', 'f5Cm', 'Qbase', 'ac4Cm', 'imG-14', 'cm5s
2U', 'mnm5s2U', 'm227G', 'yW-58', 'I', 'g6A', 'nm5U', 'm7G',
's2Um', 'Y', 'hm5C', 'm5U', 'preQ0', 'o2yW', 'm5Um', 'preQ1',
'm66Am', 'ac6A', 'ms2io6A', 'Am', 'Im', 'mnm5U', 'm22G', 't6A'
, 'm8A', 'm7GpppN', 'm27GpppN', 'm227GpppN', 'mpppN', 'm28A',
'acp3D', 'acp3Y', 'imG', 'D', 'N', 'C+', 'm27Gm', 'ho5C', 'inm
5U', 'inm5Um', 'inm5s2U', 'pppN', 'GpppN', 'CoApN', 'm44C',
...
'dG*', 'dU*', 'dT*')
-modifications:variable <mods> Variable modifications (valid: 'io6A', 's2U', 'k2C', 'm2Gm',
'Ym', 'f5Cm', 'Qbase', 'ac4Cm', 'imG-14', 'cm5s2U', 'mnm5s2U',
'm227G', 'yW-58', 'I', 'g6A', 'nm5U', 'm7G', 's2Um', 'Y',
'hm5C', 'm5U', 'preQ0', 'o2yW', 'm5Um', 'preQ1', 'm66Am', 'ac6
A', 'ms2io6A', 'Am', 'Im', 'mnm5U', 'm22G', 't6A', 'm8A', 'm7G
pppN', 'm27GpppN', 'm227GpppN', 'mpppN', 'm28A', 'acp3D', 'acp
3Y', 'imG', 'D', 'N', 'C+', 'm27Gm', 'ho5C', 'inm5U', 'inm5Um'
, 'inm5s2U', 'pppN', 'GpppN', 'CoApN', 'm44C', 'acCoApN', 'mal
...
, 'dT*')
-modifications:variable_max_per_oligo <num> Maximum number of residues carrying a variable modification
per candidate oligonucleotide (default: '2')
-modifications:resolve_ambiguities Attempt to resolve ambiguous modifications (e.g. 'mA?' for
'mA'/'Am') based on a-B ions.
This incurs a performance cost because two modifications have
to be considered for each case.
Requires a-B ions to be enabled in parameter 'fragment:ions'.
Oligonucleotide (digestion) options (ignored if 'digest' input is used):
-oligo:min_size <num> Minimum size an oligonucleotide must have after digestion to
be considered in the search (default: '5')
-oligo:max_size <num> Maximum size an oligonucleotide must have after digestion to
be considered in the search, leave at 0 for no limit (default:
'0')
-oligo:missed_cleavages <num> Number of missed cleavages (default: '1')
-oligo:enzyme <choice> The enzyme used for RNA digestion (default: 'no cleavage')
(valid: 'RNase_T1', 'RNase_A', 'colicin_E5', 'RNase_MC1', 'RNa
se_T1_Phosphatase', 'RNase_H', 'RNase_4', 'RNase_4p', 'RNase_U
2', 'cusativin', 'RNase_4c', 'mazF', 'unspecific cleavage',
'no cleavage')
Reporting Options:
-report:precursor_percentage Report the strongest peak in the configured precursor m/z wind
ow as a percentage of the raw MS2 base peak intensity. Uses
its independent report tolerance; wide windows can include
isotope peaks. This does not integrate an isotope envelope or
measure preprocessing removal, and is omitted unless there is
exactly one precursor.
False Discovery Rate options:
-fdr:decoy_pattern <string> Std::string used as part of the accession to annotate decoy
sequences (e.g. 'DECOY_'). Leave empty to skip the FDR/q-value
calculation.
-fdr:cutoff <value> Cut-off for FDR filtering; search hits with higher q-values
will be removed (default: '1.0') (min: '0.0' max: '1.0')
-fdr:remove_decoys Do not score hits to decoy sequences and remove them when filt
ering
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:
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:
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.
1.9.8