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OpenMS
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Performs proteinSIP on peptide features for elemental flux analysis.
MetaProSIP detects and quantifies stable isotope incorporation in peptides from protein-SIP experiments. It takes centroided mzML data, featureXML with identifications (from IDMapper), and a protein FASTA database as input and produces incorporation reports as tab-separated CSV files.
Relative isotope abundances (RIA) are calculated on the peptide level and then transferred to the protein level using the median of all peptide RIAs. Protein-level RIAs are further summarized at the group level (also as medians). Groups cluster proteins with similar incorporation behavior.
The group-centric report is organized hierarchically with three levels:
Group level (one row per group):
| Column | Description |
|---|---|
| Group N | Group identifier (1-based) |
| # Distinct Peptides | Number of distinct peptide sequences in the group |
| # Unambiguous Proteins | Number of proteins identified by unique peptides only |
| Median Global LR | Median labeling ratio across all peptides in the group |
| median RIA 1, 2, ... | Median relative isotope abundance for each incorporation level |
Protein level (one row per protein within a group):
| Column | Description |
|---|---|
| Protein Accession | Protein identifier from the FASTA database |
| Description | Protein description from the FASTA header |
| # Unique Peptides | Number of peptides unique to this protein (not shared with other proteins) |
| Median Global LR | Median labeling ratio across all peptides of this protein |
| median RIA 1, 2, ... | Median relative isotope abundance for each incorporation level |
Unique peptide level (one row per peptide within a protein):
| Column | Description |
|---|---|
| Peptide Sequence | Amino acid sequence |
| RT | Retention time of the feature apex (minutes) |
| Exp. m/z | Experimentally observed m/z |
| Theo. m/z | Theoretical m/z computed from the sequence and charge |
| Charge | Charge state |
| Score | Identification score (e.g., search engine score or q-value) |
| TIC fraction | Fraction of the MS1 TIC explained by the isotope pattern decomposition |
| #non-natural weights | Number of non-zero decomposition coefficients beyond the natural isotope pattern |
| RIA N | Relative isotope abundance (%) for the Nth incorporation level |
| INT N | Intensity (abundance) for the Nth incorporation level |
| Cor. N | Correlation between observed and theoretical isotope pattern for the Nth level |
| Peak intensities | Space-separated list of isotopic peak intensities across the mass range |
| Global LR | Labeling ratio: fraction of total ion current in higher (non-natural) labeling states |
Non-unique peptides are listed separately at the end (not grouped by incorporation) with additional columns:
| Column | Description |
|---|---|
| Accessions | Comma-separated list of all protein accessions this peptide maps to |
| Descriptions | Comma-separated protein descriptions |
The remaining columns (Peptide Sequence, Score, RT, Exp. m/z, Theo. m/z, Charge, #non-natural weights, RIA/INT/Cor., Peak intensities, Global LR) are the same as for unique peptides.
The peptide-centric report lists one row per peptide (PSM) with the following columns:
| Column | Description |
|---|---|
| Peptide Sequence | Amino acid sequence |
| Feature | Feature type: "feature" (identified from feature), "id" (identified from ID), or "unidentified" |
| Quality Report Spectrum | File path to the spectrum quality report plot (if quality report output is enabled) |
| Quality report scores | File path to the scores quality report plot |
| Sample Name | Name of the input mzML file |
| Protein Accessions | Comma-separated protein accessions |
| Description | Comma-separated protein descriptions from the FASTA header |
| Unique | Whether the peptide maps to a single protein (true/false) |
| #Ambiguity members | Number of proteins this peptide maps to |
| Score | Identification score |
| RT | Retention time of the feature apex (minutes) |
| Exp. m/z | Experimentally observed m/z |
| Theo. m/z | Theoretical m/z (for unidentified features this equals the precursor m/z) |
| Charge | Charge state |
| TIC fraction | Fraction of MS1 TIC explained by the decomposition |
| #non-natural weights | Number of non-zero decomposition coefficients beyond the natural pattern |
| Peak intensities | Space-separated list of isotopic peak intensities |
| Group | Group/cluster index assigned by incorporation-based clustering |
| Global Peptide LR | Global labeling ratio for this peptide |
| RIA N | Relative isotope abundance (%) for incorporation level N (columns for up to 10 levels) |
| LR of RIA N | Labeling ratio corresponding to RIA N |
| INT N | Intensity for incorporation level N |
| Cor. N | Correlation coefficient for incorporation level N |
-in_fasta does not contain the identified accessions.The command line parameters of this tool are:
MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MetaProSIP.html
Version: 3.6.0-pre-nightly-2026-01-31 Jan 31 2026, 01:46:01, Revision: d8ac3d6
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:
MetaProSIP <options>
Options (mandatory options marked with '*'):
-in_mzML <file>* Centroided MS1 data (valid formats: 'mzML')
-in_fasta <file>* Protein sequence database (valid formats: 'fasta')
-out_csv <file>* Tab-separated, group-centric report of SIP incorporation results. Organiz
ed hierarchically by groups, proteins, and peptides. Columns for unique
peptides: Peptide Sequence, RT (min), Exp. m/z, Theo. m/z, Charge, Score,
TIC fraction, #non-natural weights, then for each incorporation: RIA
(relative isotope abundance, %), INT (intensity), Cor. (correlation),
followed by Peak intensities and Global LR (labeling ratio). Non-unique
peptides additionally list protein Accessions and Descriptions. Group
and protein summary rows report median Global LR and median RIA values.
(valid formats: 'csv')
-out_peptide_centric_csv <file>* Tab-separated, peptide-centric report of SIP incorporation results. Colum
ns: Peptide Sequence, Feature, Quality Report Spectrum (path), Quality
report scores (path), Sample Name, Protein Accessions, Description, Uniqu
e (bool), #Ambiguity members, Score, RT (min), Exp. m/z, Theo. m/z, Charg
e, TIC fraction, #non-natural weights, Peak intensities, Group, Global
Peptide LR (labeling ratio), then for each incorporation (up to 10): RIA
(%), LR of RIA, INT (intensity), Cor. (correlation). (valid formats: 'csv
')
-in_featureXML <file>* Feature data annotated with identifications (IDMapper) (valid formats:
'featureXML')
-r_executable <executable> The R executable. Provide a full or relative path, or make sure it can
be found in your PATH environment.
-labeling_element <parameter> Which element (single letter code) is labeled. (default: 'C') (valid:
'C', 'N', 'H', 'O')
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 (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:
1.9.8