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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-2026-03-12 Mar 13 2026, 01:45:58, Revision: 88f2819
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:
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