Index of all local module documentation for the nf-core/msproteomics pipeline.
Each page is named after the module directory under modules/local (the process name is the upper-cased name).
| Module | Description |
|---|---|
| checkcentroid | FragPipe's centroid check of the first LC-MS file before the search |
| tdf2mzml | Convert Bruker .d (TDF) files to mzML format |
| diatracer | diaTracer: Bruker diaPASEF .d files to mzML for DIA analysis |
| diaumpire | Generate pseudo-spectra from DIA mass spectrometry data |
| decompress | Decompress .gz/.tar/.tar.gz/.zip inputs to .mzML, .raw or Bruker .d |
| mzmlindexing | Index mzML files using OpenMS FileConverter for efficient random access |
| openmspeakpicker | Centroid peak picking using OpenMS PeakPickerHiRes |
| Module | Description |
|---|---|
| checkdbconfig | Check the database decoys the way FragPipe headless does |
| philosopherdatabase | FragPipe database update (decoys + contaminants), only with --add_philosopher_decoy / --add_philosopher_contaminants |
| splitfasta | Split a FASTA database into chunks for parallel MSFragger search |
| sortfasta | Sort the proteins of a FASTA file for the calibration search of a split-database run |
| Module | Description |
|---|---|
| msfragger | Ultrafast peptide identification using MSFragger database search engine |
| msfraggercalibrate | Mass calibration and parameter optimization for split-database search |
| msfraggerapplycalibration | Apply MSFragger's calibration output to the search params and spectra of a split-database search |
| mergesplitsearch | Merge MSFragger split-database search results per sample |
| crystalc | Remove chimeric artifact PSMs from pepXML search results |
| Module | Description |
|---|---|
| msbooster | Deep learning-based PSM rescoring using predicted retention time and spectra |
| percolator | Semi-supervised PSM validation and FDR control using Percolator |
| philosopherpeptideprophet | Statistical validation of peptide assignments using PeptideProphet |
| ptmprophet | PTM site localization using PTMProphet |
| Module | Description |
|---|---|
| philosopheriprophet | Philosopher iProphet over all validated pepXMLs |
| philosopherproteinprophet | Statistical protein inference using ProteinProphet |
| philosopherfilter | FDR filtering and report generation using Philosopher |
| philosopherreport | Generate TSV reports from Philosopher workspace binaries |
| philosopherabacus | Philosopher abacus multi-experiment report |
| Module | Description |
|---|---|
| ionquant | Label-free and isobaric quantification with match-between-runs and MaxLFQ |
| freequant | Label-free quantification using Philosopher's freequant command |
| philosopherlabelquant | Extract TMT/isobaric reporter ion intensities using Philosopher labelquant |
| tmtintegrator | TMT-Integrator for isobaric labeling quantification |
| iq | Protein quantification using the iq R package with MaxLFQ algorithm |
| msstatslfq | Statistical analysis of label-free quantification data using MSstats |
| diannfragpipe | FragPipe-mode DIA-NN quantification with FragPipe's bundled DIA-NN and its post-steps |
| Module | Description |
|---|---|
| ptmshepherd | Post-translational modification analysis and mass shift characterization |
| Module | Description |
|---|---|
| pairscans | Pair parent and child scans of one LC-MS file for O-Pair |
| mbg | Mass-based glycoproteomics matching for glycan identification |
| opair | O-glycoproteomics analysis for O-glycan identification and site localization |
| Module | Description |
|---|---|
| tmtlabelcheckanalyze | Analyze TMT labeling efficiency from PSM data |
| Module | Description |
|---|---|
| saintexpress | Score protein-protein interactions from AP-MS data using SAINTexpress |
| reprinttosaintinput | SAINTexpress inputs from a REPRINT table |
| fpop | Fast Photochemical Oxidation of Proteins (FPOP) analysis |
| fpopcoadaptr | FPOP coADAPTr converter over the whole FragPipe work dir |
| exportmatchedfragments | FragPipe "Export matched fragments": matched fragment ions per PSM in psm.tsv |
| metaproteomics | Metaproteomics database optimization and taxonomy analysis |
| speclibgen | Generate spectral libraries with FragPipe's gen_con_spec_lib.py (FragPipe-SpecLib) |
| Module | Description |
|---|---|
| fragpipeheadless | Run FragPipe in headless mode as a single all-in-one process |
| parsefragpipeworkflow | Parse FragPipe workflow files into per-tool configuration files |
| fragpipesaveworkflow | Write FragPipe's saved UI state (fragpipe.workflow) for a run |
| fragpipesecondpass | FragPipe's second-pass workflow and manifest after a Write sub mzML run |
| writesubmzml | FragPipe "Write sub mzML": the scans no confident PSM explains |
| Module | Description |
|---|---|
| generatesdrffromsamplesheet | Convert a samplesheet CSV to SDRF format |
| fragpipesdrf | Write the FragPipe SDRF template (sdrf.tsv) for a run |
| writetextfile | Write a text file whose body was built outside the tool modules |