Extracts TMT/isobaric reporter ion intensities from mzML spectra using Philosopher labelquant.
This module runs Philosopher labelquant to extract TMT/isobaric reporter ion intensities from mzML spectra.
It runs inside the results directory workspace (containing .meta/ from PHILOSOPHERFILTER or FREEQUANT), reading .meta/ binaries and mzML files.
The updated .meta/ workspace is passed to downstream PHILOSOPHERREPORT, which regenerates TSVs with TMT intensity columns.
| Channel | Type | Description |
|---|---|---|
| meta | val(map) | Sample/experiment metadata |
| results_dir | path | Directory with psm.tsv and .meta/ workspace from PHILOSOPHERFILTER or FREEQUANT |
| mzml_dir | path | Directory containing mzML files for the experiment/group |
| annot | path | TMT annotation file mapping channels to samples |
| config_cli | val(string) | Labelquant CLI flags (--tol, --level, --plex, --brand, --minprob, --purity, --removelow) |
| Channel | Type | Description |
|---|---|---|
| results_dir | tuple(val, path) | Output directory ${prefix} with updated .meta/ containing TMT intensities |
| versions_philosopher | topic: versions | Philosopher version |
| versions_fragpipe | topic: versions | FragPipe version |
| Parameter | Default | Description |
|---|---|---|
| ext.args | '' | Additional command-line arguments appended after config_cli and --annot/--dir flags |
| ext.prefix | ${meta.id} |
Output directory name |
| ext.fragpipe_tools_dir | /fragpipe_bin/fragpipe-24.0/fragpipe-24.0/tools |
FragPipe tools directory |
The licensed FragPipe image given with --fragpipe_container.
Used in the FRAGPIPE_QUANT subworkflow (subworkflows/local/fragpipe_quant/main.nf) for TMT reporter ion extraction.
The output .meta/ workspace is then passed to PHILOSOPHERREPORT to generate final TSV files with quantification data.