Label-free and isobaric quantification with match-between-runs and MaxLFQ.
IonQuant is a fast and comprehensive tool for MS1 quantification of label-free and isobaric labeled proteomics data, providing accurate feature detection, match-between-runs (MBR), and MaxLFQ normalization. It operates as an aggregate step across all samples, generating a filelist pointing to per-sample psm.tsv files and spectra directories, and supports TMT isobaric quantification via annotation files. Used within the FRAGPIPE_QUANT subworkflow and the TMT Label Check workflow for quantification.
| Channel | Type | Description |
|---|---|---|
| meta | val(map) | Sample metadata map |
| psm_dirs | path | PHILOSOPHERFILTER output directories (named by sample, containing psm.tsv) |
| spec_files | path | Spectral files (*.mzML or *.raw) staged in spectra/ subdirectory |
| annotation_file | path | TMT annotation file (2-column or 6-column TSV; pass [] if not applicable) |
| config_cli | val(string) | IonQuant parameters as CLI string (e.g., --mbr 1 --maxlfq 1) |
| modmasses | val(string) | Comma-separated modification masses for --modlist (empty = skip) |
| ionquant_dir | path | Unzipped IonQuant tool directory (optional, pass [] when not using) |
| Channel | Type | Description |
|---|---|---|
| results_dir | tuple(meta, path) | Directory containing all IonQuant output files |
| ions | tuple(meta, path) | Ion-level quantification (ion.tsv, optional) |
| combined_ions | tuple(meta, path) | Combined ion-level quantification across samples (combined_ion.tsv, optional) |
| combined_protein | tuple(meta, path) | Combined protein-level quantification (combined_protein.tsv, optional) |
| combined_peptide | tuple(meta, path) | Combined peptide-level quantification (combined_peptide.tsv, optional) |
| combined_modified_peptide | tuple(meta, path) | Combined modified-peptide-level quantification (combined_modified_peptide.tsv, optional) |
| combined_site | tuple(meta, path) | Combined site-level quantification (combined_site_*.tsv, optional) |
| all_tsv | tuple(meta, path) | All TSV output files |
| license_agreement | path | License agreement marker file |
| versions_ionquant | tuple | IonQuant software version (topic channel) |
| versions_fragpipe | tuple | FragPipe software version (topic channel) |
| Parameter | Default | Description |
|---|---|---|
| ext.args | '' | Additional CLI arguments appended to the IonQuant Java command |
| ext.prefix | meta.id | Override for the output directory name |
| ext.fragpipe_tools_dir | (auto-detected) | Override for the FragPipe tools directory path |
| ext.agree_fragpipe_license_agreement | (required) | Must be true or the process exits with an error |
Inherited from pipeline configuration (requires FragPipe container).
Used in the FRAGPIPE_QUANT subworkflow (subworkflows/local/fragpipe_quant/main.nf) as IONQUANT, IONQUANT_MS1, and IONQUANT_ISOBARIC for different quantification modes.
Its combined_modified_peptide.tsv also feeds the TMT label check analysis (workflows/tmt_labelcheck.nf).
Includes a guard that skips execution when both --perform-isoquant 0 and --perform-ms1quant 0 are set.