Workflows

quantms supports two DDA proteomics workflows. Choose based on your experimental design.

DDA-LFQ (Label-Free Quantification)

For experiments without chemical labeling. Protein abundance is estimated from peptide ion intensities.

nextflow run bigbio/quantms \
    -profile docker \
    --input samplesheet.csv \
    --database uniprot_human.fasta \
    --outdir results/

Pipeline Steps

1. File conversion — Raw files converted to mzML (ThermoRawFileParser)
2. Database search — Peptide identification with Comet and/or MS-GF+
3. PSM rescoring — ML-based rescoring with MS2PIP + DeepLC + Percolator
4. Peptide indexing — FDR filtering and protein inference
5. Feature detection — Chromatographic feature finding (OpenMS)
6. Feature linking — Align and match features across runs
7. Protein quantification — Aggregate peptide intensities to protein level
8. Quality control — Generate pmultiqc interactive QC report

Input Requirements

• Raw files: .mzML, .raw (Thermo), or .d (Bruker)
• FASTA database: protein sequences for search
• Sample sheet: CSV mapping files to samples and conditions

Sample Sheet Format

sample,spectra_file,sdrf_file,condition
sample1,/path/to/sample1.mzML,experiment.sdrf.tsv,control
sample2,/path/to/sample2.mzML,experiment.sdrf.tsv,treatment

DDA-ISO (Isobaric Labeling: TMT/iTRAQ)

For multiplexed experiments using TMT or iTRAQ chemical labels.

nextflow run bigbio/quantms \
    -profile docker \
    --input samplesheet.csv \
    --database uniprot_human.fasta \
    --labelling_type isobaric \
    --outdir results/

Pipeline Steps

1. File conversion — Raw to mzML
2. Database search — With reporter ion extraction
3. PSM rescoring — ML rescoring + FDR control
4. Reporter ion quantification — Extract TMT/iTRAQ channel intensities
5. Protein summarization — Aggregate to protein level per channel
6. Normalization — Median normalization across channels
7. Quality control — pmultiqc report with TMT-specific plots

Supported Labels

Label	Plex	Flag
TMT6	6-plex	--label_type TMT6plex
TMT10	10-plex	--label_type TMT10plex
TMT11	11-plex	--label_type TMT11plex
TMT16	16-plex	--label_type TMT16plex
TMT18	18-plex	--label_type TMT18plex
iTRAQ4	4-plex	--label_type iTRAQ4plex
iTRAQ8	8-plex	--label_type iTRAQ8plex

Choosing a Workflow

Feature	DDA-LFQ	DDA-ISO
Labeling	None	TMT or iTRAQ
Multiplexing	No (1 sample per file)	Yes (6-18 samples per file)
Dynamic range	Higher	Ratio compression
Missing values	More frequent	Fewer (within plex)
Best for	Discovery, large cohorts	Precise quantification, time-course

DIA Workflow

For DIA (Data-Independent Acquisition) experiments, use the dedicated quantmsdiann pipeline:

nextflow run bigbio/quantmsdiann \
    -profile docker \
    --input samplesheet.csv \
    --database uniprot_human.fasta \
    --outdir results/

See quantmsdiann documentation for details.