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Output

quantms produces standardized output files organized into predictable directories under --outdir. All primary result files follow open HUPO-PSI standards.

DIA users: DIA output files and structure are described in the quantmsdiann documentation.

Output Structure

DDA-LFQ Output

results_lfq/
├── pipeline_info/             # Nextflow execution reports and software versions
├── sdrf/                      # SDRF files and OpenMS config files used
├── spectra/                   # Spectra-related data (when --mzml_features is enabled)
│   └── mzml_statistics/       # Per-run mzML statistics
├── quant_tables/              # All quantification results
│   ├── out.mzTab              # mzTab with identifications and quantities
│   ├── msstats_in.csv         # MSstats-ready long-format table
│   └── out.consensusXML       # OpenMS internal format (debugging/downstream)
├── msstats/                   # MSstats-processed results
│   └── out_msstats.mzTab      # mzTab with MSstats input format (for downstream analysis)
└── pmultiqc/                  # Interactive QC report
    ├── multiqc_report.html
    ├── multiqc_data/
    └── multiqc_plots/
        ├── png/
        ├── svg/
        └── pdf/

DDA-ISO Output (TMT / iTRAQ)

results_iso/
├── pipeline_info/
├── sdrf/
├── quant_tables/
│   ├── out.mzTab              # mzTab with channel intensities and identifications
│   ├── peptide_out.csv        # Peptide-level quantities per channel
│   ├── protein_out.csv        # Protein-level quantities per channel
│   └── out_msstats_in.csv     # MSstats-ready table
├── msstats/
│   └── out_msstats.mzTab
└── pmultiqc/
    ├── multiqc_report.html
    └── ...

Verbose Output

For debugging or detailed intermediate-file inspection, run with -c verbose_modules:

nextflow run bigbio/quantms -profile docker -c verbose_modules -params-file params.yaml

The verbose structure exposes all intermediate steps:

results/
├── pipeline_info/
├── sdrf/
├── spectra/
│   ├── mzml_indexing/
│   └── mzml_statistics/
├── peptide_identification/
│   ├── comet/
│   ├── msgf/
│   └── sage/
├── peptide_postprocessing/
│   ├── psm_features/
│   ├── psm_clean/
│   ├── percolator/
│   ├── consensusid/
│   ├── fdr_consensusid/
│   └── id_filter/
├── quant_tables/
├── msstats/
└── pmultiqc/

Key Output Files

mzTab

The primary result file. Generated for both DDA-LFQ and DDA-ISO workflows.

  • Location: quant_tables/out.mzTab
  • Standard: HUPO-PSI mzTab
  • Suitable for: PRIDE submission, downstream quantification tools (mokume, qpx)

mzTab is a multi-section TSV file. Each line starts with a section identifier:

Prefix Section
MTD Metadata
PRH/PRT Protein header / entry
PEH/PEP Peptide header / entry
PSH/PSM PSM header / entry

Notable optional columns in the PRT section:

  • opt_global_Posterior_Probability_score — Posterior probability from protein inference
  • opt_global_nr_found_peptides — Number of identified peptides per protein
  • opt_global_result_type — single_protein, indistinguishable_protein_group, or protein_details

Notable optional columns in the PEP section:

  • opt_global_cv_MS:1000889_peptidoform_sequence — Sequence with modifications
  • opt_global_q-value — Experiment-wide q-value
  • opt_global_mass_to_charge_study_variable[n] — Precursor m/z in sample n

Notable optional columns in the PSM section:

  • opt_global_cv_MS:1000889_peptidoform_sequence — Modified sequence for this match
  • opt_global_SpecEValue_score — Spectral E-value (MS-GF+ engine)
  • opt_global_q-value — Experiment-wide q-value

Score columns vary depending on which search engines and rescoring tools were used; consult their individual documentation for definitions.

MSstats Input Table

  • Location: quant_tables/msstats_in.csv (LFQ) or quant_tables/out_msstats_in.csv (ISO)
  • Format: Long-format CSV compatible with the OpenMStoMSstats() function in the MSstats R package
  • Use: Statistical modeling of differential expression

MSstats Input Export

  • Location: msstats/out_msstats.mzTab
  • Contains: MSstats-compatible CSV exported for downstream statistical analysis with the MSstats R package

Parquet PSM Tables

When running the identification-only subworkflow, PSM results are written in quantms.io parquet format:

  • Location: psm_tables/
  • Use: Efficient downstream processing with pandas, DuckDB, or qpx

OpenMS Formats (LFQ only)

  • quant_tables/out.consensusXML — ConsensusXML with linked features across runs. Useful for debugging and OpenMS-based downstream analysis.
  • quant_tables/peptide_out.tsv — Peptide-level quantities from ProteinQuantifier
  • quant_tables/protein_out.tsv — Protein-level quantities from ProteinQuantifier

pmultiqc QC Report

  • Location: pmultiqc/multiqc_report.html
  • Open in any web browser — no installation required

The pmultiqc plugin generates an interactive HTML report summarizing:

  • Peptide and protein identification counts per run
  • FDR distributions
  • Charge state distributions
  • Missed cleavage rates
  • Precursor mass error distributions
  • Quantification intensity distributions
  • TMT channel balance (isobaric workflows)
  • Software versions used

Plots are also exported as static images under pmultiqc/multiqc_plots/ in PNG, SVG, and PDF formats.

Pipeline Info

  • Location: pipeline_info/
  • Contents:
  • execution_report.html — Interactive Nextflow execution report
  • execution_timeline.html — Per-process timing
  • execution_trace.txt — Detailed resource usage per task
  • pipeline_dag.svg — Workflow directed acyclic graph
  • software_versions.yml — Exact versions of all tools used
  • params_<timestamp>.json — Full parameter set used for the run

SDRF-Driven Parameter Precedence

When an SDRF file is used as input, the following parameters are read from the SDRF and override any values provided on the command line:

  • labelling_type
  • dissociationmethod
  • fixedmodifications
  • variablemodifications
  • precursormasstolerance / precursormasstoleranceunit
  • fragmentmasstolerance / fragmentmasstoleranceunit
  • enzyme
  • acquisition_method

Input File Types (Reference)

Spectra

quantms natively supports:

  • .mzML — Open standard (preferred)
  • .raw — Thermo Fisher RAW files (auto-converted via ThermoRawFileParser)
  • .d — Bruker timsTOF (converted when --convert_dotd is set)

Compressed variants (.gz, .tar, .tar.gz, .zip) are also accepted.

Protein Database

Standard FASTA format. Remove stop-codon characters (*) before use. Decoys are added automatically by the pipeline when --add_decoys true (default).