Converter Coverage Matrix

This page lists which QPX data views each converter produces. Use it to see at a glance what output to expect from each tool.

Views produced per converter

Converter	PSM	Feature	PG	Pepmap	Sample	Run	Dataset	Ontology	Provenance	mz
MaxQuant	Yes	Yes	Yes	No	If SDRF	If SDRF	Yes	If SDRF	No	No
FragPipe	Yes	Yes	Yes	No	If SDRF	If SDRF	Yes	If SDRF	No	No
DIA-NN	No	Yes	Yes	No	Yes	Yes	Yes	If terms	Yes	No
Spectronaut	No	Yes	Yes	No	If SDRF	If SDRF	Yes	Yes	Yes	No
OpenMS native QPX	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes	Yes	No
OpenMS consensusXML	Yes	Yes	Yes	No	If SDRF	If SDRF	Yes	If terms	Yes	No
CDAP	Yes	Yes	Yes	No	If PDC	If PDC	Yes	Yes	Yes	No
mzIdentML	Yes	No	No	Yes	If SDRF	If SDRF	Yes	Yes	Yes	No
QuantMS MSstats	No	Yes	No	No	Yes	Yes	Yes	Yes	Yes	No
SDRF	No	No	No	No	Yes	Yes	No	Optional	No	No

• Yes — the converter produces this view.
• No — the converter does not produce this view (e.g. DIA-NN has no PSM view; mzIdentML has no Feature/PG).
• If SDRF — the view is produced only when an SDRF file is provided. Whether SDRF is optional or required depends on the converter; see its CLI contract below.
• If terms — the view is produced when the converter discovers resolvable ontology entries.
• If PDC — CPTAC/PDC studies ship no SDRF, and CDAP .psm files carry no sample metadata. When run through qpxc pdc2qpx (default), the sample/run views are built from PDC GraphQL metadata, which also recovers the TMT/iTRAQ channel → biological-sample mapping. Disable with --no-metadata.

The mz (full-spectra) view is produced by the standalone qpxc convert mz command, or automatically by qpxc pdc2qpx --include-spectra; it is not emitted by the per-tool converters above.

CLI commands

Converter	Command
MaxQuant	qpxc convert maxquant
FragPipe	qpxc convert fragpipe
DIA-NN	qpxc convert diann
Spectronaut	qpxc convert spectronaut
OpenMS native QPX	qpxc convert openms
OpenMS consensusXML	qpxc convert openms-consensus
CDAP	qpxc convert cdap
mzIdentML	qpxc convert mzidentml
QuantMS MSstats	qpxc convert quantms-msstats
SDRF only	qpxc convert sdrf

Input files (summary)

Converter	Typical inputs
MaxQuant	msms.txt, evidence.txt, proteinGroups.txt
FragPipe	psm.tsv, combined_ion, combined_protein
DIA-NN	report (TSV or Parquet), pg_matrix (optional); required SDRF
Spectronaut	report.tsv; optional SDRF
OpenMS native QPX	-out_qpx Parquet directory; SDRF; optional companion consensusXML
OpenMS consensusXML	consensusXML; optional SDRF
CDAP	CPTAC CDAP .psm files in one study directory
mzIdentML	.mzid / .mzid.gz; optional MGF or mzML (file/folder) for spectra; optional SDRF
QuantMS MSstats	QuantMS-generated *_msstats_in.csv; required SDRF
SDRF	Single SDRF TSV file

For field-level mappings from each tool’s columns to QPX, see Tool Field Mappings.