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	If SDRF	If SDRF	Yes	If SDRF	No	No
quantms	Yes	Yes	Yes	No	If SDRF	If SDRF	Yes	Yes	No	No
mzIdentML	Yes	No	No	Yes	If SDRF	If SDRF	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 (sample and run metadata). SDRF is optional for all converters.

CLI commands

Converter	Command
MaxQuant	qpxc convert maxquant
FragPipe	qpxc convert fragpipe
DIA-NN	qpxc convert diann
quantms	qpxc convert quantms
mzIdentML	qpxc convert mzidentml
SDRF only	qpxc convert sdrf

Input files (summary)

Converter	Typical inputs
MaxQuant	msms.txt, evidence.txt, proteinGroups.txt
FragPipe	psm.tsv, combined_ion/combined_peptide, combined_protein
DIA-NN	report (tsv), pg_matrix (optional)
quantms	mzTab; optional MSstats, optional SDRF
mzIdentML	.mzid / .mzid.gz; optional MGF or mzML (file/folder) for spectra; optional SDRF
SDRF	Single SDRF TSV file

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