bigbio/qpx

View on GitHub

qpx (Quantitative Proteomics eXchange) format (aka quantms.io) a format to capture a full proteomics experiment

Stars: 26
Forks: 8
Open beginner issues: 0
Indexed issues: 11
Avg merge: 5h 13m
Merged PRs (30d): 27

Dominant language: Python
License: Apache-2.0
Last GitHub push: Sep 13, 2026
Latest indexed: Sep 14, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Open All

11 open issues indexed

Discussion: Ontology versioning? Open

bigbio/qpx#157 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Additional metadata to store? Open

bigbio/qpx#162 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 14, 2026
psm/feature: no field carries the native spectrum reference, and the `scan` component convention is undefined outside Waters Open

bigbio/qpx#259 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
pg: a (group, quantification unit, label) with no quantity — labelled row with null intensity, or no row? Open

bigbio/qpx#280 · 8 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
design_matrix(fillna=None) turns a stored NULL pg intensity into 0.0; the in-memory and out-of-core pivots disagree Open

bigbio/qpx#281 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Conversion summary calls n_features_without_pg "identified-but-not-quantified", but it counts features with no PG link Open

bigbio/qpx#282 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
feature.parquet confidence fields are always null (peptide_qvalue in both converters; all three in OpenMS) Open

bigbio/qpx#284 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
collection.md documents an API (open_collection) that does not exist Open

bigbio/qpx#290 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
perf: DIA-NN pg adapter loops per (protein group, run) in Python — 49x available Open

bigbio/qpx#291 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Declared fields populated by one converter and null in another, with no documented reason Open

bigbio/qpx#300 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Issue representing SILAC Open

bigbio/qpx#308 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

bigbio/qpx

Get new issues in your inbox