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New Working Group: Making Proteomics AI-Ready

The HUPO-PSI AI-readiness Working Group has launched, bringing together researchers to make public proteomics data more usable for AI through better metadata, formats, and reprocessing workflows. Chaired by Tine Claeys, with co-chairs Samuel Wein and Ralf Gabriels, the group welcomes anyone interested in shaping practical, community-driven solutions. Get involved and follow our progress!

Documents in progress and new documents

  • The mzQC format, a data standard for reporting and exchanging quality-related information in biological mass spectrometry, has been been released on February 21st, 2024
  • The mzIdentML 1.3.0 specification and its crosslinking extension have been released on July 4th, 2024.
  • The mzPAF (Peak Annotation Format – Peptides) specification has been released on September 22nd, 2025 
  • The mzSpecLib specification, a formal standard and file format to store and distribute spectral libraries, has been released on September 22nd, 2025
  • The Proforma 2.1 specification (Proteoform and Peptidoform Notation, https://www.psidev.info/proforma) is in public review until December 10th, 2025. Please participate and send your comments to the HUPO-PSI editor (sylvie.ricard-blum(at)univ-lyon1.fr).

See more details on these documents in progress.

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HUPO-PSI Working groups and Outputs

The HUPO Proteomics Standards Initiative defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification.

Working Groups Guidelines v. Formats v. Controlled Vocabularies  v.
Molecular
Interactions
Group charter 		MIMIx
MIABE
MIAPAR		 1.1.2
1.0.0
1.0.0		 PSI-MI XML
PSI-MI XML
MITAB
FeatureTAB		 2.5.4
3.8.8
2.8
1.0		 PSI-MI CV  2.5.0
Mass Spectrometry
Group charter

 

Proteomics Informatics
Group charter

Mass spectrometry (MIAPE-MS)
Identification (MIAPE-MSI)
Mass spectrometry Quantification (MIAPE-Quant)

2.98
1.1
1.0

 mzML
TraML 
mzData†
mzIdentML 
mzQuantML†
mzTab
mzTab-M
proBed 
proBAM 
PEFF 
USI
SDRF‑Proteomics
mzSpecLib*
mzPAF*
ProForma

1.1.0
1.0.0
NA
1.3.0
1.0.0
1.0.0
2.0.0
1.0.0
1.0.0
1.0.0
1.0.0
1.0.0
1.0.0
1.0.0
2.0.0

 PSI-MS 
XLMOD 		 4.0.15
1.1.0
Protein Modifications
Group charter		 PSI-MOD
Quality Control
Group charter		 mzQC 1.0.0
Disordered Proteins
Group charter		 Minimum Information About Disorder Experiments (MIADE) 1.0
Protein Separation
(Inactive)		 Gel electrophoresis (MIAPE-GE) 
Gel informatics (MIAPE-GI) 
Column chromatography (MIAPE-CC) 
Capillary electrophoresis (MIAPE-CE) 
Phosphoproteomics (MIASSPE) 		 1.4
1.0
1.1
0.9.3
0.9		 GelML 
spML 		 1.1.0
1.0.0		 sepCV  1.0.0
AI-readiness
Group charter		 – – – – – –

†deprecated, * in development