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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. An edited version of  the mzPAF (Peak Annotation Format – Peptides) has been released on May 7th, 2026.
  • The mzSpecLib specification, a formal standard and file format to store and distribute spectral libraries, has been released on September 22nd, 2025
  • The FeatureTab, an exchange format for molecular interactions features, has been released on January 8th, 2026.
  • The Proforma 2.1 specification (Proteoform and Peptidoform Notation) has been released on June 21th, 2026.
  • The MIDAP (Minimum Information Describing a Proteoform) document v.1.0.0 is under revision after the external and public review phase that ended on April 19th, 2026.
  • The recommendation for encoding data independent acquisition, ion mobility data, subsampled data arrays, and additional compression types in mzML 1.1 (https://www.psidev.info/mzml) is under public and external review until September 12th. Please participate and send comments to sylvie.ricard-blum :at: univ-lyon1.fr.

See more details on these documents in progress.

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 1.1.2 PSI-MI XML 2.5.4 PSI-MI CV 2.5.0
MIABE 1.0.0 PSI-MI XML 3.8.8
MIAPAR 1.0.0 MITAB 2.8
FeatureTAB 1.0
Mass Spectrometry
Group charter

Proteomics Informatics
Group charter		 Mass spectrometry (MIAPE-MS) 2.98 mzML 1.1.0 PSI-MS 4.1.248
Identification (MIAPE-MSI) 1.1 TraML 1.0.0 XLMOD 1.5.3
Mass spectrometry Quantification (MIAPE-Quant) 1.0 mzData† NA
mzIdentML 1.3.0
mzQuantML† 1.0.0
mzTab 1.0.0
mzTab-M 2.0.0
proBed 1.0.0
proBAM 1.0.0
PEFF 1.0.0
USI 1.0.0
SDRF‑Proteomics 1.0.0
mzSpecLib 1.0.1
mzPAF 1.0.1
ProForma 2.1.0
Protein Modifications
Group charter		 PSI-MOD 1.033.0
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) 1.4 GelML 1.1.0 sepCV 1.0.0
Gel informatics (MIAPE-GI) 1.0 spML 1.0.0
Column chromatography (MIAPE-CC) 1.1
Capillary electrophoresis (MIAPE-CE) 0.9.3
Phosphoproteomics (MIASSPE) 0.9
AI-readiness
Group charter		 – – – – – –
†deprecated, * in development