Standards > terminology artifact > bsg-s000068

ready HUPO PSI Mass Spectrometry Controlled Vocabulary

Abbreviation:PSI-MS CV

General Information
The PSI-MS Controlled Vocabulary is developed in common with the PSI-Proteomics Informatics group. It consists of a large collection of structured terms covering description and use of Mass Spectrometry instrumentation as well as Protein Identification and Quantitation software. The source of the terms are multiple: they include vocabulary and definitions in chapter 12 of the IUPAC nomenclature book, instrument and software vendors and developers and other user-submitted terms. Although its structure and use is linked to mzML, mzIdentML and mzQuantML, it is dynamically maintained in a OBO format. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS–related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary.

This record is maintained by HUPO PSI  (HUPOPSI)

Record updated: May 4, 2017, 2:11 p.m. by The FAIRsharing Team.

Access / Retrieve Data

MS Ontology Display

View in BioPortal.

Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Implementing Databases (3)
MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. We offer user-submission tools and have strong reporting capabilities. We will utilise and further develop de-facto standard formats where various components are encapsulated, such as the encoded spectral and chromatographic data, and associated information about the chemical structure, as well as metadata describing assays and the study as a whole. We are dedicated to collaborate closely with major parties in world-wide metabolomics communities, such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.

Japan Proteome Standard Repository
jPOSTrepo (Japan ProteOme STandard Repository) is a data repository of sharing MS raw/processed data.

Implementing Policies

This record is not implemented by any policy.


Record Maintainer



Grant Number(s)

  • BB/H024654/1 (Biotechnology and Biological Sciences Research Council)

  • BB/I000909/1 (Biotechnology and Biological Sciences Research Council)

  • EU FP7 grant number 260558 (ProteomeXchange)

  • P50 GM076547 (NIGMS NIH)

  • R01 GM087221 (NIGMS NIH)

  • WT085949MA (Wellcome Trust, UK)


The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G,Montecchi-Palazzi L,Ovelleiro D,Jones AR,Binz PA,Deutsch EW,Chambers M,Kallhardt M,Levander F,Shofstahl J,Orchard S,Vizcaino JA,Hermjakob H,Stephan C,Meyer HE,Eisenacher M
Database (Oxford) 2013

View Paper (PubMed) View Paper (DOI)