Standards > model/format > bsg-s000112

ready mz Markup Language


General Information
From 2005-2008 there has existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming effort. Therefore the PSI, with full participation by ISB, has developed a new format by taking the best aspects of each of the precursor formats to form a single one. It is intended to replace the previous two formats. This new format was originally given a working name of dataXML. The final name is mzML.

This record replaces or incorporates the following deprecated resources:


Developed in France , Germany , United Kingdom

Created in 2008

Taxonomic range

This record is maintained by HUPO PSI  (HUPOPSI)

Record updated: June 29, 2016, 1:23 p.m. by The FAIRsharing Team.



Additional Information


    No tools defined


Access / Retrieve Data

Conditions of Use


Implementing Databases (6)
Model Organism Protein Expression Database
Model Organism Protein Expression Database

MitoZoa is a specialized database collecting complete and nearly-complete (longer than 7 kb) mtDNA entries of metazoan species, excluding Placozoa. MitoZoa contains curated entries, whose gene annotation has been significantly improved using a semi-automatic reannotation pipeline and by manual curation of mitogenomics experts. MitoZoa has been specifically designed to address comparative analyses of mitochondrial genomic features in a given metazoan group or in species belonging to the same genus (congeneric species). MitoZoa focuses on mitochondrial gene order, non-coding regions, gene content, and gene sequences.

PRoteomics IDEntifications database
The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.

The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.

The World-2DPAGE database
A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.

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

Scroll for more...


mzML--a community standard for mass spectrometry data.

Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.
Mol. Cell Proteomics 2011

View Paper (PubMed) View Paper (DOI)

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaino JA,Deutsch EW,Wang R,Csordas A,Reisinger F,Rios D,Dianes JA,Sun Z,Farrah T,Bandeira N,Binz PA,Xenarios I,Eisenacher M,Mayer G,Gatto L,Campos A,Chalkley RJ,Kraus HJ,Albar JP,Martinez-Bartolome S,Apweiler R,Omenn GS,Martens L,Jones AR,Hermjakob H
Nat Biotechnol 2014

View Paper (PubMed) View Paper (DOI)

mzML--a community standard for mass spectrometry data.

Martens L,Chambers M,Sturm M,Kessner D,Levander F,Shofstahl J,Tang WH,Rompp A,Neumann S,Pizarro AD,Montecchi-Palazzi L,Tasman N,Coleman M,Reisinger F,Souda P,Hermjakob H,Binz PA,Deutsch EW
Mol Cell Proteomics 2010

View Paper (PubMed) View Paper (DOI)