title: A common open representation of mass spectrometry data and its application to proteomics research.
abstract: A broad range of mass spectrometers are used in mass spectrometry (MS)-based proteomics research. Each type of instrument possesses a unique design, data system and performance specifications, resulting in strengths and weaknesses for different types of experiments. Unfortunately, the native binary data formats produced by each type of mass spectrometer also differ and are usually proprietary. The diverse, nontransparent nature of the data structure complicates the integration of new instruments into preexisting infrastructure, impedes the analysis, exchange, comparison and publication of results from different experiments and laboratories, and prevents the bioinformatics community from accessing data sets required for software development. Here, we introduce the 'mzXML' format, an open, generic XML (extensible markup language) representation of MS data. We have also developed an accompanying suite of supporting programs. We expect that this format will facilitate data management, interpretation and dissemination in proteomics research.
authors.affiliation: Institute for Systems Biology, 1441 North 34 Street, Seattle, Washington 98103-8904, USA.
authors.forename: Patrick G A
authors.initials: PG
authors.lastname: Pedrioli
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.forename: Robert
authors.initials: R
authors.lastname: Hubley
authors.forename: Mathijs
authors.initials: M
authors.lastname: Vogelzang
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Brian
authors.initials: B
authors.lastname: Raught
authors.forename: Brian
authors.initials: B
authors.lastname: Pratt
authors.forename: Erik
authors.initials: E
authors.lastname: Nilsson
authors.forename: Ruth H
authors.initials: RH
authors.lastname: Angeletti
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
authors.forename: Kei
authors.initials: K
authors.lastname: Cheung
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Costello
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Sequin
authors.initials: S
authors.lastname: Huang
authors.forename: Randall K
authors.initials: RK
authors.lastname: Julian
authors.forename: Eugene
authors.initials: E
authors.lastname: Kapp
authors.forename: Mark E
authors.initials: ME
authors.lastname: McComb
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
authors.forename: Gilbert
authors.initials: G
authors.lastname: Omenn
authors.forename: Norman W
authors.initials: NW
authors.lastname: Paton
authors.forename: Richard
authors.initials: R
authors.lastname: Simpson
authors.forename: Richard
authors.initials: R
authors.lastname: Smith
authors.forename: Chris F
authors.initials: CF
authors.lastname: Taylor
authors.forename: Weimin
authors.initials: W
authors.lastname: Zhu
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D003628:Database Management Systems; D016208:Databases, Factual; D033181:Information Dissemination / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods* / Q000592:standards; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards; D020543:Proteome / Q000032:analysis / Q000737:chemistry / Q000145:classification; D040901:Proteomics / Q000379:methods* / Q000592:standards; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome