A common open representation of mass spectrometry data and its application to proteomics research.
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.
Pedrioli
Patrick G A
PG
Institute for Systems Biology, 1441 North 34 Street, Seattle, Washington 98103-8904, USA.
Eng
Jimmy K
JK
Hubley
Robert
R
Vogelzang
Mathijs
M
Deutsch
Eric W
EW
Raught
Brian
B
Pratt
Brian
B
Nilsson
Erik
E
Angeletti
Ruth H
RH
Apweiler
Rolf
R
Cheung
Kei
K
Costello
Catherine E
CE
Hermjakob
Henning
H
Huang
Sequin
S
Julian
Randall K
RK
Kapp
Eugene
E
McComb
Mark E
ME
Oliver
Stephen G
SG
Omenn
Gilbert
G
Paton
Norman W
NW
Simpson
Richard
R
Smith
Richard
R
Taylor
Chris F
CF
Zhu
Weimin
W
Aebersold
Ruedi
R
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
D020543:Proteome