Open AccessAn efficient data format for mass spectrometry-based proteomics
Author(s) -
Anuj R. Shah,
Jennifer L. Davidson,
Matthew Monroe,
Anoop Mayampurath,
William F. Danielson,
Yan Shi,
A.C. Robinson,
Brian H. Clowers,
Mikhail E. Belov,
Gordon A. Anderson,
Richard Smith
Publication year - 2010
Publication title -
journal of the american society for mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.961
H-Index - 127
eISSN - 1879-1123
pISSN - 1044-0305
DOI - 10.1016/j.jasms.2010.06.014
Subject(s) - computer science , xml , data exchange , database , robustness (evolution) , application programming interface , information retrieval , data mining , proteomics , chemistry , world wide web , programming language , biochemistry , gene
The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However, these efforts have yet to gain significant attention, mostly because they have not demonstrated significant performance benefits over existing standards, but also due to issues such as extensibility to multidimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times, and extensibility to accommodate multidimensional separation systems.