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Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
Author(s) -
Martens Lennart,
Nesvizhskii Alexey I.,
Hermjakob Henning,
Adamski Marcin,
Omenn Gilbert S.,
Vandekerckhove Joël,
Gevaert Kris
Publication year - 2005
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200401302
Subject(s) - raw data , proteomics , milestone , proteome , computer science , data collection , data science , information repository , database , bioinformatics , computer data storage , chemistry , biology , geography , archaeology , biochemistry , statistics , mathematics , gene , programming language , operating system
With the human Plasma Proteome Project (PPP) pilot phase completed, the largest and most ambitious proteomics experiment to date has reached its first milestone. The correspondingly impressive amount of data that came from this pilot project emphasized the need for a centralized dissemination mechanism and led to the development of a detailed, PPP specific data gathering infrastructure at the University of Michigan, Ann Arbor as well as the protein identifications database project at the European Bioinformatics Institute as a general proteomics data repository. One issue that crept up while discussing which data to store for the PPP concerns whether the raw, binary data coming from the mass spectrometers should be stored, or rather the more compact and already significantly processed peak lists. As this debate is not restricted to the PPP but relates to the proteomics community in general, we will attempt to detail the relative merits and caveats associated with centralized storage and dissemination of raw data and/or peak lists, building on the extensive experience gained during the PPP pilot phase. Finally, some suggestions are made for both immediate and future storage of MS data in public repositories.