title: Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community.
abstract: Mass spectrometry-based proteomics has emerged as a technology of choice for global analysis of cell signaling networks. However, reporting and sharing of MS data are often haphazard, limiting the usefulness of proteomics to the signaling community. We argue that raw data should always be provided with proteomics studies together with detailed peptide and protein identification and quantification information. Statistical criteria for peptide identification and their posttranslational modifications have largely been established for individual projects. However, the current practice of indiscriminately incorporating these individual results into databases such as UniProt is problematic. Because of the vast differences in underlying data quality, we advocate a differentiated annotation of data by level of reliability. Requirements for the reporting of quantitative data are being developed, but there are few mechanisms for community-wide sharing of these data.
authors.affiliation: Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark. jesper.olsen@cpr.ku.dk
authors.forename: Jesper V
authors.initials: JV
authors.lastname: Olsen
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
mesh_terms: D003628:Database Management Systems / Q000592:standards*; D030562:Databases, Protein / Q000592:standards; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods* / Q000592:standards / Q000706:statistics & numerical data; D015398:Signal Transduction