PeptideAtlasapplication/xmlftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_RAW.tarftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_prot_179_201104181136.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_mzXML_201104181135.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_prot_179_201104181136.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_READMEftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_mzXML_201104181135.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_179_sequest.paramsftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_179_search.params.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_Search_Results_179_201104181135.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000181/PAe000181_Search_Results_179_201104181135.propertiesprimaryOK200Y. A. Goo, E. C. Yi, N. S. Baliga, W. A. Tao, M. Pan, R. Aebersold, D. R. Goodlett, L. Hood and W. V. NgTPP'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=208'nbaliga@systemsbiology.orgPeptideAtlasProteomicsUnknownHalobacterium Nrc-1 (halobacterium)The newly available techniques for sensitive proteome analysis and the resulting amount of data require a new bioinformatics focus on automatic methods for spectrum reprocessing and peptide/protein validation. Manual validation of results in such studies is not feasible and objective enough for quality relevant interpretation. The necessity for tools enabling an automatic quality control is, therefore, important to produce reliable and comparable data in such big consortia as the Human Proteome Organization Brain Proteome Project. Standards and well-defined processing pipelines are important for these consortia. We show a way for choosing the right database model, through collecting data, processing these with a decoy database and end up with a quality controlled protein list merged from several search engines, including a known false-positive rate.Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.Stephan Christian C, Reidegeld Kai A KA, Hamacher Michael M, van Hall André A, Marcus Katrin K, Taylor Chris C, Jones Philip P, Müller Michael M, Apweiler Rolf R, Martens Lennart L, Körting Gerhard G, Chamrad Daniel C DC, Thiele Herbert H, Blüggel Martin M, Parkinson David D, Binz Pierre-Alain PA, Lyall Andrew A, Meyer Helmut E HEfalseyagsn2_1120rptreplicate enrichment for soluble proteins; 1100-2000 m/z; Goo et al., 2003, Mol Cell Proteomics 2(8):5102006-12-312016-03-29PAe0001811692743264091