PeptideAtlasapplication/xmlftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_RAW.tarftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_prot_216_201104181136.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_mzXML_201104181136.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_Search_Results_216_201104181136.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_READMEftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_Search_Results_216_201104181136.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_mzXML_201104181136.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_prot_216_201104181136.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_216_search.params.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000218/PAe000218_216_sequest.paramsprimaryOK200Y. 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=245'nbaliga@systemsbiology.orgPeptideAtlasProteomicsUnknownHalobacterium Nrc-1 (halobacterium)A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.Chamrad Daniel C DC, Körting Gerhard G, Schäfer Heike H, Stephan Christian C, Thiele Herbert H, Apweiler Rolf R, Meyer Helmut E HE, Marcus Katrin K, Blüggel Martin MfalseYAGsn2_48rptreplicate enrichment for soluble proteins; 400-800 m/z; Goo et al., 2003, Mol Cell Proteomics 2(8):5112006-12-312016-03-29PAe0002181691297364091