title: Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.
abstract: 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.
authors.affiliation: Protagen AG, Dortmund, Germany. Daniel.Chamrad@protagen.de
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Chamrad
authors.forename: Gerhard
authors.initials: G
authors.lastname: Körting
authors.forename: Heike
authors.initials: H
authors.lastname: Schäfer
authors.forename: Christian
authors.initials: C
authors.lastname: Stephan
authors.forename: Herbert
authors.initials: H
authors.lastname: Thiele
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
authors.forename: Katrin
authors.initials: K
authors.lastname: Marcus
authors.forename: Martin
authors.initials: M
authors.lastname: Blüggel
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001921:Brain / Q000378:metabolism*; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval; D013058:Mass Spectrometry; D051379:Mice; D008969:Molecular Sequence Data; D010865:Pilot Projects; D020543:Proteome / Q000378:metabolism*; D012984:Software; D038202:alpha-Crystallin A Chain / Q000378:metabolism
chemical_list: D020543:Proteome; D038202:alpha-Crystallin A Chain