title: Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.
abstract: 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.
authors.affiliation: Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany. Christian.Stephan@rub.de
authors.forename: Christian
authors.initials: C
authors.lastname: Stephan
authors.forename: Kai A
authors.initials: KA
authors.lastname: Reidegeld
authors.forename: Michael
authors.initials: M
authors.lastname: Hamacher
authors.forename: André
authors.initials: A
authors.lastname: van Hall
authors.forename: Katrin
authors.initials: K
authors.lastname: Marcus
authors.forename: Chris
authors.initials: C
authors.lastname: Taylor
authors.forename: Philip
authors.initials: P
authors.lastname: Jones
authors.forename: Michael
authors.initials: M
authors.lastname: Müller
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Gerhard
authors.initials: G
authors.lastname: Körting
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Chamrad
authors.forename: Herbert
authors.initials: H
authors.lastname: Thiele
authors.forename: Martin
authors.initials: M
authors.lastname: Blüggel
authors.forename: David
authors.initials: D
authors.lastname: Parkinson
authors.forename: Pierre-Alain
authors.initials: PA
authors.lastname: Binz
authors.forename: Andrew
authors.initials: A
authors.lastname: Lyall
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
mesh_terms: D000465:Algorithms; D001921:Brain / Q000378:metabolism*; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval; D013058:Mass Spectrometry; D015337:Multicenter Studies as Topic; D010865:Pilot Projects; D020543:Proteome / Q000032:analysis* / Q000378:metabolism
chemical_list: D020543:Proteome