Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.

STEPHAN, Christian, REIDEGELD, Kai A, HAMACHER, Michael, VAN HALL, André, MARCUS, Katrin, TAYLOR, Chris, JONES, Philip, MÜLLER, Michael, APWEILER, Rolf, MARTENS, Lennart, KÖRTING, Gerhard, CHAMRAD, Daniel C, THIELE, Herbert, BLÜGGEL, Martin, PARKINSON, David, BINZ, Pierre-Alain, LYALL, Andrew and MEYER, Helmut E (2006). Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics, 6 (18), 5015-5029.

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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.

Item Type:	Article
Research Institute, Centre or Group - Does NOT include content added after October 2018:	Biomedical Research Centre
Identification Number:	https://doi.org/10.1002/pmic.200600294
Page Range:	5015-5029
Depositing User:	Jamie Young
Date Deposited:	03 Jun 2015 08:35
Last Modified:	18 Mar 2021 23:15
URI:	https://shura.shu.ac.uk/id/eprint/9981

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