IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics
| Autor: | Paola Picotti, Ruedi Aebersold, Roger Higdon, Winston A. Haynes, Natali Kolker, Lukas Reiter, Andrew T. Bauman, Elizabeth Stewart, Gerald van Belle, Alexander Schmidt, Gregory Hather, Eugene Kolker |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
False discovery rate
Proteomics Proteomics methods Computer science Biophysics High throughput proteomics Computational biology computer.software_genre 01 natural sciences Biochemistry Mass Spectrometry 03 medical and health sciences Research environment False Positive Reactions Databases Protein 030304 developmental biology 0303 health sciences 010401 analytical chemistry Proteins 0104 chemical sciences High-Throughput Screening Assays Spire Identification (information) Models Chemical Protein model Data mining computer |
| Zdroj: | Journal of Proteomics Journal of proteomics |
| ISSN: | 1874-3919 |
| DOI: | 10.1016/j.jprot.2011.06.003 |
| Popis: | In high-throughput mass spectrometry proteomics, peptides and proteins are not simply identified as present or not present in a sample, rather the identifications are associated with differing levels of confidence. The false discovery rate (FDR) has emerged as an accepted means for measuring the confidence associated with identifications. We have developed the Systematic Protein Investigative Research Environment (SPIRE) for the purpose of integrating the best available proteomics methods. Two successful approaches to estimating the FDR for MS protein identifications are the MAYU and our current SPIRE methods. We present here a method to combine these two approaches to estimating the FDR for MS protein identifications into an integrated protein model (IPM). We illustrate the high quality performance of this IPM approach through testing on two large publicly available proteomics datasets. MAYU and SPIRE show remarkable consistency in identifying proteins in these datasets. Still, IPM results in a more robust FDR estimation approach and additional identifications, particularly among low abundance proteins. IPM is now implemented as a part of the SPIRE system. |
| Databáze: | OpenAIRE |
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