title: IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
abstract: 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.
authors: Bioinformatics & High-throughput Analysis Laboratory, Seattle, WA, USA. Roger.Higdon@seattlechildrens.org
authors: Roger
authors: R
authors: Higdon
authors: Lukas
authors: L
authors: Reiter
authors: Gregory
authors: G
authors: Hather
authors: Winston
authors: W
authors: Haynes
authors: Natali
authors: N
authors: Kolker
authors: Elizabeth
authors: E
authors: Stewart
authors: Andrew T
authors: AT
authors: Bauman
authors: Paola
authors: P
authors: Picotti
authors: Alexander
authors: A
authors: Schmidt
authors: Gerald
authors: G
authors: van Belle
authors: Ruedi
authors: R
authors: Aebersold
authors: Eugene
authors: E
authors: Kolker
mesh_terms: D030562:Databases, Protein; D005189:False Positive Reactions; D057166:High-Throughput Screening Assays / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D008956:Models, Chemical; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D011506:Proteins