Estimating probabilities of peptide database identifications to LC-FTICR-MS observations

Proteome Science
Kevin K AndersonDon S Daly

Abstract

The field of proteomics involves the characterization of the peptides and proteins expressed in a cell under specific conditions. Proteomics has made rapid advances in recent years following the sequencing of the genomes of an increasing number of organisms. A prominent technology for high throughput proteomics analysis is the use of liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS). Meaningful biological conclusions can best be made when the peptide identities returned by this technique are accompanied by measures of accuracy and confidence. After a tryptically digested protein mixture is analyzed by LC-FTICR-MS, the observed masses and normalized elution times of the detected features are statistically matched to the theoretical masses and elution times of known peptides listed in a large database. The probability of matching is estimated for each peptide in the reference database using statistical classification methods assuming bivariate Gaussian probability distributions on the uncertainties in the masses and the normalized elution times. A database of 69,220 features from 32 LC-FTICR-MS analyses of a tryptically digested bovine serum albumin (BSA) sample was matched...Continue Reading

References

Apr 27, 2004·Omics : a Journal of Integrative Biology·Samuel PurvineEugene Kolker
Nov 3, 2004·BioTechniques·Ljiljana Pasa-TolićRichard D Smith
Jun 28, 2005·Journal of the American Society for Mass Spectrometry·Angela D NorbeckRichard D Smith
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates

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Citations

Aug 20, 2011·Bioinformatics·Melissa M MatzkeBobbie-Jo M Webb-Robertson
Mar 7, 2014·The Journal of Venomous Animals and Toxins Including Tropical Diseases·Jaya VejayanHalijah Ibrahim
Jan 1, 2009·Molecular & Cellular Proteomics : MCP·Benjamin RietschelAnsgar Poetsch
Oct 15, 2011·Electrophoresis·Carolina FernándezJosé-Luis Capelo-Martínez
Mar 6, 2008·Rapid Communications in Mass Spectrometry : RCM·Christophe D MasselonJérôme Garin
Apr 30, 2008·Journal of Proteome Research·Xiuxia DuMary S Lipton

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Software Mentioned

KKA
METMBS
SEQUEST
MEM
PRISM Data Analysis system
SEQUEST XCorr

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