Proteomic data mining using predicted peptide chromatographic retention times.
Correct identification of proteins from peptide fragments is important for proteomic analyses. Peptides are initially separated by Reversed-Phase High-Performance Liquid Chromatography (RP-HPLC) before Mass Spectrometry (MS) identification. At the present time, peptide fragment retention (separation) time is not used as a useful scoring filter for identification of the peptide fragments and their parent proteins. In the present paper, we present a new web-based tool for the prediction of peptide fragment retention times and its use in compiling a database of approximately 133,000 peptide fragments computationally obtained by digestion with trypsin of 4,265 E. coli - K12 proteins. The retention calculation is based on the described formulae and the fragments/protein identification was carried out using a simple search-scoring algorithm.
Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA. brian.tripet@uchsc.edu
Brian
B
Tripet
Megha
M
Renuka Jayadev
Don
D
Blow
Cao
C
Nguyen
Robert
R
Hodges
Krzysztof
K
Cios
D000595:Amino Acid Sequence; D002845:Chromatography / Q000379:methods*; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry*; D013058:Mass Spectrometry / Q000379:methods; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D013997:Time Factors; D014357:Trypsin / Q000494:pharmacology
D029968:Escherichia coli Proteins; D010455:Peptides; D014357:Trypsin