title: Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS.
abstract: A new algorithm, sequence-specific retention calculator, was developed to predict retention time of tryptic peptides during RP HPLC fractionation on C18, 300-A pore size columns. Correlations of up to approximately 0.98 R2 value were obtained for a test library of approximately 2000 peptides and approximately 0.95-0.97 for a variety of real samples. The algorithm was applied in conjunction with an exclusion protocol based on mass (15 ppm tolerance) and retention time (2-min tolerance for 0.66% acetonitrile/min gradient), MART criteria to significantly reduce the instrument time required for complete MS/MS analysis of a digest separated by RP HPLC. This was confirmed by reanalyzing the set of HPLC-MALDI MS/MS data with no loss in protein identifications, despite the number of virtually executed MS/MS analyses being decreased by 57%.
authors.affiliation: Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada. krokhino@cc.umanitoba.ca
authors.forename: Oleg V
authors.initials: OV
authors.lastname: Krokhin
authors.forename: Stephen
authors.initials: S
authors.lastname: Ying
authors.forename: John P
authors.initials: JP
authors.lastname: Cortens
authors.forename: Dhiman
authors.initials: D
authors.lastname: Ghosh
authors.forename: Victor
authors.initials: V
authors.lastname: Spicer
authors.forename: Werner
authors.initials: W
authors.lastname: Ens
authors.forename: Kenneth G
authors.initials: KG
authors.lastname: Standing
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Beavis
authors.forename: John A
authors.initials: JA
authors.lastname: Wilkins
mesh_terms: D045744:Cell Line, Tumor; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D007477:Ions / Q000737:chemistry; D009862:Online Systems; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*; D013997:Time Factors
chemical_list: D007477:Ions; D010455:Peptides; D011506:Proteins