title: Peptide Shifter: enhancing separation reproducibility using correlated expression profiles.
abstract: Chromatographic protein and peptide separation technologies enable comprehensive proteomic analysis of plasma and other complex biological samples by mass spectrometry. However, as the number of separations and/or fractions increases, so does the number of peptides split across fraction boundaries. Irreproducibility of peptide chromatographic separation results in peptides on or near the boundary moving partially or entirely into adjacent fractions. Peptide shifting across fraction boundaries increases the variability of measured peptide abundance, and so there is a trade-off between proteomic comprehensiveness using separation technologies and accurate quantitative proteomic measurements. In this paper, a method for detecting and correcting split peptides, called Peptide Shifter, is introduced and evaluated. An essential component of Peptide Shifter is a global peptide expression profile analysis that allows the inference of the underlying peptide shift pattern without the use of peptide labeling or internal standards. A controlled proteomic analysis of plasma samples demonstrates a 34% decrease in peptide intensity variability after the application of Peptide Shifter.
authors: Caprion Proteomics, Montreal, Quebec, Canada. dsitnikov@caprion.com
authors: Dmitri
authors: D
authors: Sitnikov
authors: Joanna M
authors: JM
authors: Hunter
authors: Clive
authors: C
authors: Hayward
authors: Kevin
authors: K
authors: Eng
authors: Isabelle
authors: I
authors: Migneault
authors: Sylvain
authors: S
authors: Tessier
authors: Gregory J
authors: GJ
authors: Opiteck
authors: Paul
authors: P
authors: Kearney
mesh_terms: D000465:Algorithms; D001774:Blood Chemical Analysis / Q000379:methods*; D001798:Blood Proteins / Q000032:analysis*; D002845:Chromatography / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000032:analysis*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013223:Statistics as Topic
chemical_list: D001798:Blood Proteins; D020543:Proteome
references: Brief Funct Genomic Proteomic. 2006 Jun;5(2):112-20
references: 16772272
references: J Exp Bot. 2005 Jan;56(410):219-43
references: 15618298
references: Proteomics. 2005 Aug;5(13):3246-61
references: 16104057
references: Proteomics. 2005 Aug;5(13):3226-45
references: 16104056
references: Mol Cell Proteomics. 2005 Oct;4(10):1487-502
references: 15979981
references: Anal Chem. 1985 Oct;57(12):2178-82
references: 4061834
references: Clin Immunol. 2004 May;111(2):186-95
references: 15137951
references: Mol Cell Proteomics. 2006 Apr;5(4):589-607
references: 16399765
references: Anal Chem. 2006 Apr 1;78(7):2286-96
references: 16579610
references: J Chromatogr. 1984 Apr 27;289:277-98
references: 6736157
references: Nat Biotechnol. 2001 Mar;19(3):242-7
references: 11231557
references: Mol Cell Proteomics. 2005 Sep;4(9):1328-40
references: 16048906
references: Mol Cell Proteomics. 2006 Jan;5(1):144-56
references: 16219938
references: Nat Biotechnol. 2001 Oct;19(10):946-51
references: 11581660
references: Anal Chem. 2005 Apr 1;77(7):2187-200
references: 15801753
references: Anal Chem. 1985 Oct;57(12):2168-77
references: 4061833
references: Cell Biochem Biophys. 2006;44(1):11-29
references: 16456231