title: Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification.
abstract: Fourier transform-all reaction monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ions against every fragmentation spectrum across the entire acquisition. A dot product score is calculated against each spectrum to generate a score chromatogram used for both identification and quantification. Chromatographic elution profile characteristics are not used to cluster precursor peptide signals to their respective fragment ions. FT-ARM identifications are demonstrated to be complementary to conventional data-dependent shotgun analysis, especially in cases where the data-dependent method fails because of fragmenting multiple overlapping precursors. The sensitivity, robustness, and specificity of FT-ARM quantification are shown to be analogous to selected reaction monitoring-based peptide quantification with the added benefit of minimal assay development. Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides.
authors.affiliation: Department of Genome Sciences, University of Washington , 815 Mercer Street, Seattle, Washington 98109, United States.
authors.forename: Chad R
authors.initials: CR
authors.lastname: Weisbrod
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.forename: Michael R
authors.initials: MR
authors.lastname: Hoopmann
authors.forename: Tahmina
authors.initials: T
authors.lastname: Baker
authors.forename: James E
authors.initials: JE
authors.lastname: Bruce
mesh_terms: D000595:Amino Acid Sequence; D029968:Escherichia coli Proteins / Q000737:chemistry; D005583:Fourier Analysis; D057230:Limit of Detection; D016014:Linear Models; D008969:Molecular Sequence Data; D008970:Molecular Weight; D010446:Peptide Fragments / Q000737:chemistry*; D010449:Peptide Mapping / Q000379:methods* / Q000592:standards; D020543:Proteome / Q000737:chemistry; D012015:Reference Standards; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D012710:Serum Albumin, Bovine / Q000737:chemistry; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods* / Q000592:standards
chemical_list: D029968:Escherichia coli Proteins; D010446:Peptide Fragments; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D012710:Serum Albumin, Bovine