Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

Citations Over TimeTop 10% of 2012 papers

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.

Related Papers

• → Mass Spectra of β-Keto Esters(1972)3 cited
• → Mass spectra of bithiophthalide and related compounds(1971)11 cited
• → Fragmentation in doubly charged ion mass spectra of anhydropisatin and related compounds(1976)4 cited
• → Structure Analysis of High Molecular Organic Compounds with their Fragment Ions produced by Electron Impact(1964)
• → Mass spectra of cyclodipeptides.(1984)