Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification
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- 作者：Chad R. Weisbrod ; Jimmy K. Eng ; Michael R. Hoopmann ; Tahmina Baker ; James E. Bruce
- 刊名：Journal of Proteome Research
- 出版年：2012
- 出版时间：March 2, 2012
- 年：2012
- 卷：11
- 期：3
- 页码：1621-1632
- 全文大小：520K
- 年卷期：v.11,no.3(March 2, 2012)
- ISSN：1535-3907
文摘
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.