Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification

J Proteome Res. 2012 Mar 2;11(3):1621-32. doi: 10.1021/pr2008175. Epub 2012 Feb 21.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Escherichia coli Proteins / chemistry
  • Fourier Analysis
  • Limit of Detection
  • Linear Models
  • Molecular Sequence Data
  • Molecular Weight
  • Peptide Fragments / chemistry*
  • Peptide Mapping / methods*
  • Peptide Mapping / standards
  • Proteome / chemistry
  • Reference Standards
  • Saccharomyces cerevisiae Proteins / chemistry
  • Serum Albumin, Bovine / chemistry
  • Software*
  • Tandem Mass Spectrometry / methods*
  • Tandem Mass Spectrometry / standards


  • Escherichia coli Proteins
  • Peptide Fragments
  • Proteome
  • Saccharomyces cerevisiae Proteins
  • Serum Albumin, Bovine