{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Weisbrod CR"],"funding":["NCRR NIH HHS","NIGMS NIH HHS"],"pagination":["1621-32"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC3319072"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(3)"],"pubmed_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."],"journal":["Journal of proteome research"],"pubmed_title":["Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification."],"pmcid":["PMC3319072"],"funding_grant_id":["S10 RR025107","R01 GM086688-03","R01 GM086688","1R01GM097112","S10 RR025107-02","7S10RR025107","R01 RR023334","R01 GM097112-01","5R01RR023334","R01 RR023334-04","R01 GM097112","5R01GM086688"],"pubmed_authors":["Hoopmann MR","Weisbrod CR","Eng JK","Bruce JE","Baker T"],"additional_accession":[]},"is_claimable":false,"name":"Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification.","description":"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.","dates":{"release":"2012-01-01T00:00:00Z","publication":"2012 Mar","modification":"2025-04-21T16:33:29.385Z","creation":"2019-03-27T00:51:56Z"},"accession":"S-EPMC3319072","cross_references":{"pubmed":["22288382"],"doi":["10.1021/pr2008175"]}}