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dc.contributor.authorAlghanem, Bandar
dc.contributor.authorNikitin, Frederic
dc.contributor.authorStricker, Thomas
dc.contributor.authorDuchoslav, Eva
dc.contributor.authorLuban, Jeremy
dc.contributor.authorStrambio-De-Castillia, Caterina
dc.contributor.authorMuller, Markus
dc.contributor.authorLisacek, Frederique
dc.contributor.authorVaresio, Emmanuel
dc.contributor.authorHopfgartner, Gerard
dc.date2022-08-11T08:10:18.000
dc.date.accessioned2022-08-23T17:03:41Z
dc.date.available2022-08-23T17:03:41Z
dc.date.issued2017-05-15
dc.date.submitted2018-05-10
dc.identifier.citation<p>Rapid Commun Mass Spectrom. 2017 May 15;31(9):753-761. doi: 10.1002/rcm.7839. <a href="https://doi.org/10.1002/rcm.7839">Link to article on publisher's site</a></p>
dc.identifier.issn0951-4198 (Linking)
dc.identifier.doi10.1002/rcm.7839
dc.identifier.pmid28199054
dc.identifier.urihttp://hdl.handle.net/20.500.14038/44482
dc.description.abstractRATIONALE: In peptide quantification by liquid chromatography/mass spectrometry (LC/MS), the optimization of multiple reaction monitoring (MRM) parameters is essential for sensitive detection. We have compared different approaches to build MRM assays, based either on flow injection analysis (FIA) of isotopically labelled peptides, or on the knowledge and the prediction of the best settings for MRM transitions and collision energies (CE). In this context, we introduce MRMOptimizer, an open-source software tool that processes spectra and assists the user in selecting transitions in the FIA workflow. METHODS: MS/MS spectral libraries with CE voltages from 10 to 70 V are automatically acquired in FIA mode for isotopically labelled peptides. Then MRMOptimizer determines the optimal MRM settings for each peptide. To assess the quantitative performance of our approach, 155 peptides, representing 84 proteins, were analysed by LC/MRM-MS and the peak areas were compared between: (A) the MRMOptimizer-based workflow, (B1) the SRMAtlas transitions set used 'as-is'; (B2) the same SRMAtlas set with CE parameters optimized by Skyline. RESULTS: 51% of the three most intense transitions per peptide were shown to be common to both A and B1/B2 methods, and displayed similar sensitivity and peak area distributions. The peak areas obtained with MRMOptimizer for transitions sharing either the precursor ion charge state or the fragment ions with the SRMAtlas set at unique transitions were increased 1.8- to 2.3-fold. The gain in sensitivity using MRMOptimizer for transitions with different precursor ion charge state and fragment ions (8% of the total), reaches a ~ 11-fold increase. CONCLUSIONS: Isotopically labelled peptides can be used to optimize MRM transitions more efficiently in FIA than by searching databases. The MRMOptimizer software is MS independent and enables the post-acquisition selection of MRM parameters. Coefficients of variation for optimal CE values are lower than those obtained with the SRMAtlas approach (B2) and one additional peptide was detected.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=28199054&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://doi.org/10.1002/rcm.7839
dc.subjectAmino Acids, Peptides, and Proteins
dc.subjectBiochemistry
dc.subjectChemistry
dc.titleOptimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry
dc.typeJournal Article
dc.source.journaltitleRapid communications in mass spectrometry : RCM
dc.source.volume31
dc.source.issue9
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/pmm_pp/76
dc.identifier.contextkey12103875
html.description.abstract<p>RATIONALE: In peptide quantification by liquid chromatography/mass spectrometry (LC/MS), the optimization of multiple reaction monitoring (MRM) parameters is essential for sensitive detection. We have compared different approaches to build MRM assays, based either on flow injection analysis (FIA) of isotopically labelled peptides, or on the knowledge and the prediction of the best settings for MRM transitions and collision energies (CE). In this context, we introduce MRMOptimizer, an open-source software tool that processes spectra and assists the user in selecting transitions in the FIA workflow.</p> <p>METHODS: MS/MS spectral libraries with CE voltages from 10 to 70 V are automatically acquired in FIA mode for isotopically labelled peptides. Then MRMOptimizer determines the optimal MRM settings for each peptide. To assess the quantitative performance of our approach, 155 peptides, representing 84 proteins, were analysed by LC/MRM-MS and the peak areas were compared between: (A) the MRMOptimizer-based workflow, (B1) the SRMAtlas transitions set used 'as-is'; (B2) the same SRMAtlas set with CE parameters optimized by Skyline.</p> <p>RESULTS: 51% of the three most intense transitions per peptide were shown to be common to both A and B1/B2 methods, and displayed similar sensitivity and peak area distributions. The peak areas obtained with MRMOptimizer for transitions sharing either the precursor ion charge state or the fragment ions with the SRMAtlas set at unique transitions were increased 1.8- to 2.3-fold. The gain in sensitivity using MRMOptimizer for transitions with different precursor ion charge state and fragment ions (8% of the total), reaches a ~ 11-fold increase.</p> <p>CONCLUSIONS: Isotopically labelled peptides can be used to optimize MRM transitions more efficiently in FIA than by searching databases. The MRMOptimizer software is MS independent and enables the post-acquisition selection of MRM parameters. Coefficients of variation for optimal CE values are lower than those obtained with the SRMAtlas approach (B2) and one additional peptide was detected.</p>
dc.identifier.submissionpathpmm_pp/76
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.contributor.departmentProgram in Molecular Medicine
dc.source.pages753-761


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