Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
10825974 | Methods | 2013 | 12 Pages |
Abstract
Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow.
Keywords
FDRITRAQFWHMSISStable isotope-labeled internal standardMRMSISCAPAMudPITSRMNISTLC–MS/MSMS/MSDatabaseisobaric tag for relative and absolute quantitationBioinformaticsTandem MSELISAEnzyme-linked immunosorbent assayStable isotope dilutionSiDSILACCoefficient of VariationMass spectrometryPrideMultidimensional protein identification technologyNational Institute of Standards and Technologyfalse discovery ratestable isotope labeling by amino acids in cell cultureselective reaction monitoringmultiple reaction monitoringTargeted proteomics
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Authors
Christopher M. Colangelo, Lisa Chung, Can Bruce, Kei-Hoi Cheung,