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BMC Bioinformatics DOI:10.1186/1471-2105-13-S16-S9

Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.

Publication TypeJournal Article
Year of Publication2012
AuthorsMani, DR, Abbatiello, SE, Carr, SA
JournalBMC Bioinformatics
Volume13 Suppl 16
Date Published2012
KeywordsBiomarkers, Data Interpretation, Statistical, Indicator Dilution Techniques, Isotopes, Limit of Detection, Mass Spectrometry, Peptides, Proteins, Proteomics

Multiple reaction monitoring mass spectrometry (MRM-MS) with stable isotope dilution (SID) is increasingly becoming a widely accepted assay for the quantification of proteins and peptides. These assays have shown great promise in relatively high throughput verification of candidate biomarkers. While the use of MRM-MS assays is well established in the small molecule realm, their introduction and use in proteomics is relatively recent. As such, statistical and computational methods for the analysis of MRM-MS data from proteins and peptides are still being developed. Based on our extensive experience with analyzing a wide range of SID-MRM-MS data, we set forth a methodology for analysis that encompasses significant aspects ranging from data quality assessment, assay characterization including calibration curves, limits of detection (LOD) and quantification (LOQ), and measurement of intra- and interlaboratory precision. We draw upon publicly available seminal datasets to illustrate our methods and algorithms.


Alternate JournalBMC Bioinformatics
PubMed ID23176545
PubMed Central IDPMC3489552
Grant ListHHSN268201000033C / / PHS HHS / United States
R01 CA126219 / CA / NCI NIH HHS / United States
U24CA126476 / CA / NCI NIH HHS / United States