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

• Main Authors: Mani D R, Abbatiello Susan E, Carr Steven A
• Format: Article
• Language: English
• Published: BMC 2012-11-01
• Series: BMC Bioinformatics
• Subjects: Multiple reaction monitoring mass spectrometry (MRM-MS); stable isotope dilution (SID); quantification; interference detection; limits of detection and quantification; intra- and interlaboratory precision
• Online Access: http://www.biomedcentral.com/1471-2105/13/S16/S9

<p>Abstract</p> <p>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.</p>