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Statistical Characterization of MRM-MS Assays for Quantitative Proteomics

Published: Friday, November 30, 2012
Last Updated: Friday, November 30, 2012
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MRM-MS assays are increasingly being deployed to measure and quantify peptides and proteins, this article provides a complete toolkit for the analysis and interpretation of MRM-MS experiments.

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 inter-laboratory precision. We draw upon publicly available seminal datasets to illustrate our methods and algorithms.

The article is published online in the journal BMC Bioinformatics and is free to access.  

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