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IsoTopics™ – November 2016

Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue.

Described here is the rigorous development and application of highly multiplexed assays for the in-depth quantitation of hundreds of proteins in mouse plasma and heart tissue samples. The method features a targeted MRM approach with stable isotope-labeled peptides used as internal standards. The validated assays have disease relevance and association to biological/molecular processes, and are suitable for molecular phenotyping as well as biomarker assessment studies. A collection of the validated plasma assays have been assembled into a quality control (QC) and a biomarker assessment kit (BAK) for the research community. The PeptiQuant™ BAK-81, for example, enables 81 proteins spanning a four order of magnitude concentration range to be quantified in mouse plasma samples through bottom-up LC-MRM/MS and a reverse standard curve approach.


The mouse is the most commonly used laboratory animal, with more than 14 million mice being used for research each year in North America alone. The number and diversity of mouse models is increasing rapidly through genetic engineering strategies, but detailed characterization of these models is still challenging because most phenotypic information is derived from time-consuming histological and biochemical analyses. To expand the biochemists' toolkit, we generated a set of targeted proteomic assays for mouse plasma and heart tissue, utilizing bottom-up LC/MRM-MS with isotope-labeled peptides as internal standards. Protein quantitation was performed using reverse standard curves, with LC-MS platform and curve performance evaluated by quality control (QC) standards. The assays comprising the final panel (101 peptides for 81 proteins in plasma; 227 peptides for 159 proteins in heart tissue) have been rigorously developed under a fit-for-purpose approach and utilize stable-isotope labeled peptides for every analyte to provide high-quality precise relative quantitation. In addition, the peptides have been tested to be interference-free and the assay is highly multiplexed, with reproducibly determined protein concentrations spanning >4 orders of magnitude. The developed assays have been used in a small pilot study to demonstrate their application to molecular phenotyping or biomarker discovery/verification studies. This article is protected by copyright. All rights reserved.


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