Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry- based Assay Development Using a Fit- for- Purpose Approach

• Type of Material: Article
• Authors: Steve A. Carr, Broad Institute of MIT and Harvard; Susan E. Abbatiello, Broad Institute of MIT and Harvard; Bradley L. Ackermann, Eli Lilly and Company; Christoph Borchers, University of Victoria; Bruno Domon, Luxembourg Clinical Proteomics Center; Eric W. Deutsch, Institute for Systems Biology; Russell P. Grant, Laboratory Corporation of America® Holdings; Andrew N. Hoofnagle, University of Washington; Ruth Huettenhain, Institute of Molecular Systems Biology; James Ritchie, Emory University
• Language: English
• Date: 2014-03-01
• Publisher: American Society of Biochemistry Molecular Biology Inc.
• Publication Version: Final Published Version
• Copyright Statement: © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
• Final Published Version (URL): http://dx.doi.org/10.1074/mcp.M113.036095
• Title of Journal or Parent Work: Molecular and Cellular Proteomics
• Volume: 13
• Issue: 3
• Start Page: 907
• End Page: 917
• Grant/Funding Information: This work was supported in part by the Broad Institute of MIT and Harvard and by the following grants from the US National Institutes of Health: grant U24CA160034 from the National Cancer Institute Clinical Proteomics Tumor Analysis Consortium Initiative (to S.A.C.) and grants HHSN268201000033C and R01HL096738 from the National Heart, Lung, and Blood Institute (to S.A.C.)
• Keywords: BIOANALYSIS; LC-MS/MS ASSAY; Life Sciences & Biomedicine; Biochemistry & Molecular Biology; Science & Technology; VERIFICATION; INBORN-ERRORS; PROTEIN IDENTIFICATION DATA; BIOMARKER DISCOVERY; ABSOLUTE QUANTIFICATION; CLINICAL VALIDATION; QUANTITATIVE-ANALYSIS; PLASMA; Biochemical Research Methods
• Research Categories: Chemistry, Biochemistry

Abstract

Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.