Journal
PROTEOMICS
Volume 9, Issue 21, Pages 4834-4836Publisher
WILEY
DOI: 10.1002/pmic.200900310
Keywords
Animal proteomics; MS; MS-data validation; Protein quantification; Selected reaction monitoring
Funding
- RDA [200901FHT010305191, 20070401034017]
- Institute of Biomedical Science and Technology of Konkuk University [IBST-2007-03-04]
- Ministry of Health and Welfare [A080611]
- Ministry of Education, Science and Technology, Republic of Korea [SC-2120]
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Simultaneous quantification of multiple proteins by selected reaction monitoring (SRM) has several applications in cell signaling studies including embryo proteomics. However, concerns have recently been raised over the specificity of SRM assays due to possible ion redundancy and/or sequence similarity of selected peptide with multiple non-related proteins. In this Viewpoint article, we discuss some simple measures that can increase our confidence in the accuracy of SRM scans used in proteomic experiments. At least in embryonic samples from porcine species, these measures were found to be useful in validating MS-identified differentially expressed proteins. Among the nine proteins analyzed by SRM assay, all the proteins that were found to be up- or down-regulated in MS experiment were also faithfully up- or down-regulated in SRM assay.
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