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Proteomics. 2009 Nov;9(21):4834-6. doi: 10.1002/pmic.200900310.

Combining selected reaction monitoring with discovery proteomics in limited biological samples.

Author information

1
Department of Animal Biotechnology, Bio-Organ Research Center / Animal Resources Research Center, Institute of Bio-Science and Technology, Konkuk University, Hwayang-dong, Gwangjin-Gu, Seoul, South Korea.

Abstract

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.

PMID:
19810035
DOI:
10.1002/pmic.200900310
[Indexed for MEDLINE]

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