title: Combining selected reaction monitoring with discovery proteomics in limited biological samples.
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.
authors.affiliation: 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.
authors.forename: Mukesh Kumar
authors.initials: MK
authors.lastname: Gupta
authors.forename: Jin Woo
authors.initials: JW
authors.lastname: Jung
authors.forename: Sang Jun
authors.initials: SJ
authors.lastname: Uhm
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.forename: Hoon Taek
authors.initials: HT
authors.lastname: Lee
authors.forename: Kwang Pyo
authors.initials: KP
authors.lastname: Kim
mesh_terms: D000818:Animals; D004622:Embryo, Mammalian / Q000737:chemistry*; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D013552:Swine; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D011506:Proteins