Targeted mass spectrometry assays for protein quantitation monitor peptide surrogates, which are easily multiplexed to target many peptides in a single assay. However, these assays have generally not taken advantage of sample multiplexing, which allows up to ten analyses to occur in parallel. We present a two-dimensional multiplexing workflow that utilizes synthetic peptides for each protein to prompt the simultaneous quantification of >100 peptides from up to ten mixed sample conditions. We demonstrate that targeted analysis of unfractionated lysates (2 hr) accurately reproduces the quantification of fractionated lysates (72 hr analysis) while obviating the need for peptide detection prior to quantification. We targeted 131 peptides corresponding to 69 proteins across all 60 National Cancer Institute cell lines in biological triplicate, analyzing 180 samples in only 48 hr (the equivalent of 16 min/sample). These data further elucidated a correlation between the expression of key proteins and their cellular response to drug treatment.
Erickson, Brian KRose, Christopher MBraun, Craig RErickson, Alison RKnott, JeffreyMcAlister, Graeme CWuhr, MartinPaulo, Joao AEverley, Robert AGygi, Steven PP50 GM107618/GM/NIGMS NIH HHS/K01 DK098285/DK/NIDDK NIH HHS/R01 GM103785/GM/NIGMS NIH HHS/R01 GM067945/GM/NIGMS NIH HHS/U54 HL127365/HL/NHLBI NIH HHS/Mol Cell. 2016 Dec 21. pii: S1097-2765(16)30818-8. doi: 10.1016/j.molcel.2016.12.005.