An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies

ABSTRACT: Phosphorylation-mediated signaling pathways have major implications in cellular regulation and disease. Mass spectrometry-based proteomics is a well-established approach for quantifying thousands of phosphorylation events in a single experiment. However, proteins with roles in signaling pathways are frequently less abundant and phosphorylation is often sub-stoichiometric. As such, the efficient enrichment and subsequent recovery of phosphorylated peptides is vital. To understand better phosphopeptide recovery from enrichment strategies, we designed a peptide internal standard-based assay directed toward sample preparation strategies for mass spectrometry analysis. We coupled mass-differential tandem mass tag (mTMT) reagents (specifically, TMTzero and TMTsuper-heavy), nine mass spectrometry-amenable phosphopeptides (phos9), and peak area measurements from extracted ion chromatograms to determine phosphopeptide recovery. We showcase this mTMT/phos9 recovery assay by evaluating three commercial phosphopeptide enrichment workflows. Our assay provides data on the recovery of phosphopeptides, which complement other metrics, namely the number of identified phosphopeptides and enrichment specificity. Our mTMT/phos9 assay is applicable to any enrichment protocol in a typical experimental workflow irrespective of sample origin or labeling strategy.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Joao Paulo  

LAB HEAD: Joao A. Paulo

PROVIDER: PXD008966 | Pride | 2018-12-04

REPOSITORIES: Pride