Assessment of current mass spectrometric workflows for the quantification of low abundant proteins and phosphorylation sites.

ABSTRACT: The data described here provide a systematic performance evaluation of popular data-dependent (DDA) and independent (DIA) mass spectrometric (MS) workflows currently used in quantitative proteomics. We assessed the limits of identification, quantification and detection for each method by analyzing a dilution series of 20 unmodified and 10 phosphorylated synthetic heavy labeled reference peptides, respectively, covering six orders of magnitude in peptide concentration with and without a complex human cell digest background. We found that all methods performed very similarly in the absence of background proteins, however, when analyzing whole cell lysates, targeted methods were at least 5-10 times more sensitive than directed or DDA methods. In particular, higher stage fragmentation (MS3) of

SUBMITTER: Bauer M 

PROVIDER: S-EPMC4596922 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature