Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms.

ABSTRACT: Discovery proteomics experiments include many options for sample preparation and MS data acquisition, which are capable of creating datasets for quantifying thousands of proteins. To define a strategy that would produce a dataset with sufficient content while optimizing required resources, we compared (1) single-sample LC-MS/MS with data-dependent acquisition to single-sample LC-MS/MS with data-independent acquisition and (2) peptide fractionation with label-free (LF) quantification to peptide fractionation with relative quantification of chemically labeled peptides (sixplex tandem mass tags (TMT)). These strategies were applied to the same set of four frozen lung squamous cell carcinomas and four adjacent tissues, and the overall outcomes of each experiment were assessed. We identified 66

SUBMITTER: Stewart PA 

PROVIDER: S-EPMC5606153 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature