Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms.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)). 
LC-MS/MS
Data are available via ProteomeXchange with identifiers PXD004682, PXD004683, PXD004684, and PXD005733.
ProteomeXchange