Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes.

ABSTRACT: In-depth, reproducible coverage of complex proteomes is challenging because the complexity of tryptic digests subjected to LC-MS/MS analysis frequently exceeds mass spectrometer analytical capacity, which results in undersampling of data. In this study, we used cancer cell lysates to systematically compare the commonly used GeLC-MS/MS (1-D protein + 1-D peptide separation) method using four repetitive injections (2-D/repetitive) with a 3-D method that included solution isoelectric focusing and involved an equal number of LC-MS/MS runs. The 3-D method detected substantially more unique peptides and proteins, including higher numbers of unique peptides from low-abundance proteins, demonstrating that additional fractionation at the protein level is more effective than repetitive analyses at o

SUBMITTER: Wang H 

PROVIDER: S-EPMC2870931 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature