DeMix workflow for efficient identification of cofragmented peptides in high resolution data-dependent tandem mass spectrometry.

ABSTRACT: Based on conventional data-dependent acquisition strategy of shotgun proteomics, we present a new workflow DeMix, which significantly increases the efficiency of peptide identification for in-depth shotgun analysis of complex proteomes. Capitalizing on the high resolution and mass accuracy of Orbitrap-based tandem mass spectrometry, we developed a simple deconvolution method of "cloning" chimeric tandem spectra for cofragmented peptides. Additional to a database search, a simple rescoring scheme utilizes mass accuracy and converts the unwanted cofragmenting events into a surprising advantage of multiplexing. With the combination of cloning and rescoring, we obtained on average nine peptide-spectrum matches per second on a Q-Exactive workbench, whereas the actual MS/MS acquisition rate was

SUBMITTER: Zhang B 

PROVIDER: S-EPMC4223503 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature