Systematic comparison of a two-dimensional ion trap and a three-dimensional ion trap mass spectrometer in proteomics.

ABSTRACT: The utility and advantages of the recently introduced two-dimensional quadrupole ion trap mass spectrometer in proteomics over the traditional three-dimensional ion trap mass spectrometer have not been systematically characterized. Here we rigorously compared the performance of these two platforms by using over 100,000 tandem mass spectra acquired with identical complex peptide mixtures and acquisition parameters. Specifically we compared four factors that are critical for a successful proteomic study: 1) the number of proteins identified, 2) sequence coverage or the number of peptides identified for every protein, 3) the data base matching SEQUEST X(corr) and S(p) score, and 4) the quality of the fragment ion series of peptides. We found a 4-6-fold increase in the number of peptides and p

SUBMITTER: Mayya V 

PROVIDER: S-EPMC1487187 | biostudies-literature | 2005 Feb

REPOSITORIES: biostudies-literature