We describe the application of capillary liquid chromatography (LC) time-of-flight (TOF) mass spectrometric instrumentation for the rapid characterization of microbial proteomes. Previously (Lipton et al. Proc. Natl Acad. Sci. USA, 99, 2002, 11049) the peptides from a series of growth conditions of Deinococcus radiodurans have been characterized using capillary LC MS/MS and accurate mass measurements which are logged in a accurate mass and time (AMT) tag database. Using this AMT tag database, detected peptides can be assigned using measurements obtained on a TOF due to the additional use of elution time data as a constraint. When peptide matches are obtained using AMT tags (i.e. using both constraints) unique matches of a mass spectral peak occurs 88% of the time. Not only are AMT tag matches unique in most cases, the coverage of the proteome is high; ~3500 unique peptide AMT tags are found on average per capillary LC run. From the results of the AMT tag database search, ~900 ORFs detected using LC-TOFMS, with ~500 ORFs covered by at least two AMT tags. These results indicate that AMT databases searches with modest mass and elution time criteria can provide proteomic information for approximately one thousand proteins in a single run of
Revised: November 10, 2005 |
Published: September 1, 2003
Citation
Strittmatter E.F., P.L. Ferguson, K. Tang, and R.D. Smith. 2003.Proteome Analyses Using Accurate Mass and Elution Time Peptide Tags with Capillary LC Time-of-Flight Mass Spectrometry.Journal of the American Society for Mass Spectrometry 14, no. 9:980-991.PNNL-SA-38208.