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Protein Identification Protocol

For general methods and basics on protein identification by mass spectrometry, please review the following articles:

  1. Peptide mass fingerprinting. Bernd Thiede, Wolfgang Höhenwarter, Alexander Krah, Jens Mattow,
    Monika Schmid, Frank Schmidt, Peter R. Jungblut. Methods 35 (2005) 237-247
  2. Protein identification using MS/MS data. John S. Cottrell doi:10.1016/j.jprot.2011.05.014
  3. Current Chemical tagging strategies for proteome analysis by mass spectrometry. Alexander Leitner and Wolfgang Lindner. jopurnal of chromatography doi:10.1016/j.jchromb.2004.09.057 

MALDI data acquisition

ESI MS data acquisition

MudPIT data acquisition

Data analysis

  • Local Search engines: MASCOT, SEQUEST (BioWorks Browser and Proteome Discoverer), OMSSA, X!Tandem and PEAKS
  • MaxQuant and PEAKS for protein quantitation.
  • DHX MS analysis: HDExaminer, HDXFinder and MagTran (for manual analysis)
Mass Spectrometry/Proteomics Core Laboratory

University of Kansas Medical Center
Mass Spectrometry/Proteomics Core Laboratory
1058 Hemenway
3901 Rainbow Boulevard
Kansas City, Kansas 66160