Chapter 7: Bioinformatic Tools for the LC-MS/MS Analysis of Proteins and Peptides
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Published:22 Jul 2011
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Special Collection: 2011 ebook collection , 2011 ebook collection , 2011-2015 analytical chemistry subject collection
C. Webhofer and M. Schrader, in Protein and Peptide Analysis by LC-MS: Experimental Strategies, ed. T. Letzel, The Royal Society of Chemistry, 2011, ch. 7, pp. 87-103.
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Tandem mass spectrometry coupled to liquid chromatography became a major analytical method in protein and peptide analysis after soft ionization methods were introduced. Highly sophisticated software tools are available to interpret the wealth of information represented within MS/MS spectra.
First, we give a basic introduction to the principal functionality of MS/MS analysis for peptide identification. The identification of a tryptic E. coli peptide by database comparison is used as an example and may be traced by the reader.
Next, the much more complex procedure of automated LC-MS/MS protein quantification by 15N in vivo metabolic labelling is described using mouse tissue. Workflow and stepwise analysis, using different software tools, are explained in detail. In addition, we illustrate the first steps towards biological interpretation.
