Mass spectrometry has become a standard
method for the identification, quantification and characterization of
proteins present over a wide dynamic range in complex biological matrices.
To this end in practice proteins are most often digested into peptides,
measured by mass spectrometry and matched to known sequences through
algorithm-based searching. While instrumentation and bioinformatics
ultimately determine the depth of complexity in which a sample can be
measured, efficient digestion and high quality proteases are necessary to
produce an experimental data set that will maximize the potential for
correct identification and characterization. In this presentation we will
discuss several parameters from "the biological side" of protein analysis to
help get the most out of protein identification and characterization
experiments. The focus will be on the complimentary use of proteases and
conditions for their use.
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