Quantitation: Average protocol
This is label-free, absolute quantitation for the proteins in a mixture based on the
application of a rule to the intensities of extracted ion chromatograms (XICs) for the
peptide matches in a database search result. The method is described in
Silva, J. C.,
et al., Absolute quantification of proteins by LCMSE - A virtue of parallel MS
acquisition, Molecular & Cellular Proteomics 5 144-156 (2006). The observation
was that the average MS signal response for
the three most intense tryptic peptides per mole of protein
was constant within a coefficient of variation of less than
±10%.
This protocol requires information from the raw data file that is not
present in the peak list, so the quantitation report is
generated in Mascot Distiller, which has access to both the Mascot
search results and the raw data.
More detailed information about quantitation reports for the average protocol
will be available as soon as the Mascot Distiller Quantitation Toolbox is released.
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