The Spectra Count option on the Compare menu the MS2 Runs web part allows you to export summarized MS2 data from multiple runs. This export format is easy to work with in an external tool such as Microsoft Excel or a scripting language such as R.

A common application for such views is label-free quantitation. The object of which is to assess the relative quantities of identified proteins in two different samples. As the name implies, this technique does not require the input samples to be differentially labeled, as they are in an ICAT experiment for example. Instead, label-free quantitation involves using many MS2 runs of each of the same paired samples. Then the number of times a given peptide is identified by the search engine is statistically analyzed to determine whether there are any significant differences seen between the runs from the two different samples.






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