This project and its two subfolders (demoset and ms1ms2matching ) contain sample data loaded into LabKey/CPAS to illustrate label-free quantitation approaches. This data was published with the PEPPeR study from the Broad Institute; see the details page for a description of the data sets and acknowlegement of the sources.
"MS2" (MS/MS) analysis searches were done on all 50 mzXML files using the same X!Tandem search parameters, followed by running the TPP tools PeptideProphet, XPRESS, and ProteinProphet.
The demoset folder demonstrates a label-free approach using spectra counts. In that folder are 50 MS2 runs, evenly divided into an Alpha group and a Beta group based on the input sample. (For a complete description of this example, see the documentation topic on label-free quantitation. )In this folder is a 6-run subset from the same two samples, shown in the list below.
To demonstrate spectral counting using either the 6-run set or the 50-run set, do the following:
The documentation topic on the ms1/ms2 matching approach to this example data has not yet been written, but the underlying MS1 facilities are documented under the topic MS1 Pipelines .