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:

  1. Select the checkbox for "all runs in list" in the upper left of the MS2 Runs grid.
  2. Press the Compare button at the bottom of the grid.  Choose the "Spectra Count" option.
  3. Choose the third Grouping Option, "Peptide sequence, ProteinProphet protein assignment".
  4. Choose the middle filtering option, " All peptides with PeptideProphet probability >= " and fill in 0.75 as the value.
  5. Press go.
  6. When the result data set is visible, press the Views button and select DoExampleRunScoring.
  7. In this folder, the example spectra counting calculation will begin immediately.  In the demoset folder, the calculation runs as a pipeline job.  Press Start Job to start this, and wait for the job status messages.
  8. When the results are visible, scroll down to see the graph.
  9. To demonstrate the implementation of a published counting algorithm, try the DoSASPECT view in step 7. (There is no graph in the result.)

 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 .

MS2 Export
minTest/VARMIX_B_04 (kscorev5)2008-05-12 09:02AlphaMixSmallSetPepper12v4pluscRAPplusMouseIPI.fasta
minTest/VARMIX_M_02 (kscorev5)2008-05-12 09:02BetaMixSmallSetPepper12v4pluscRAPplusMouseIPI.fasta
minTest/VARMIX_M_04 (kscorev5)2008-05-12 09:02BetaMixSmallSetPepper12v4pluscRAPplusMouseIPI.fasta
minTest/VARMIX_N_03 (kscorev5)2008-05-12 09:02BetaMixSmallSetPepper12v4pluscRAPplusMouseIPI.fasta
minTest/VARMIX_B_03 (kscorev5)2008-05-12 09:02AlphaMixSmallSetPepper12v4pluscRAPplusMouseIPI.fasta
minTest/VARMIX_D_03 (kscorev5)2008-05-12 09:02AlphaMixSmallSetPepper12v4pluscRAPplusMouseIPI.fasta
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This list only shows protein lists that have been loaded into this folder. When constructing queries, annotations in the project are visible from all the folders in that project.
Protein name *?
Minimum prob?
Search in subfolders?
Exact matches only?