LabKey's proteomics tools support loading quantitation output for analysis from XPRESS, Q3, and Libra. If ProteinProphet processes the quantitation and rolls it up at the protein level, LabKey Server will also import that data.

When using LabKey Server to kick off searches, you can add the following snippet to your tandem.xml settings to run XPRESS:

<note label="pipeline quantitation, residue label mass" type="input">9.0@C</note>

Whether LabKey Server initiated the search or not, as long as the quantitation data is in the .pep.xml file at the time of import, LabKey Server will load the data.

Add Quantitation Columns

When viewing runs with quantitation data, you will want to add the columns that hold the quantitation data.

Add Peptide Quantitation Columns

  • Navigate to the run you would like to modify.
  • In the Peptides section, select Grid Views > Customize Grid
    • To add XPRESS or Q3 peptide quantitation columns, expand the Quantitation node.
    • To add Libra peptide quantitation columns, expand the iTRAQ Quantitation node.
  • Choose columns.
  • Save the grid.

Add Protein Quantitation Columns

  • Navigate to the run you would like to modify.
  • In the Peptides section, select Grid Views > ProteinProphet.
  • Then Grid Views > Customize Grid.
  • Open the nodes Protein Prophet Data > Protein Group > Quantitation or iTRAQ Quantitation.
  • Choose columns.
  • Save the grid.

To view the elution profile for a peptide, click on the peptide's sequence or scan number. You can click to view other charge states, and for XPRESS quantitation you can edit the elution profile to change the first and last scans. LabKey Server will recalculate the areas and update the ratios for the peptide, but currently will not bubble up the changes to the protein group quantitation.

Excluding Specific Peptides from Quantitation Results

If you have XPRESS or Q3 quantitation data, you can exclude specific peptides from the quantitation results. The server will automatically recalculate the rollup quantitation values at the protein group level. Follow these steps:

Exclude Specific Peptides

  • Add the peptide quantitation columns (see above).
  • Navigate to the peptide you would like to exclude. (Expand a particular protein record to see the peptides available and then click the name of the peptide.)
  • On the peptide's details page, scroll down and click the Invalidate Quantitation Results button.
  • Refresh the run page and note that the peptide's Invalidated column now has the value "true" and the quantitation rollup values for the protein have been recalculated.

Include a Previously Excluded Peptide

  • To include a previously excluded peptide, navigate to the peptide's details page, and click the Revalidate Quantitation Results button.

Related Topics

Label-Free Quantitation

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