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To specify which columns to display for protein results when viewing an MS2 run, use the guidance in this topic.

  • Navigate to the run you would like to work with.
  • In the Peptides section, select Grid Views > ProteinProphet.
  • Then Grid Views > Customize Grid.
  • In the Available Fields pane, select which columns to display in the current grid.
  • Click Save to name and save the grid.

The currently displayed columns appear in the Selected Fields pane. You can edit the columns that appear in this list manually for finely tuned control over which columns are displayed in what order.

Available Protein Columns

The following table describes some of the available protein columns. Not all columns are available for all data sets.

Protein ColumnColumn AbbrevDescription
Protein   The name of the sequence from the protein database.
SequenceMass   The mass of the sequence calculated by adding the masses of its amino acids.
Peptides PP Peps The number of filtered peptides in the run that were matched to this sequence.
UniquePeptides PP Unique The number of unique filtered peptides in the run that were matched to this sequence.
AACoverage   The percent of the amino acid sequence covered by the matched, filtered peptides.
BestName   A best name, either an accession number or descriptive word, for the identified protein.
BestGeneName   The most useful gene name associated with the identified protein.
Description   Short description of the protein’s nature and function.
GroupNumber Group A group number assigned to the ProteinProphet group.
GroupProbability Prob ProteinProphet probability assigned to the protein group.
PctSpectrumIds Spectrum Ids Percentage of spectrum identifications belonging to this protein entry.  As a semi-quantitative measure, larger numbers reflects higher abundance.
ErrorRate   The error rate associated with the ProteinProphet probability for the group.
ProteinProbability Prob ProteinProphet probability assigned to the protein(s).
FirstProtein   ProteinProphet entries can be composed of one or more indistinguishable proteins and are reflected as a protein group. This column represents the protein identifier, from the protein sequence database, for the first protein in a protein group.
FirstDescription   Protein description of the FirstProtein.
FirstGeneName   Gene name, if available, associated with the FirstProtein.
FirstBestName   The best protein name associated with the FirstProtein. This name may come from another protein database file.
RatioMean L2H Mean The light-to-heavy protein ratio generated from the mean of the underlying peptide ratios.
RatioStandardDev L2H StdDev The standard deviation of the light-to-heavy protein ratio.
RatioNumberPeptides Ratio Peps The number of quantified peptides contributing to the protein ratio.
Heavy2LightRatioMean H2L Mean The heavy-to-light protein ratio generated from the mean of the underlying peptide ratios.
Heavy2LightRatioStandardDev H2L StdDev The heavy-to-light standard deviation of the protein ratio.


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