The following table describes the columns on the Protein Groups page.

Protein Groups page columns

Column

Description

# Peptides

Displays the total number of peptides identified from all included searches for the master protein of the protein group.

# Proteins

Displays the total number of identified proteins in the protein group.

# PSMs

Displays the total number of peptide spectrum matches identified from all included searches for the master protein of the protein group. Includes those redundantly identified.

# Unique Peptides

Displays the number of unique peptide sequences identified from all included searches for the master protein of the protein group.

Checked

Indicates whether the item is selected.

Found in Files

Represents the best confidence of the PSMs of the protein that the application identified in the files:

  • Green: High confidence
  • Yellow: Medium confidence
  • Red: Low confidence
  • Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Files parameter to True.

Found in Fractions

Represents the best confidence of the PSMs of the protein that the application identified in the fractions:

  • Green: High confidence
  • Yellow: Medium confidence
  • Red: Low confidence
  • Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Fractions parameter to True.

Found in Sample Groups

Represents the best confidence of the PSMs of the protein that the application identified in the sample groups:

  • Green: High confidence
  • Yellow: Medium confidence
  • Red: Low confidence
  • Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.
  • Grey: n/a

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Sample Groups parameter to True.

Found in Samples

Represents the best confidence of the PSMs of the protein that the application identified in the samples:

  • Green: High confidence
  • Yellow: Medium confidence
  • Red: Low confidence
  • Blue: Found but unidentified PSM. Only the results from precursor ion quantification searches contain blue boxes.

This column appears only when you include the Data Distributions node in the consensus workflow and set its Show Found in Samples parameter to True.

Group Description

Displays a description of the master protein of the protein group.

Protein Group ID

Displays a simple number assigned to the protein group. All protein groups are enumerated.