The following table describes the columns on the Decoy Peptide Groups page.

Decoy Peptide Groups page columns

Column

Description

# Missed Cleavages

Displays the number of cleavage sites in a peptide sequence that a cleavage reagent (enzyme) did not cleave. This number excludes cases where an amino acid such as proline inhibits the cleaving enzyme. For example, if proline resides next to lysine or arginine, trypsin does not cleave the lysine or arginine. The application returns a 0 value for the # Missed Cleavages when all peptides have been completely digested.

# Protein Groups

Displays the number of decoy protein groups containing the peptide.

# Proteins

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

# PSMs

Displays the total number of identified peptide sequences (peptide spectrum matches) in the decoy peptide group, including those redundantly identified.

Charge (by Search Engine)

Displays the charge state of the peptide.

Checked

Indicates whether the item is selected.

Concatenated Rank (by Search Engine)

Displays the value for the “best” PSM that the search engine found. This value includes the rank of the normal PSMs for the same spectra.

Confidence

Indicates a confidence level associated with the decoy peptide group at the top level: green for high confidence, yellow for medium confidence, and red for low confidence.

Confidence (by Search Engine)

Indicates a confidence level associated with the peptide group at the top level: green for high confidence, yellow for medium confidence, and red for low confidence.

Dm/z [Da] (by Search Engine)

Displays the difference between the measured charged mass (m/z [Da]) and the theoretical mass of the same charge (z).

Modifications

Displays the modification found in the PSMs of the peptide group.

Modifications (All Possible Sites)

Displays the modifications found in the PSMs of the protein.

Percolator PEP (by Search Engine)

Displays the posterior error probability (PEP) of the best PSM of the peptide group that the search node identified.

This column appears when the consensus workflow includes the Percolator node. For information on how this node calculates the posterior error probability, see Percolator node .

Percolator q-Value (by Search Engine)

Display the q-Value by each search engine.

Percolator SVM_Score (by Search Engine)

Displays the maximum Percolator score for the identified decoy peptide group.

This column appears when the consensus workflow includes the Peptide Validator node. For information about this node, see Peptide Validator node.

Protein Accessions

Displays the unique identifiers (accessions) of all proteins from all protein groups that include the given peptide sequence.

The identifiers displayed in the Protein Group Accessions column are the same as those displayed in the Accession column on the Proteins and PSMs pages.

PSM Ambiguity

Displays the grouping status of the PSM in the decoy peptide group from the following:

  • Unambiguous: This PSM is the only match that the application considered for this spectrum. There is no ambiguity that it needs to resolve.
  • Selected: The application selected this PSM from a set of two or more matches that it considered for the protein group inference process.
  • Rejected: The application rejected this PSM from a set of two or more matches that it considered for the protein group inference process.
  • Ambiguous: The application considered two or more peptide matches to the same spectrum for the protein group inference process. If you set the Apply Strict Parsimony Principle parameter of the Protein Grouping node to True, the application resolves this ambiguity to Selected or Rejected.
  • Unconsidered: The application did not consider this PSM for the protein group inference process because it did not meet the requirements specified by the settings of the Protein Grouping node.

For more information on the protein group inference process that the application uses to assign the grouping status of PSMs, see Understanding protein grouping.

Quality PEP

Displays the posterior error probability (PEP) for the identified peptide group.

This column appears when the consensus workflow includes the Peptide Validator node. For information on how this node calculates the posterior error probability, see Peptide Validator node.

Quality q-value

Displays the q-value for the identified peptide group.

This column appears when the consensus workflow includes the Peptide Validator node. For information on how this node calculates the q-value, see Peptide Validator node.

Rank (by Search Engine)

Displays the ordering of peptides by rank.

Search Engine Rank (by Search Engine)

Displays the original rank that the search engine assigned to all PSMs and peptide groups.

Sequence

Displays the sequence of amino acids that compose the peptide in the decoy peptide group.

Sequence Length

Displays the number of amino acids in a sequence.

Theo. MH+ [Da]

Displays the mass calculated from the sequence, the amino acid masses, and the defined modification masses, as opposed to the measured mass.

DCn (by Search Engine)

Displays the normalized score difference between the currently selected PSM and the highest-scoring PSM for that spectrum.

DM [ppm] (by Search Engine)

Displays the difference between the theoretical mass of the peptide and the experimental mass of the precursor ion, in parts per million.

Dm/z [Da] (by Search Engine)

Displays the mass-to-charge ratio of the precursor ion, in daltons.