Mass Spec Results Definitions

Source: Proteome Discoverer Version 1.4 User Guide

Protein Score

The sum of the ion scores of all peptides that were identified.

# PSM's

The number of peptide spectrum matches. The number of PSM's is the total number of identified peptide spectra matched for the protein.  The PSM value may be higher than the number of peptides identified for high-scoring proteins because peptides may be identified repeatedly.


The percentage of the protein sequence covered by identified peptides.

# Proteins

The number of identified proteins in a protein group, that is, the number of proteins displayed in the Protein Group Members view.

# Unique Peptides

The number of peptide sequences that are unique to a protein group.  These are the peptides that are common to the proteins of a protein group, and which do not occur in the proteins of any other group.  The number of unique peptides that determine a protein group can be set in Proteome Discoverer.

# Peptides

The total number of distinct peptide sequences identified in the protein group.


Xcorr (cross correlation) is a measure of the goodness of fit of experimental peptide fragments to theoretical spectra created from the sequence b and y ions.

Delta CN

Delta Correlation is a measure of the specificity of the fit.  It describes how much better the primary candidate's sequence fits the experimental data vs. the secondary candidate's sequence.  A smaller number implies a better fit.

Delta M (ppm)

Delta Mass is the deviation of the measured mass from the theoretical mass of the peptide, in ppm.

q Value

q value is the minimal false discovery rate at which the identification is considered correct.

Posterior Error Probability (PEP)

The posterior error probability (PEP) is the probability that the observed PSM is incorrect.