MassQC Help > Metrics > Identifications > Search Score          
Search Score

Search Score is the score assigned by the software (the search engine) that associates the spectra with the peptides.

Higher Search Scores correlate with a higher frequency of good identifications of peptides.

The Search Score metric depends upon the analysis method used when loading the standard sample. MassQC supports simple standard samples.

Simple standard samples > A common simple sample is BSA but in general simple samples have only a few proteins. For these samples, the analysis method specifies that the search engine will be OMSSA.

  • Search Score is the log of the OMSSA e-value.
  • The Search Score metric is the median search score for all peptides.

OMSSA has a standard threshold that all peptide to spectrum matches must pass before the peptide is considered identified.

Spectrum with a good search score.

This spectrum was given a good score by the search engine for matching to peptide TNWYDNGSNQVAFGR.

Spectra with poor search score

This spectrum was given a poor score by the search engine for matching to peptide TNWYDNGSNQVAFGR.


For OMSSA, the Search Score is the log of the e-value.


Higher: Good Search Scores correspond to peptides which are solidly identified.

The most reproducible LC-MS performance is when this metric remains in a narrow range over a series of runs. Wide variability in any metric means your process is not reproducible.

What the Metric Detects:

The Search Score tells how good the MS2 spectra are in the sense of how easily they are matched to peptides by a search engine. Low values of the Search Score may be caused by:

  • Contaminants which cause chemical noise and extra non-identifiable peaks in the spectrum
  • In-source decay which causes the b and y ion peaks used by search engines to fragment
  • Poor fragmentation which is seen as only a few peaks in the MS2 spectrum and is perhaps caused by incorrect collision energy
Related Metrics:

Spectra with high Search Scores are easily identified by search engines because they have a good MS2 Signal to Noise, have a reasonable number of Peaks per Spectrum and the major peaks in the MS spectrum are the fragment ion peaks of the peptide.

Related Troubleshooting Topics:

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