Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases.
It was also the first to take into account the non-uniform distribution of peptide sizes, caused by the enzymatic digestion of a protein that is needed for mass spectrometry analysis.
However, MOWSE was only applicable to peptide mass fingerprint searches and was dependent on pre-compiled databases which were inflexible with regard to post-translational modifications and enzymes other than trypsin.
To overcome these limitations, to take advantage of multi-processor systems and to add non-enzymatic search functionality, development was begun again from scratch by David Perkins at the Imperial Cancer Research Fund.
The program cleaves every protein in the specified search database in silico according to specific rules depending on the cleavage enzyme used for digestion and calculates the theoretical mass for each peptide.
Mascot employs the widely used significance level of 0.05, meaning that in a single test the probability of observing an event at random is less than or equal to 1 in 20.
[1] In addition to the calculated peptide scores, Mascot also estimates the False Discovery Rate (FDR) by searching against a decoy database.
The decoy matches are certain to be spurious identifications, but we can't discriminate between true and false positives identified in the target database.