What does the Mascot Score mean?

Oct 9. 2015


What does the Mascot Score mean?

I just got my protein identification report. Can you tell me what the Mascot Score means?


The Protein Identification report contains a list of proteins that were positively identified by a significant Mascot Score in the Mascot database search [1, 2].

For protein identification, the protein is typically first cleaved by trypsin, and then nanoLC-MS/MS analyzes the resulting peptides. The mass spectrometric data contain a list of the accurate peptide masses and peptide fragment masses. Using the Mascot database search software, these are searched against sequence databases containing known protein amino acid sequences. The Mascot Score is a statistical score for how well the experimental data match the database sequence [1, 2].

What makes a positive Mascot Protein identification?

The Mascot score for a protein is the summed score for the individual peptides, e.g., peptide masses and peptide fragment ion masses, for all peptides matching a given protein. The mascot score has to be above the 95% confidence level for positive protein identification. For a database search in the nrbd protein database from NCBI containing 18 million known protein sequences, the 95% confidence level is around a Score of 90 [1, 2].

The Mascot score is logarithmic. If you need more information, you can find a detailed description of it on the Matrix Science website (http://www.matrixscience.com/).

More information

If you want to learn more about mass spectrometric identification of proteins from 1D and 2D gels using mass spec, read here: Protein Identification

You may also want to check out this blog post on preparing samples for analysis to optimize how much protein you load onto the gel.

Increase protein concentration on PVDF membrane


[1]          Perkins et al.: “Probability-based protein identification by searching sequence databases using mass spectrometry data,” Electrophoresis, 1999

[2]          Koenig et al.Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics.“, Journal of Proteome Research, 2008

More posts about Database Searching & Protein Identification
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  • Speedy and detailed protein ID of SDS gel bands

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