Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Posted by Web Master (March 30, 2020)

New databases and greater maximum search size

We want to make this public Mascot Server as useful as possible to people having to work remotely during the current emergency.

First of all, the limit on the number of spectra in an individual MS/MS search is being increased from 1200 spectra to 20,000 spectra.

Secondly, for the vast majority of searches, the appropriate Uniprot proteome plus a contaminants database gives the most meaningful results with the best sensitivity. We have added 18 Uniprot proteomes, covering the organisms most commonly used in proteomics projects. If your organism of interest is missing, and Uniprot has a proteome with at least 75% coverage, please contact us to request that it be added.

We have also added the Uniprot pre-release database of protein sequences for the SARS-CoV-2 virus. This database will be updated whenever a new version is available.

These changes require us to drop one of the sequence databases. A great deal of processing time is currently spent on searches of NCBIprot, the NCBI non-identical protein database. This gigantic collection should be the database of last resort, for use when the target sequences cannot be found in a more selective database. Unfortunately, we see many searches on this site of PMFs and poor quality MS/MS data against the entire NCBIprot that cannot possibly give statistically meaningful results. We have decided that NCBIprot will only be available on special request. Contact us to explain why none of the other databases are suitable for your searches, and we can provide a temporary login to enable access to NCBIprot.

(If you have an in-house Mascot Server, the above restrictions do not apply. NCBIprot, the 18 UniProt proteomes and the pre-release SARS-CoV-2 database are pre-defined in Database Manager, so that any of them can be enabled with a couple of mouse clicks.)

If you have any suggestions for further improvements, please don’t hesitate to get in touch.

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