Posted by Web Master (February 16, 2009)

Larger searches permitted on free public Mascot Server

The IBM BladeCenterTM on this site has been upgraded with new blades containing dual 2.83 GHz quad core E5440 processors and 8 GB memory. This increased capacity has allowed us to raise the limit on the number of spectra in a single MS/MS search from 300 to 1200. Of course, this is still an artificially low limit, designed to ensure that as many people as possible can submit searches in peak hours. If you need to submit larger searches, the answer is to license a copy of Mascot to run in-house. Even a 1 cpu licence can handle searches of 1,000,000 spectra.

We have also decided to remove the facility to run no-enzyme searches from the public guest account. This is because no-enzyme searches take 100 times longer than searches with tryptic specificity. In most cases, there is no value in running a no-enzyme search because a semi-specific enzyme, such as semiTrypsin, will do a better job of picking up the occasional non-specific cleavage product. If you are working with samples that are not the result of digestion with a known enzyme, e.g. endogenous peptides, and need to evaluate Mascot with such data, please email to make a special arrangement.

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