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Topic: databasee search with Protein Prospector MS-Tag

Hi Martin.

Thank you for keeping up the work at this great piece of software. I use it practically every day. =)

Recently I often need to do database searches to identify peptides from MS/MS spectra. Unfortunately the peptides are not generated by activity of a specific protease but rather through unspecific cleavages. The Mascot web tool offeres such a search option but only for paying customers and not for guest users since the computational load is much heavier compared with the use of specific proteases like trypsin.
The webpage of MS-Tag / Protein Prospector also features such a functionality. However, I can't find the corresponding entry in the mMass dialogue Tools -> Protein Prospector - MS-Tag -> Enzyme. According to the webpage it should read "No enzyme" and it is certainly different from "Full Protein". Is it possible to implement this function into the next version of mMass?

best wishes
Martin

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Re: databasee search with Protein Prospector MS-Tag

Hi Martin,
I'm happy to hear that you are every-day-user of mMass :-)

It should be easy to add such as parameter to the dialog. Unfortunately, Protein Prospector doesn't provide any sort of on-line list of available options for their parameters, so all the values has to be hard-coded inside mMass. For the Mascot that's completely different - they provide such a list so the form is always up-to-date. I'll update the form for the next version.

Best wishes,
Martin

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Re: databasee search with Protein Prospector MS-Tag

Great!
Thanks a lot!

best wishes,
Martin