Hi,

I know mMass very well and the Mascot identification is very easy using this software. Just open your spectrum in mMass, process your spectrum (smoothing, baseline correction and peak picking) - it is in processing tab - and when your peaks are labelled just click either on Tools/Mascot PMF or ProFound. It will open dialog where you need to define search settings (mass tolerance, taxonomy etc.). Then click search and if the mascot server is selected it will automatically send your data to Matrix Science server a run the PMF search. 

If you want to open raw data, you will probably need converter (I have experience just with Bruker software). mMass should open simple ascii, mzXML and mzML formats whithout any need of converter.

Hope it helps,

Lukas

There also is a great screencast taking you through the whole process:

https://www.youtube.com/watch?v=RA44uq4JZH0

You should be able to process your files directly with mmass. If not you may get CompassXport from brukers home page (its free, but you'll have to register) and use it to convert the files.

Dear Jitendra,

Actually what you want to know???

Do you want to know molecular weight?

Do you want to know about peptide mass fingerprint similarity with other proteins?

or

You just want to identify your protein whether it is novel?

or

you want to deduce the amino acid sequence using the MS/MS (tandem MS) data.?

Please let me know what is exact query.

I have done such type of work and will let you know definitely.

Regards,

A K Dubey