"Use at least three different ExPSAy tools to characterise the identified protein – justify choice and present the findings", I have data from mass spectrometer, the mass values and it is my first time working with such data. I do not know where else I can use Mass spectrometer data apart from MASCOT to identify and characterise my protein.
There are three proven ways of using mass spectrometry data for protein identification. The first of these is known as a peptide mass fingerprint. This was the original method to be developed, and uses the molecular weights of the peptides resulting from digestion of a protein by a specific enzyme.
I do not fully understand your question, is it what other tools beside Mascot are available to interpret MS/MS data?
If so there are also several free tools although they require some experience on the command line such as X!Tandem or MSGF+, the latter is quite good (in my experience). Depending on the instrument used you may also take MaxQuant.
If you want to use tools to further get information about an identified protein it really depends on what you want to know or what you expect.
Hopefully that was helpful.
cheers
I did identify my protein but the assessments asks, to characterise the protein using 3 ExPASY tools. I have got the amino acid sequence from peptide finger printing. So my question is which ExPASY sequence should I use?
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