I have isolated peptides from venom proteins and I would like to identify it by matching it to database. Since there is no genome sequence for my snake species, I would like to use database that contains entire set of small peptides.
Hi,
As indicated by the Dr. Ivanova above, I don't think such a database exists, neither as freeware, nor as commercial product.
I think animal venoms, and the peptides therein, are some of the most complex mixtures you can spray into your mass spec, as these contain uncommon amino acids, modifications and can be partly cyclic.
Therefore, the key in annotating these peptides is in mass accuracy and persistance (in manual annotation).
Good luck!
You could consider creating your own transcriptome from e.g. the gland that produces your venom, create a database and use ESI-Q-TOF to create and analyze your database as described here: Article Transcriptomic and Neuropeptidomic Analysis of the Stick Ins...
Depending on the size of the transcriptome you will need a quiet powerful machine to run PEAKS with such a huge database. Also known characteristic amino acids motif would be useful to create the database from scratch...
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