Hi Sudeep, > I am trying to figure out how molecular weight of the peptide fragments in > EMBOSS program "DIGEST" is calculated if enzyme used for digestion is Trypsin. > > Monoisotopic mass of each constituent AA residues in a given peptide sequence+ > monoisotopic mass of water > or > Average mass of each constituent AA residues in a given peptide sequence > +average mass of water
Average mass. as far as I am aware ... but we do need more documentation of the molecular weights in Eamino.dat You can set the masses in a local data file if you want to use monoisotopic values. Add -aadata filename to the commandline or put a file Eamino.dat in your current directory. For the water the values are currently hardcoded in nucleus/embprop.c as: H 1.00782 OH 17.00274 But we could add values to Eamino.dat. If you can provide alternative values we can also add an alternative local data file to the EMBOSS distribution. Hope that helps. Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
