[EMBOSS] Monoisotopic or Average mass

[Peter Rice]

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