[EMBOSS] Algorithms for pI and molecular weight in pepstats
pmr at ebi.ac.uk
Tue Jul 26 07:28:14 UTC 2011
On 26/07/2011 00:42, Jake Rothenbuhler wrote:
> What are the algorithms used to compute the molecular weight and
> isoelectric point in pepstats? We are currently using pepstats to
> measure these properties in our in-house bioinformatics tools and some
> users are concerned because the results can differ from those returned
> by ExPASy.
There was discussion on this last year on this list too.
There is no single correct answer. Molecular weights can use the average
value for each amino acid to calculate the molecular weight of a
protein, or monoisotopic values top calculate peptide masses for
mass-spec data. Pepstats has a command line option -mono to use the
monoisotopic weights. We use amino acid molecular weights from ExPASy
findmod in the calculations.
The isoelectric point can be calculated for various conditions. When I
checked last, ExPASy's protparam was set up the isoelectric focus phase
of 2D gels under high urea conditions. It was unclear at the time where
to find all the values needed to reproduce their calculation.
We would like to update EMBOSS's protein property calculations, possibly
with additional options or alternative parameter sets.
Any suggestions from anyone on the list?
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