[EMBOSS] Algorithms for pI and molecular weight in pepstats

[Peter Rice]

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?

regards,

Peter Rice
EMBOSS Team