[EMBOSS] pepstats pI values (vs protparam)

[Peter Rice]

On 24/06/2010 11:20, Ingo P. Korndoerfer wrote:
> oh no ... i need some help again ...
>
> my colleagues tell me (similar to the issue resolved last week)
> peptstats and protparam calculate different pIs.
>
> alternatively, of course, if i can convince my team pepstats values are
> better then protparam values, that would be fine, too ...

That may be the easiest option for now...

I checked on what protparam does ... and it is very specific to running 
2D gels under high urea conditions. It also looks as though the 
publication does not have all the values (only a few N-terminal resudie 
values were given, for the proteins they analysed) so I have to dig 
deeper to calculate the others. The values are defined only for acidic 
proteins (and for acidic residues, values are given to 2 decimal places, 
for basic residues they are to the nearest integer! Are there any more 
recent calculatioins for basic resudues we can use?

It does lead to some interesting options, especially for eukaryote 
proteins, but we will not be able to change the calculations in time for 
this release.

Meanwhile we would like to hear more from users who calculate pIs what 
conditions they are interested in (and why).

regards,

Peter Rice