Hi,

There are a range of tools for generating MW and pI, and plotting them like a 'theroretical 2D gels', MW (Y axis) and pI (X axis).

I've not worked on human proteomes, primarily microbial, so i'm not sure how well they'll scale up. But, programs i've used include:

To get the MW and pIs

>Protein Digestion Simulator from the PNNL - its a standalone program which can generate MW and pIs (but be sure not to check any of the digestion options).

>Expasy tools

To plot the distributions from the protein sequence (fasta) directly you can use this online tool and it'll do the rest

>Virtual 2D @ http://proteo.cnb.csic.es:8080/virtual2d/

To plot the MW and pIs

>Gelprint @ http://www.igs.cnrs-mrs.fr/gelprint/

>Or once you've got the MW and pIs just do a scatter plot in excel

Hope it helps,

Raju