If you have an OFFGEL(TM) system, I highly recommend you check out this paper in press at Electrophoresis here.
This group came up with markers that migrate with the pI of the sample wells and can give you a quick heads up on the progress of your fractionation!
One of the challenges with this offline separation technique is that it can be difficult to tell when your fractionation has proceeded to completeness. This team evaluated the use of a several markers with known pIs. For example, the markers dark orange and yellow, have pIs of 3.9 and 10.1 respectively. If the diluted colors focus in wells or IPG strip can we assume that the peptides have completed migration?
They find that they can, and confirm with MS/MS. Even better? They can use these markers with peptides that have been isobaric labeled!
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