This is a continuation of experiments that I began to describe in April of this year
Please see Part 1 and Part 2, for more information.
Since I finished part 2 of this short experiment, 3 separate readers have written me with this exact same question: how many unique peptides were discovered in each experiment?
As (I hope) you can see in the grainy .JPEG from Excel above, the peptide OFFGEL separation provided the largest number of both unique protein groups and peptides of the 4 methods evaluated. Surprisingly, the SCX came in second, suggesting that (at least for this very simply study) methods that separated digested plasma proteins were superior to separation of plasma proteins at the un-digested level.
Disclaimer: This study was not for the purpose of discovering large numbers of proteins or peptides. This method was purely for the evaluation of 4 different separation techniques for the identification of depleted plasma proteins. All 4 methods began with the same amount of protein, either pre- or post- digestion, with the assumption that the loss during digestion whether in-gel or in-solution would be roughly equivalent. The method was a standard Top10 high/low with a dynamic exclusion at 2 events and a mass width of 0.01 Da.
As always, please email me directly if you would like further information (and sorry for the delay!). Keep those questions coming!