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The in‐depth analysis of complex proteome samples requires fractionation of the sample into subsamples prior to  LC ‐ MS / MS  in shotgun proteomics experiments. We have established a 3 D  workflow for shotgun proteomics that relies on protein separation by 1 D PAGE , gel fractionation, trypsin digestion, and peptide separation by in‐gel  IEF , prior to  RP ‐ HPLC‐MS / MS . Our results show that applying peptide  IEF  can significantly increase the number of proteins identified from  PAGE  subfractionation. This method delivers deeper proteome coverage and provides a large degree of flexibility in experimentally approaching highly complex mixtures by still relying on protein separation according to molecular weight in the first dimension.

Increased proteome coverage by combining PAGE and peptide isoelectric focusing: Comparative study of gel‐based separation approaches