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Updated: May 8, 2026

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
Published on: April 1, 2017
Increased proteome coverage by combining PAGE and peptide isoelectric focusing: comparative study of gel-based
Ilian Atanassov1, Henning Urlaub
1Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Abstract:
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 3D workflow for shotgun proteomics that relies on protein separation by 1D 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.
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