Methods for fractionation, separation and profiling of proteins and peptides

Electrophoresis. 2002 Sep;23(17):3048-61. doi: 10.1002/1522-2683(200209)23:17<3048::AID-ELPS3048>3.0.CO;2-L.


In the last few years there has been an increased effort to develop technologies capable of identifying and quantifying large numbers of proteins expressed within a cell system (i.e., the proteome). The complexity of the mixtures being analyzed has made the development of effective fractionation and separation methods a critical component of this effort. This review highlights many of the protein and peptide fractionation and separation methods, such as electrophoresis and high-performance liquid chromatography (HPLC), which have experienced significant development over the past forty years. Modern instrumental strategies for the resolution of cell proteins, based on separations employing a single high-resolution or multidimensional approach, and the relative merits of each, will be discussed. The focus of this manuscript will be on the development of multidimensional separations such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), HPLC/HPLC, and HPLC-capillary electrophoresis and their application to the characterization of complex proteome mixtures.

Publication types

  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Animals
  • Chromatography / instrumentation
  • Chromatography / methods*
  • Electrophoresis / instrumentation
  • Electrophoresis / methods*
  • Equipment Design
  • Humans
  • Peptides / analysis
  • Peptides / isolation & purification*
  • Proteins / analysis
  • Proteins / isolation & purification*


  • Peptides
  • Proteins