This article was originally published in Electrophoresis 2010, 31, 3580–3585, DOI 10.1002/elps.201000298

New method for prefractionation of plasma for

proteomic analysis

Anna Fitzgerald and Bradley J. Walsh

Keywords:

2-DE / IEF / Plasma / Prefractionation

The depth of proteome analysis is severely limited in

complex samples with a wide dynamic range of protein

abundance such as plasma. Removal of high-abundance

proteins should reveal the signal of lower abundance plasma

proteins. However, smaller proteins may be part of larger

protein complexes and hence the removal of proteins

involved in complexes with high-abundance proteins such

as albumin may inhibit the search for disease biomarkers.

Prefractionation of a sample divides it into fractions of

reduced complexity, allowing improved detection of lower

abundance proteins. Using a prefractionation device, which

employs GradiflowTM technology, we were able to separate

small volume plasma samples into multiple fractions based

on the molecular weight and/or charge. The resulting

samples of reduced complexity were directly compatible

with 2-DE. The use of this prefractionation machine may

therefore be useful in the hunt for disease biomarkers.

Time course experiment showing native separation of plasmaafter fractionation based on MW in the MF-10 Gradiflow.

Proteomics Clin. Appl. 2011, 5, 205–209 209