Protein Fractionation for Quantitative Plasma Proteomics by Semi-Selective Precipitation
Ekaterina Mostovenko*, Hannah C. Scott, Oleg Klychnikov, Hans Dalebout, André M. Deelder and Magnus Palmblad
Bio molecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
- *Corresponding Author:
- Ekaterina Mostovenko
Biomolecular Mass Spectrometry Unit
Department of Parasitology, Leiden University Medical Center
P.O. Box 9600, 2300 RC Leiden, The Netherlands
E-mail: [email protected]
Received Date: August 06, 2012; Accepted Date: September 01, 2012; Published Date: September 03, 2012
Citation: Mostovenko E, Scott HC, Klychnikov O, Dalebout H, Deelder AM, et al. (2012) Protein Fractionation for Quantitative Plasma Proteomics by Semi-Selective Precipitation. J Proteomics Bioinform 5: 217-221. doi: 10.4172/jpb.1000239
Copyright: © 2012 Mostovenko E, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Blood plasma is a highly complex mixture of proteins, metabolites and lipids, and a rich source of potential biomarkers for a range of diseases and conditions. The wide range in protein abundance poses a tremendous challenge for plasma proteomics. However, as a relatively small number of proteins make up most of the total protein pool, the concentration range can be compressed by depletion of abundant proteins, such as albumin. To reduce sample complexity and increase the protein coverage, we have developed a sample preparation method based on semi-selective precipitation with acetonitrile at different pH and built a data analysis pipeline, combining different search strategies. The method we propose is reproducible and easily parallelised (high throughput), and may be well suited to fractionate plasma for label-free quantitative proteomics in large clinical studies. Up to 90% of albumin and other abundant proteins were removed by adding an equal volume of acetonitrile to the samples adjusted to pH 5.