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Journal of Biomedicine and Biotechnology
Volume 2011, Article ID 245291, 14 pages
Review Article

Sample Preparation Techniques for the Untargeted LC-MS-Based Discovery of Peptides in Complex Biological Matrices

1Laboratory for Analytical Biotechnology and Innovative Peptide Biology, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 3706 AV Zeist, The Netherlands
2Netherlands Proteomics Centre, Delft University of Technology, Julianalaan 67, 3706 AV Zeist, The Netherlands
3TNO Triskelion, 3700 AV Zeist, The Netherlands
4Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium

Received 16 June 2011; Accepted 1 September 2011

Academic Editor: Isabel Sá-Correia

Copyright © 2011 Inez Finoulst et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Although big progress has been made in sample pretreatment over the last years, there are still considerable limitations when it comes to overcoming complexity and dynamic range problems associated with peptide analyses from biological matrices. Being the little brother of proteomics, peptidomics is a relatively new field of research aiming at the direct analysis of the small proteins, called peptides, many of which are not amenable for typical trypsin-based analytics. In this paper, we present an overview of different techniques and methods currently used for reducing a sample's complexity and for concentrating low abundant compounds to enable successful peptidome analysis. We focus on techniques which can be employed prior to liquid chromatography coupled to mass spectrometry for peptide detection and identification and indicate their advantages as well as their shortcomings when it comes to the untargeted analysis of native peptides from complex biological matrices.