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Journal of Biomedicine and Biotechnology
Volume 2010 (2010), Article ID 840518, 6 pages
Review Article

Mass Spectrometry-Based Label-Free Quantitative Proteomics

1Center on Proteolytic Pathways, Burnham Institute for Medical Research, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
2Department of Dermatology, University of California, San Diego, CA 92093, USA

Received 1 July 2009; Accepted 1 September 2009

Academic Editor: Pieter C. Dorrestein

Copyright © 2010 Wenhong Zhu 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.


In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies.