Table of Contents
International Journal of Proteomics
Volume 2013, Article ID 756039, 13 pages
Review Article

Issues and Applications in Label-Free Quantitative Mass Spectrometry

1Department of Cellular & Integrative Physiology, Biotechnology Research & Training Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
2School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA

Received 2 October 2012; Revised 17 October 2012; Accepted 31 October 2012

Academic Editor: Bomie Han

Copyright © 2013 Xianyin Lai 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.


To address the challenges associated with differential expression proteomics, label-free mass spectrometric protein quantification methods have been developed as alternatives to array-based, gel-based, and stable isotope tag or label-based approaches. In this paper, we focus on the issues associated with label-free methods that rely on quantitation based on peptide ion peak area measurement. These issues include chromatographic alignment, peptide qualification for quantitation, and normalization. In addressing these issues, we present various approaches, assembled in a recently developed label-free quantitative mass spectrometry platform, that overcome these difficulties and enable comprehensive, accurate, and reproducible protein quantitation in highly complex protein mixtures from experiments with many sample groups. As examples of the utility of this approach, we present a variety of cases where the platform was applied successfully to assess differential protein expression or abundance in body fluids, in vitro nanotoxicology models, tissue proteomics in genetic knock-in mice, and cell membrane proteomics.