Mass spectrometry-based label-free quantitative proteomics

Abstract

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.

Figure 1

General approaches of quantitative proteomics. (a) Shotgun isotope labeling method. After labeling by light and heavy stable isotope, the control and sample are combined and analyzed by LC-MS/MS. The quantification is calculated based on the intensity ratio of isotope-labeled peptide pairs. (b) Label-free quantitative proteomics. Control and sample are subject to individual LC-MS/MS analysis. Quantification is based on the comparison of peak intensity of the same peptide or the spectral count of the same protein.