Quantitative Proteomics

Abstract

Quantitative proteomics technologies have been evolving rapidly, but have reached a level of maturity where reliable results of well‐understood statistical significance can be expected from experiments intended to measure changes in protein abundance in paired samples of case versus control or in multiple comparison studies with substantial numbers of biological replicates and multiple treatments. This review provides an overview of the progress and challenges in the field and highlights specific methods to examine changes in protein abundance where the intact protein species are separated and quantified (top‐down proteomics) and where proteins are digested and separated and peptide abundance is quantified (bottom‐up or shotgun proteomics) to infer relative protein abundance. This paper provides specific examples of two‐dimensional (2‐D) gel‐based quantification along with shotgun methods using 18 O‐labeling and label‐free quantification methods. In each case, issues of sample numbers, target variance, sample prefractionation, and other considerations that are informative to the practical use of these techniques are highlighted. The future prospects of this field are bright, but the challenges of integrating the wealth of proteomics data available into an informative biological context remain an area of important future development.

Differential expression of serum proteins in multiple myeloma

“…LabScan software version 6.0 on an ImageScanner was used to obtain digital images of the silver stained gels, which were then analyzed using ImageMaster 2D Platinum 7.0 software (all GE Healthcare, Chicago, IL, USA). Both spot standardization and spot intensity or volume were performed according to standard protocols (16).…”