Quantitative proteomics: the next logical step in molecular phenotyping

Abstract

The past era of proteomics has been dominated by global studies whose primary aim was to characterize as much of the proteome as possible. The progress was remarkable. Early in this decade, the ability to identify a thousand proteins from a single proteome sample using mass spectrometry (MS) was limited to a handful of laboratories. Presently, the ability to identify upwards of 3000 proteins is pretty much commonplace. This ability to gain comprehensive proteomic coverage was used to conduct a variety of different studies ranging from simply determining the protein content of a complex sample to comparing the phosphoproteomes of different cell types. Unfortunately, the ability to identify large numbers of proteins comes at a price: the amount of information obtained per protein is not very high. The hope of these global studies was that by surveying as much of the proteome as possible, at least identification of a few proteins of biological interest would facilitate important discoveries and expand boundaries of systems biology. Global proteomic studies have had a number of successes with a large number of important findings being made. Unfortunately, most basic researchers are not equipped with bioinformatics tools capable of thorough meta-analysis of these data sets and are interested in more specific information on a small number of proteins. Fortunately, MS has many more attributes than simply being able to identify large numbers of molecules in complex mixtures. For a long time, MS has been the technology of choice for quantitating metabolites because of its sensitivity and specificity. The last decade has witnessed remarkable progress in adopting targeted approaches to quantitate specific proteins within complex mixtures such as serum and plasma. The conventional thinking used to be that MS would play a major role in the discovery of potential disease-specific biomarkers for example; validation would be conducted using antibody-based methods. However, as demonstrated by the many articles present within this special edition of Briefings inFunctional Genomics andProteomics, MS will be a major contributor for quantitating these potential markers across the thousands of samples necessary for validation. Beyond validation of potential biomarkers, translation of targeted quantitative methods to other types of proteins, such as glycosylated or phosphorylated proteins will be key for using MS to specifically define the roles proteins play in cellular systems. As co-editors, we wish to thank each author who contributed a manuscript to the special edition. We understand that your time is valuable and we appreciate you sacrificing some of it to make this an outstanding issue. To the reader, we hope you find this collection of articles enjoyable to read and that they stimulate ideas that you can test and explore within your own facilities.