Quantitative Proteomics: (Volume 1 New Developments in Mass Spectrometry)

As a component of post-genome science, the field of proteomics has assumed great prominence in recent years. Whereas quantitative analyses focussed initially on relative quantification, a greater emphasis is now placed on absolute quantification and consideration of proteome dynamics. Coverage of the topic of quantitative proteomics requires consideration both of the analytical fundamentals of quantitative mass spectrometry and the specific demands of the problem being addressed. Quantitative Proteomics aims to outline the state of the art in mass spectrometry-based quantitative proteomics, describing recent advances and current limitations in the instrumentation used, together with the various methods employed for generating high quality data. Details on both strategies describing how stable isotope labelling can be applied and methods for performing quantitative analysis of proteins in a label-free manner are given. The utility of these strategies to understanding cellular protein dynamics are then exemplified with chapters looking at spatial proteomics, dynamics of protein function as determined by quantifying changes in protein post-translational modification and protein turnover. Finally, a key application of these techniques to biomarker discovery and validation is presented, together with the rapidly developing area of quantitative analysis of protein-based foodstuffs. This exemplary book is essential reading for analytical and biological mass spectrometrists working in proteomics research, as well as those undertaking either fundamental or clinical-based investigations with an interest in understanding protein dynamics and/or biomarker assessment.

Table of Contents:
Practical Considerations and Current Limitations in Quantitative Mass Spectrometry-Based Proteomics; Targeted Proteomics Based on High Resolution Accurate Mass Spectrometry Measurement; Making Sense Out of the Proteome: The Utility of iTRAQ and TMT; Getting Absolute: Determining Absolute Protein Quantities via Selected Reaction Monitoring Mass Spectrometry; Proteomics Standards with Controllable Trueness - Absolute Quantification of Peptides, Phosphopeptides and Proteins Using ICP- and ESI-MS Label-Free Strategies for Protein Quantification; Overview and Implementation of Mass Spectrometry-Based Label-Free Quantitative Proteomics; MS1 Label-Free Quantification Using Ion Intensity Chromatograms in Skyline (Research and Clinical Applications); Label-Free Quantification of Proteins Using Data-Independent Acquisition; Spatial Proteomics: Practical Considerations for Data Acquisition and Analysis in Protein Subcellular Localisation Studies; Quantitative Analyses of Phosphotyrosine Cellular Signalling in Disease; Next Generation Proteomics: PTMs in Space and Time; Experimental and Analytical Approaches to Quantification of Protein Turnover on a Proteome-Wide Scale; Protein Quantification by MRM for Biomarker Validation; MRM-based Protein Quantification with Labelled Standards for Biomarker Discovery, Verification, and Validation in Human Plasma; Mass Spectrometry-Based Quantification of Proteins and Peptides in Food; Subject Index

Review :
"Quantitative Proteomics should not be regarded only as an updated reference book of cutting-edge bottom-up strategies for quantitative proteomics. Its reading makes us reflect on the enormous experimental progress made possible by the recent developments magnificently summarized in the 15 chapters in this new volume of the series New Developments in Mass Spectrometry." Bio-molecular cycles are to say the least exceedingly complex. Although many cycles have already been defined, relatively little is known about the macromolecular workhorses that are embedded in the cells that actually do the work. It is only in the last two decades, with major advances in instrumentation, that insights into these complex mechanisms have been possible. Analysing a moving target is difficult at any time. When that target is the determination of protein composition as a function of the cell cycle, its age and its response to extracellular stimuli, the process becomes one of taking a snapshot in time. By definition this monitors the quantitative changes taking place over time and mass spectrometry is one of very few techniques capable of achieving this objective. Even with this very powerful tool, a very careful selection of appropriate strategies is called for, and this book describes those that have achieved at least a degree of success. The greatest limitation is that quantitative proteomics relies on the use of peptide surrogates as read-outs for the actual protein amount. Such simulations are not always reliable, a major fact recognised and emphasised throughout all chapters. With this in mind the editors have assembled authors with the necessary knowledge combined with an ability to explain current practices whilst simultaneously stating the limitations. Most authors also propose new ideas and possible extensions that may well apply in the future. The book is divided into a description of the technology (two chapters); label-based protein quantification (three chapters); label-free protein quantification (three chapters); dynamic protein quantification (four chapters); and application of quantitative proteomics (three chapters). The division between labelled and label-free quantification is most useful. It allows for a rapid comparison between methods and easier selection of the most appropriate method. The challenge in any method is to determine the absolute protein quantification at any given time and then reproduce it. At the forefront of current methods are HPLC and electrospray MS. As always with this technology, a major issue is how to identify the most appropriate sample preparation method, an issue recognised by most authors. The most intriguing chapters are the last two. It is encouraging to see a chapter on blood plasma. The blood processing industry is a key to human survival, is a massively important industry, and yet receives relatively little publicity. It is in effect largely hidden from public view. Non-communicable diseases account for 60 % of the world’s fatalities, and yet many could be detected by biomarkers if the technology were available—and quantitative proteomics offers the promise of inexpensive automated procedures on the millions of samples of blood taken daily. Similarly, in the chapter on food, application of similar methods offers the prospect of determining allergies in food, the new plague of allergic reaction now suffered by some 30 % of the western populace. It is regrettable that this book is unlikely to be read by those responsible for allocation of research funding. Development of the described technology holds significant promise in delivering automated methods capable of early detection and therefore easier and cheaper treatment of many diseases. "the editors have assembled authors with the necessary knowledge combined with an ability to explain current practices whilst simultaneously stating the limitations. Most authors also propose new ideas and possible extensions that may well apply in the future."