Rune Matthiesen (editor) - Mass Spectrometry Data Analysis in Proteomics (Methods in Molecular Biology, Band 2051)

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The third edition of Mass Spectrometry Data Analysis in Proteomics starts as the previous editions with a basic introduction to mass spectrometry-based proteomics. The following chapters are written by experts in specific subdomains of proteomics. The aim is to provide detailed information on each topic to allow newcomers to follow the content but at the same time present novel ideas and views that can influence future developments in mass spectrometry-based proteomics. The authors have been offered to provide complete coverage of their domains with no page restriction. The first edition of the book was published in 2007, and we have witnessed a strong improvement in sensitivity and reproducibility of mass spectrometry-based proteomics. Furthermore, quality of computational methods has also improved. Consequently, all chapters have been updated to provide the newest and most relevant information on each topic. In contrast to the previous editions, this edition aims to also provide instructions on how to perform the most relevant computational methods such as database-dependent searches, although the focus is still on computational concepts.

There are now several examples demonstrating that clinical proteomics is reproducible, and we and many others believe that mass spectrometry will play a major role in clinical research in the coming years. Criticism of mass spectrometry often revolves around lack of throughput and it will never compete with genomics because of the lack of a method to amplify the analyte. However, clinical proteomics provides complementary information to genomics which we refer to as proteogenomics, and several methods exist to amplify the signal of protein-based targets. The analogy that the genome is like a cookbook for the organisms is justifiable. Furthermore, the sample preparation steps are often more straightforward for mass spectrometry, and new workflows allow analysis of more than 300 blood samples per day using a single instrument. However, to cook a delicious cake more is needed: a good chef, functional working tools, and fresh ingredients. To answer questions about the quality of the cake, it is often more informative to taste it rather than reading the recipe. In fact, many diseases have a major environmental component that potentially is better reflected in the proteome than the genome.