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Part Theory, Part Lab Manual, Proteomics in Practice Hopes to Fill Gap in Basic Training

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By necessity, training researchers in the basics of proteomics must involve more than just book learning, but a new textbook published this month by Wiley-VCH tries hard to bridge the gap between theory and the laboratory. Written by Reiner Westermeier and Tom Naven, two Amersham Biosciences researchers based in Germany, Proteomics in Practice attempts to walk the reader through the basics of 2D gel electrophoresis and MALDI-TOF mass spectrometry — the theory and laboratory practice — and for the novice proteomics researcher, should provide a valuable introduction to these pillars of proteome analysis technology.

The origins of the new book are rooted in the training courses Westermeier and co-author Naven led while touring the world for Amersham last year. Westermeier, well-versed in electrophoresis technology, and Naven, a mass spectrometrist, had developed a training manual for the course, and the positive feedback they received during their final stop in South Africa led the two to contact Wiley about weaving additional text around the manual. It helped that Westermeier had already authored Electrophoresis in Practice, another Wiley title.

Although the scope of the book is limited, Westermeier and Naven said they chose to focus on 2D gel electrophoresis and MALDI-TOF mass spectrometry because of their stability — the techniques should be around for at least the next 10 years, the authors claim in the book. Furthermore, Westermeier and Naven said the book’s specificity is one of its primary strengths. Other books, Naven said, tend to use collections of essays from various authors to provide overviews of different proteomics technologies, but Proteomics in Practice touches only on the use of 2D gels and MALDI mass spectrometry, giving detailed instruction in a well-entrenched proteomics approach.

“This book says straight from the start that it will tell you how to do proteomics by the 2D/MS approach — 2D electrophoresis, followed by peptide mass fingerprinting, and then using CAF [chemical assisted fragmentation] MALDI sequence analysis to improve your protein identification rate,” said Naven. “That’s what the book concentrates on.”

To provide this focused instruction, the book is split roughly evenly between a first section providing introductory theory and explanations of tools and techniques, and a course manual providing specifics on reagents and laboratory protocols for carrying out typical 2D/MALDI MS analyses of protein samples. As an appendix, the authors included a trouble-shooting guide describing frequent problems, their causes, and terse instructions for their remedy.

As a whole, the book is laid out cleverly and with attention to visual aid when necessary. Rather than list footnotes at the end of each chapter or section, the margins of each page include tips, asides, and references to journal articles where the reader can find a more thorough investigation of the question at hand. Nor is the theory section — even on mass spectrometry — cluttered with abstruse formulas; for the novice proteomics researcher with a background in genetics or biochemistry the theory is sufficient.

Not surprisingly, given the book’s origins in an Amersham training course, Proteomics in Practice focuses on techniques for proteome analysis that are possible to perform using Amersham tools and instruments. CAF MALDI sequencing analysis, Naven admitted, is one technique specific to Amersham’s Ettan MALDI-TOF mass spectrometer and instrumentation. But the general approach to protein separation and identification described in the book, he added, is applicable to many vendors’ instrumentation platforms.

But Westermeier and Naven don’t intend for the book’s contents to remain static. Instead, they plan to update its coverage — on average every six months on the Wiley website and in two to three years as a future edition. Westermeier mentioned adding the analysis of posttranslational modifications to the book’s contents, as well as chromatography techniques for separating proteins. On the mass spectrometry side, Naven said updates would include MS/MS sequencing techniques.

“This is a living book,” Westermeier said. “We’ll add complementary techniques when in our eyes they are stable enough.”

— JSM