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• W179968103 abstract "Protein protocols on CD-ROM, Version 2.0, edited by John M. Walker. 2002. Totowa, NJ, USA: Humana Press. $595 (CD-ROM; content claimed to be more than 13,000 pages, with 2659 figures). Protein purification protocols, 2nd ed., edited by Paul Cutler. 2004. Totowa, NJ, USA: Humana Press. 496 pp. $115 (hardcover). Both products claim to be geared toward novice and experienced investigators in the field of protein science. In my opinion, neither of these groups is well served by either of these publications: Both are older texts, despite the recent publication dates, and there is considerable overlap (read “identity”) in their content. I expected Walker's Version 2 of the Protein Protocols on CD-ROM to be not only an expanded, but also a revised and an improved version of the first edition. Although Version 2 is indeed expanded, claiming to present over 5000 methods (vs. 2500 for the first version) in over 13,000 pages, it appears to be minimally revised and only marginally improved. Because I have never seen the first version, I cannot make a detailed comparison. However, the contents of the only independent review (Hsuan 1999) I found could be applied almost word for word to the present version. Given Hsuan's (1999) surprise over the inclusion of “extra” methods in the first version, I decided to look at some of these in the second version. The first mentioned, in situ PCR, is presented in Version 2 as section 4.60 by Bagasra et al. It is incredible that of the 105 literature citations in this article, one is from 1995 and the rest are from 1994 or earlier. This would have hardly been considered timely in 2002, let alone 2004. Version 2 is divided into 23 chapters, entitled (in order): Quantitation of Proteins; Electrophoresis of Proteins and Peptides and Detection in Gels; Blotting and Detection Methods; Expression and Detection of Recombinant Genes; Protein Purification; Membrane Proteins; Chemical Modification of Proteins and Peptide Production and Purification; Protein/Peptide Characterization and Sequencing; Glyco-proteins; Immunochemical Techniques; Antibodies; ELISA; Epitope Mapping; NMR of Proteins and Peptides; Mass Spectrometry of Proteins and Peptides; Other Physical Methods of Analysis; Peptide Synthesis; Proteolytic Enzymes; Enzyme and Other Assays; Named Proteins and Domains: Purification and Analysis; Protein–Protein Interactions; Protein Bioinformatics; and Combinatorial Libraries. All told, there are 951 separate sections (individual contributions). There is no preface or index. One would hope that the lack of an index would be more than compensated for by the presence of a powerful search function. Unfortunately, computer search functions only find what you tell them to find. For example, searching the whole collection with the words “HIV protease” yields 31 hits (both with or without “Query Enhancement and Expansion”); unfortunately, section 17.19 (“Chemical Synthesis of the Aspartic Proteinase from Human Immunodeficiency Virus [HIV]” by Paul D. Hoeprich Jr.) is not among them. It would have been nice if the software had been able to set “HIV” and “HIV-1,” as well as “protease” and “proteinase” as equivalents in the search algorithm. Human editors, in the old, pre-PC days, were quite good at this when preparing indexes for books. Although the present search function works, it is not really as good as a decent printed index for some searches, because it also finds hits in the titles of the literature cited. Although this can sometimes be useful, I became quite weary clicking the “Next” button to search through the (hidden) list of hits in any one search. The organization of the 23 chapters is just as discordant as complained about in the Hsuan (1999) review of the first edition. I was quite favorably impressed by the general organization and presentation of much of chapter 12, “ELISA.” Almost half of this chapter (the first nine of 21 sections) is devoted to a series of textbook-style articles by John Crowther, which provide all of the background anyone needs to perform successful ELISA experiments and/or be able to better comprehend the other sections that follow in this chapter. Unfortunately, this chapter also suffers from the lack of editorial input evident throughout this collection: Sections 12.19 and 12.21, while good, are direct repeats of information presented at the beginning of this chapter. Because the latest reference in either of these latter sections is from 1995, what is the justification for the duplication of information in this chapter? Likewise, the copy editor was asleep at the wheel because this chapter does not include a list of contributors, as do most of the other chapters (all except chapters 19–23). The newest reference in the entire collection is a single reference from 1999 (in section 17.31). A total of 31 references from 1998 were found, including one (reference 41 in section 17.45) listed as being in press! Kindly put, this collection was dated when it was published in 2002 and cannot be really considered cutting-edge in 2004. I spent more than 16 hours wading through this compilation of protocols, and found a lot of useful information. Unfortunately, it is poorly presented (a function of the DynaText browser and limitations imposed by the choice to compress the figures to fit onto a single CD-ROM) and quite dated (old references and text). Unlike some of the classic publications in molecular biology methods, I would hesitate to give a beginning graduate student in our department this CD-ROM and point him/her towards the lab. I would advise any prospective buyers of this CD-ROM to save their money and rather invest their time in a Google search—it's much cheaper and may get them to their desired method a lot quicker. Sounds too harsh? Not really. Enter the search phrase “in vitro transcription translation system” in the Protein Protocols search window, hit Enter, and receive the message “invalid query expression.” Modify the search phrase to “vitro transcription translation,” and only four hits are found: two in section 4.121, and one each in sections 13.29 and 21.5. Perhaps the most relevant section, section 4.10 (“Expression of cDNA-Encoded Proteins by Cell-Free Transcription and Translation”) is not found with the search function. The first page (10 hits) of a Google search in April 2004 found four commercial sources of such systems and a lot more up-to-date information about these methods than were found using the search function of the DynaText browser together with the CD-ROM. I cannot, in good conscience, recommend this product for purchase. The second edition of the book Protein Purification Protocols, edited by Paul Cutler, is an update and extension of the 1996 first edition. This book is a disappointment. Despite the 2004 publication date, 27 of the book's 44 chapters are either completely identical to or only modestly changed from contributions by the same author(s) to the Version 2 of the Protein Protocols on CD-ROM, published in 2002. Identical means “word for word,” and modestly changed means correction of inconsequential mistakes (changing of company names) or addition of newer references, but no new methods. Only 10 of the 44 chapters have no corresponding contribution in the Protein Protocols on CD-ROM. Of these new chapters, several are noteworthy for their superficial content, brevity, and unusual organization. Chapter 42, “Mass Spectrometry,” covers this broad topic in eight pages, with two figures and a single, essentially irrelevant reference. Chapter 43 covers purification of therapeutic proteins in only eight pages, including the references. Unfortunately, not all of the acronyms used in this chapter are defined, such as Q-PCR and GP-HPLC in Table 1. The last chapter of the book, chapter 44, “Purification Process Scale-Up,” could profit from a reorganization and rewrite: There are seven pages of text and eight pages of notes. In this chapter, tables and text do not always agree, and the final figure is superfluous and an insult to the reader. Aside from the single 2003 reference in chapter 42, I found only one reference from 2002 (in chapter 43); all other references were from 2001 or earlier. Although the date of a reference says little about its relevance for inclusion in a book of this type, the citation policy of many of the authors would lead me to believe that most of the articles for this book were completed no later than 2001 or 2002. Some of the chapters (such as chapters 2, 6, 39, and 43) have a disproportionately large number of citations to books, book articles, or manufacturer's instruction manuals, all of which can be more difficult to obtain than publications in the primary literature. The index is only four pages long, with only 254 entries, for a total of 480 pages of text. The index also lacks coverage, even for those entries that it does contain. The book is actually a reasonable compendium of methods for protein purification up to about the year 2000. However, there is very little useful, newer information included. The editorial input into the book appears quite minimal. The proofreading and indexing are not adequate. If one were to overlook the fact that the majority of the book is a simple reprint of the 2002 version of the Protein Protocols on CD-ROM and one had no other resources available (such as Internet access or the instruction and application manuals put out by Millipore or Amersham Biosciences), it might make sense to consider purchasing this book. Otherwise, buyer beware." @default.
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