- Email: [email protected]
New uses for tandem mass spectrometry
238
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rapid and visual output to identify the domains contained in a protein sequence of interest. The book contains two chapters about plasmid mapping, PCR design and sequencing that are more related to molecular biology than to bioinformatics. The chapter devoted to phylogenetics mentions the methods involved in building phylogenetic trees but the use of resampling procedures, such as bootstrapping and jack-knifing, to evaluate their robustness needs to be discussed2. One of the drawbacks of this book is that the Genetics Computer Group (GCG; WI, USA) package is mentioned in excruciating detail throughout. At one point, the author comments that the ‘GCG package is the most popular molecular biology software in the world today’ – a contention that may be applicable to bioinformaticists but not to an average molecular biologist – the main audience intended for this book. The figures in the book leave much to be desired and are sometimes of such low quality that the text cannot be deciphered. The duplication of some figures as color plates does not help matters either. Also, there are occasional minor errors, such as description of the ‘nr’ subset of GenBank as one that does not include high-throughput genomic sequences (HTGSs) at all whereas in fact it currently contains all ‘finished’ phase 3 sequences that account for approximately 30% of the human genomic sequence. The book comes with a CD-ROM that contains free software for both Mac and Windows applications in addition to demonstration versions of several commercially available programs. Some of the popular programs that will probably be useful to most biologists include CLUSTAL, MACAW, PHYLIP, MacVector, Signal Scan, RasMol, Tree View and Strider. Overall, the CD has an assortment of 28 programs for Windows and 31 for the Mac as well as a list of websites described in the book. Free software might be appropriate for those with limited access to the Internet whereas the demonstration programs will allow the readers to ‘test-drive’ programs to make an informed decision before a potentially expensive purchase. Overall, this book is a good buy for those beginning in molecular biology as well as bioinformatics. References 1 Schultz, J. et al. (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28, 231–234 http://tibtech.trends.com
TRENDS in Biotechnology Vol.19 No.6 June 2001
2 Hillis, D.M. et al. (1993) Analysis of DNA sequence data: Phylogenetic Inference. Methods Enzymol. 224, 456–487
Suraj Peri and Akhilesh Pandey Protein Interaction Lab, Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark. e-mail: [email protected]
New uses for tandem mass spectrometry Protein Sequencing and Identification Using Tandem Mass Spectrometry by Michael Kinter and Nicholas E. Sherman Wiley-Interscience, London, UK, 2000. (300 pages) ISBN 0 47132 249 0
This book is timely considering the increasing number of research departments and core facilities that use tandem mass spectrometry (MS) for protein identification and sequencing. The authors describe the practical aspects of protein sequencing using tandem MS, and cover the background and partner technologies of MS that essentially contribute to the great success of this interdisciplinary field. The information is arranged in several concise chapters, dealing with ‘Historical overview on protein sequencing’ (Chapter 2), ‘Fundamental mass spectrometry’ (Chapter 3), ‘Polyacrylamide gel electrophoresis’ (Chapter 5) and ‘Preparation of protein digests for mass spectrometric sequencing experiments’ (Chapter 6). Where appropriate, step-bystep protocols are provided that describe the experimental operations in detail, and that have all been tested in the authors’ laboratories. Chapters 4 and 9 are particularly valuable; Chapter 4 (‘Collisionally-induced dissociation of protonated peptide ions and interpretation of product ion spectra’) contains a remarkably clearly structured systematic approach on how to extract sequence information from a peptide product ion spectrum. The reader is guided through a set of product ion spectra of doubly charged peptide ions with increasing complexity. The progress of the sequencing process is visualized step-by-step up to the point at which the tandem spectrum is exhaustively interpreted, which might not necessarily lead to extraction of the complete peptide
sequence. One of the strong points of interactive protein identification using raw or interpreted tandem MS data and a protein database is that partial sequence information is sufficient for reliable protein identification. A personal selection of the search engines on the Internet that are currently available for this task is discussed in Chapter 8 (‘Protein identification by database searching’). The most demanding task in peptide sequencing using tandem MS is outlined and competently discussed in Chapter 9 (‘Sequence analysis of novel proteins’). It is clearly pointed out that the so-called ‘de novo’sequencing using tandem electrospray MS requires special efforts because sequence data of such completeness and confidence have to be created, so that MS data alone – without the support of a protein database – provide reliable peptide structure information. Finally, Chapter 10 provides an introduction to the analysis of covalent protein modifications, one of the key aspects in unravelling protein function. Although some areas of the interdisciplinary field addressed in this book are treated at an introductory level, the core aspects are outlined in great detail, with expert discussions and valuable experimental details. In general, the graphics are not elaborate but do adequately complement the well-written text. Instrumentally, this book is focused on data generated from electrospray LC-tandem MS and/or MS using an ion trap analyzer, with some reference to electrospray Q-TOF and MALDI data. High-resolution data and emerging alternative techniques for the generation of tandem mass spectra of peptides are not in the focus. In protein sequencing using MS and partner technologies, sample preparation, spectra acquisition and interpretation are characterized by an increasing degree of automation. Nevertheless, the situation will persist that full analytical profit can only be gained with expert knowledge on these new technologies. In this context, a book such as that of Kinter and Sherman is invaluable. It is announced as the first volume of a series of books on mass spectrometry and we look forward to the continuation of this series. Wolf D. Lehmann Central Spectroscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. e-mail: [email protected]
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rapid and visual output to identify the domains contained in a protein sequence of interest. The book contains two chapters about plasmid mapping, PCR design and sequencing that are more related to molecular biology than to bioinformatics. The chapter devoted to phylogenetics mentions the methods involved in building phylogenetic trees but the use of resampling procedures, such as bootstrapping and jack-knifing, to evaluate their robustness needs to be discussed2. One of the drawbacks of this book is that the Genetics Computer Group (GCG; WI, USA) package is mentioned in excruciating detail throughout. At one point, the author comments that the ‘GCG package is the most popular molecular biology software in the world today’ – a contention that may be applicable to bioinformaticists but not to an average molecular biologist – the main audience intended for this book. The figures in the book leave much to be desired and are sometimes of such low quality that the text cannot be deciphered. The duplication of some figures as color plates does not help matters either. Also, there are occasional minor errors, such as description of the ‘nr’ subset of GenBank as one that does not include high-throughput genomic sequences (HTGSs) at all whereas in fact it currently contains all ‘finished’ phase 3 sequences that account for approximately 30% of the human genomic sequence. The book comes with a CD-ROM that contains free software for both Mac and Windows applications in addition to demonstration versions of several commercially available programs. Some of the popular programs that will probably be useful to most biologists include CLUSTAL, MACAW, PHYLIP, MacVector, Signal Scan, RasMol, Tree View and Strider. Overall, the CD has an assortment of 28 programs for Windows and 31 for the Mac as well as a list of websites described in the book. Free software might be appropriate for those with limited access to the Internet whereas the demonstration programs will allow the readers to ‘test-drive’ programs to make an informed decision before a potentially expensive purchase. Overall, this book is a good buy for those beginning in molecular biology as well as bioinformatics. References 1 Schultz, J. et al. (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28, 231–234 http://tibtech.trends.com
TRENDS in Biotechnology Vol.19 No.6 June 2001
2 Hillis, D.M. et al. (1993) Analysis of DNA sequence data: Phylogenetic Inference. Methods Enzymol. 224, 456–487
Suraj Peri and Akhilesh Pandey Protein Interaction Lab, Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark. e-mail: [email protected]
New uses for tandem mass spectrometry Protein Sequencing and Identification Using Tandem Mass Spectrometry by Michael Kinter and Nicholas E. Sherman Wiley-Interscience, London, UK, 2000. (300 pages) ISBN 0 47132 249 0
This book is timely considering the increasing number of research departments and core facilities that use tandem mass spectrometry (MS) for protein identification and sequencing. The authors describe the practical aspects of protein sequencing using tandem MS, and cover the background and partner technologies of MS that essentially contribute to the great success of this interdisciplinary field. The information is arranged in several concise chapters, dealing with ‘Historical overview on protein sequencing’ (Chapter 2), ‘Fundamental mass spectrometry’ (Chapter 3), ‘Polyacrylamide gel electrophoresis’ (Chapter 5) and ‘Preparation of protein digests for mass spectrometric sequencing experiments’ (Chapter 6). Where appropriate, step-bystep protocols are provided that describe the experimental operations in detail, and that have all been tested in the authors’ laboratories. Chapters 4 and 9 are particularly valuable; Chapter 4 (‘Collisionally-induced dissociation of protonated peptide ions and interpretation of product ion spectra’) contains a remarkably clearly structured systematic approach on how to extract sequence information from a peptide product ion spectrum. The reader is guided through a set of product ion spectra of doubly charged peptide ions with increasing complexity. The progress of the sequencing process is visualized step-by-step up to the point at which the tandem spectrum is exhaustively interpreted, which might not necessarily lead to extraction of the complete peptide
sequence. One of the strong points of interactive protein identification using raw or interpreted tandem MS data and a protein database is that partial sequence information is sufficient for reliable protein identification. A personal selection of the search engines on the Internet that are currently available for this task is discussed in Chapter 8 (‘Protein identification by database searching’). The most demanding task in peptide sequencing using tandem MS is outlined and competently discussed in Chapter 9 (‘Sequence analysis of novel proteins’). It is clearly pointed out that the so-called ‘de novo’sequencing using tandem electrospray MS requires special efforts because sequence data of such completeness and confidence have to be created, so that MS data alone – without the support of a protein database – provide reliable peptide structure information. Finally, Chapter 10 provides an introduction to the analysis of covalent protein modifications, one of the key aspects in unravelling protein function. Although some areas of the interdisciplinary field addressed in this book are treated at an introductory level, the core aspects are outlined in great detail, with expert discussions and valuable experimental details. In general, the graphics are not elaborate but do adequately complement the well-written text. Instrumentally, this book is focused on data generated from electrospray LC-tandem MS and/or MS using an ion trap analyzer, with some reference to electrospray Q-TOF and MALDI data. High-resolution data and emerging alternative techniques for the generation of tandem mass spectra of peptides are not in the focus. In protein sequencing using MS and partner technologies, sample preparation, spectra acquisition and interpretation are characterized by an increasing degree of automation. Nevertheless, the situation will persist that full analytical profit can only be gained with expert knowledge on these new technologies. In this context, a book such as that of Kinter and Sherman is invaluable. It is announced as the first volume of a series of books on mass spectrometry and we look forward to the continuation of this series. Wolf D. Lehmann Central Spectroscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. e-mail: [email protected]