MALDI MS E-Book
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- Herausgeber: Wiley-VCH
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
This authoritative book on MALDI MS, now finally available in its second edition and edited by one of its inventors, gives an in-depth description of the many different applications, along with a detailed discussion of the technology itself.
Thoroughly updated and expanded, with contributions from key players in the field, this unique book provides a comprehensive overview of MALDI MS along with its
possibilities and limitations.
The initial chapters deal with the technology and the instrumental setup, followed by chapters on the use of MALDI MS in protein research (including proteomics), genomics, glycomics and lipidomics. The option of MALDI-MS for the analysis of polymers and small molecules are also covered in separate chapters, while new to this edition is a section devoted to the interplay of MALDI MS and bioinformatics.
A much-needed practical and educational asset for individuals, academic institutions and companies in the field of bioanalytics.
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Seitenzahl: 915
Veröffentlichungsjahr: 2013
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Table of Contents
Related Titles
Title page
Copyright page
Preface to the Second Edition
List of Contributors
1: The MALDI Process and Method
1.1 Introduction
1.2 Analyte Incorporation
1.3 Absorption of the Laser Radiation
1.4 The Ablation/Desorption Process
1.5 Ionization
1.6 Fragmentation of MALDI Ions
1.7 MALDI of Noncovalent Complexes
1.8 The Optimal Choice of Matrix: Sample Preparation
Abbreviations
2: MALDI Mass Spectrometry Instrumentation
2.1 Introduction
2.2 Lasers for MALDI-MS
2.3 Fragmentation of MALDI Ions
2.4 Mass Analyzers
2.5 Fourier Transform Ion Cyclotron Resonance Mass Spectrometers
2.6 Quadrupole Ion Trap Mass Spectrometers
2.7 Hybrid Mass Spectrometers
2.8 Future Directions
Definitions and Acronyms
3: MALDI-MS in Protein Chemistry and Proteomics
3.1 Introduction
3.2 Sample Preparation for Protein and Peptide Analysis by MALDI-MS
3.3 Strategies for Using MALDI-MS in Protein Biochemistry
3.4 Applications of MALDI-MS in Proteomics
3.5 Computational Tools for Protein Analysis by MALDI-MS
3.6 Clinical Applications of MALDI-MS
3.7 Conclusions
Acknowledgments
4: MALDI-Mass Spectrometry Imaging
4.1 Introduction
4.2 History of Mass Spectrometry Imaging (MSI) and Microprobing Techniques
4.3 MALDI in Micro Dimensions: Instruments and Mechanistic Differences
4.4 Visualization of Mass Spectrometric Information
4.5 Data Processing and Data Exchange
4.6 Matrix Deposition for High-Resolution Imaging
4.7 Organisms, Organs, and Tissues: MALDI Imaging at Various Lateral Resolutions
4.8 Whole-Cell and Single-Cell Analysis
4.9 Cell Sorting and Capturing
4.10 Direct Protein Identification and Localization
4.11 Identification and Characterization: Requirements for Mass Resolution and Accuracy
4.12 Conclusions
Acknowledgments
5: Analysis of Nucleic Acids, and Practical Implementations in Genomics and Genetics
5.1 Challenges in Nucleic Acid Analysis by MALDI-MS
5.2 Genetic Markers
5.3 Assay Formats for Nucleic Acid Analysis by MALDI-MS
5.4 Applications in Genotyping
5.5 Applications in Comparative Sequence Analysis
5.6 Applications in Quantitation of Nucleic Acids for Analysis of Gene Expression and Gene Amplification
5.7 Future Perspectives for the MALDI-MS Analysis of Nucleic Acids
Acknowledgments
6: MALDI-MS of Glycans and Glycoconjugates
6.1 Introduction
6.2 Profiling of Glycans and Glycosphingolipids
6.3 Structural Determination
6.4 Quantitative Analysis
6.5 Conclusions
7: Lipids
7.1 Introduction
7.2 Analysis of Individual Lipid Classes and Their Characteristics
7.3 MALDI-TOF-MS of Typical Lipid Mixtures
7.4 Characterization of Typical Oxidation Products of Lipids
7.5 MALDI-MS Imaging
7.6 Combining TLC and MALDI for Lipid Analysis
7.7 Summary and Outlook
Acknowledgments
Abbreviations
8: MALDI-MS for Polymer Characterization
8.1 Introduction
8.2 Technical Aspects of MALDI-MS
8.3 Attributes and Limitations of MALDI-MS
8.4 Conclusions and Perspectives
9: Small-Molecule Desorption/Ionization Mass Analysis
9.1 Introduction
9.2 Matrix Choices for Small-Molecule MALDI
9.3 Sample Preparation
9.4 Qualitative Characterization of LMM Molecules
9.5 Analyte Quantitation by MALDI
9.6 Conclusions
Acknowledgments
Abbreviations/Acronyms
10: Computational Analysis of High-Throughput MALDI-TOF-MS-Based Peptide Profiling
10.1 Introduction
10.2 MALDI-MS Data Preprocessing
10.3 Statistical Analysis of Preprocessed Data
10.4 Concluding Remarks
11: Biotyping of Microorganisms
11.1 The Technique
11.2 Standard Identification of Bacteria and Other Microorganisms
11.3 Applicability and Performance in Routine Laboratories
11.4 Direct Specimen Analysis
11.5 Subtyping
11.6 Resistance Testing
11.7 Outlook
Index
Related Titles
Editors
Prof. Dr. Franz Hillenkamp
Institute for Medical Physics
University of Münster
Robert-Koch-Str. 31
48149 Münster
Germany
Prof. Dr. Jasna Peter-Katalinic
Department of Biotechnology
University of Rijeka
Radmile Matejčić 2
51000 Rijeka
Croatia
Cover
High speed time lapse photograph of IR-MALDI plumes generated with an optical parametric oscillator (OPO) laser (for more details see Fig. 1.2)
Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty can be created or extended by sales representatives or written sales materials. The Advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.
Library of Congress Card No.: applied for
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library.
Bibliographic information published by the Deutsche Nationalbibliothek
The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.
© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany
Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley's global Scientific, Technical, and Medical business with Blackwell Publishing.
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Preface to the Second Edition
This book on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), first published in 2006, has obviously fulfilled a long felt demand among the community of bioorganic mass spectrometrists. It was sold out after only a few years. To prepare a second edition has been a considerable task. MALDI-MS is still a very active and developing field, requiring essential changes and additions to the first edition while keeping it to a handy size and particularly staying truthful to the concept of it being a “practical guide” more than an in-depth treatment of the basics.
Chapter 1 has been amended by the results of Karas and Jaskolla on new design matrices and the mechanisms of ion formation in MALDI, which has substantially added to our understanding of the processes and how to optimize them for practical applications. They have also influenced our view of the method as such and have led to revision of other parts of the chapter.
While most of the instruments described in the first edition are still in use in many laboratories, two newcomers have literally revolutionized particularly the routine applications: the orbitrap and the ion mobility instruments. Both are now covered in much detail in Chapter 2.
Proteomics had already been at a rather mature state at the time the first edition was published. Most additions and improvements in this field are somewhat special to a given problem and are not covered in detail in this book. Here, as in most of the other applications, the reader is referred to the extensive list of original literature at the end of each chapter.
Chapter 4 has been essentially rewritten. It now concentrates on MALDI imaging, a field which has seen a dramatic development in recent years and promises to continue on this path. The discussion of biomarkers has been referred to the new Chapter 10 on bioinformatics. MALDI imaging requires the treatment of the raw data with rather sophisticated software tools, specific for this application. It is, therefore, contained in Chapter 4, rather than Chapter 10.
MALDI-MS of nucleic acids, covered in Chapter 5, has still not found as widespread an application as, for example, the analysis of proteins, mostly because of competing techniques such as second generation sequencers which are now in routine use. One interesting MALDI application is the analysis of RNA and other modified nucleic acids, where straight sequencing leads to a loss of important information.
Application of MALDI-MS to analysis of protein-linked N- and O-glycans in Chapter 6 has been generally revised and updated. In consideration of growing attention to glycomics in biology and medicine, efficient protocols for glycans and glycopeptides have been described to encompass the carbohydrate complexity both for rapid mapping as well as for quantification, and those for glycosphingolipids added.
Revisions in Chapter 7 are related to the increased interest in lipid analysis, notably boosted by introduction of the new “omics” field – lipidomics – and by developments of MS imaging as a robust new application of MALDI-MS. In addition, novel potentials of lipid analysis in applications of the direct desorption from solid surfaces and MALDI-MS imaging to diagnostics using lipids as disease markers are described.
Chapter 8, on the analysis of synthetic polymers, remained essentially unchanged in the second edition.
Chapter 9, on small molecule desorption/ionization mass analysis, reflects the use of MALDI-MS in the development of new pharmaceutical agents, again a field of important applications and developments.
Bioinformatics, now covered in the new Chapter 10, was obviously missing in the first edition. Thang V. Pham and Connie R. Jimenez of the Free University of Amsterdam describe how they use bioinformatics software in their search for tumor markers in human samples. While this is a rather special application, they have taken great care to refer the reader to the original literature which describes the principles in other fields of application.
Biotyping of microorganisms, covered in Chapter 11, has been added as a last minute topic. This chapter is not as comprehensive as the others, but we considered it important, because it is the first and so far only large scale routine clinical MALDI application. It has boomed over the last two years and is still in a phase of intense development. The most important aspects of this new application are discussed in the chapter; for details, readers are referred to the many listed references.
Franz Hillenkamp
Jasna Peter-Katalinic
Münster, Rijeka, April 2013
List of Contributors
Stefan Berkenkamp
SEQUENOM Inc.
3595 John Hopkins Court
San Diego, CA 92121
USA
sberkenkamp@sequenom
Lucinda H. Cohen
Merck Research Laboratories
DMPK Bioanalytical Group
Mail Stop RY800B201
Rahway, NJ 07065
USA
Klaus Dreisewerd
University of Münster
Institute for Medical Physics and Biophysics
Robert-Koch-Str. 31
48149 Münster
Germany
Daniele Fabris
University at Albany
The RNA Institute
1400 Washington Avenue
Albany, NY 1222
USA
Beate Fuchs
University of Leipzig
Institute of Medical Physics and Biophysics, Faculty of Medicine
Härtelstr. 16–18
04109 Leipzig
Germany
Franz Hillenkamp
University of Münster
Institute for Medical Physics and Biophysics
Robert-Koch-Str. 31
48149 Münster
Germany
Karin Hjernø
University of Southern Denmark
Department of Biochemistry and Molecular Biology
Campusvej 55
5230 Odense
Denmark
Thorsten W. Jaskolla
University of Münster
Institute for Medical Physics and Biophysics
Robert-Koch-Str. 31
D-48149 Münster
Germany
Ole N. Jensen
University of Southern Denmark
Department of Biochemistry and Molecular Biology
Campusvej 55
5230 Odense
Denmark
Connie R. Jimenez
VU University Medical Center
VUmc-Cancer Center Amsterdam, Department of Medical Oncology
CCA 1-46, OncoProteomics Laboratory
De Boelelaan 1117
1081 HV Amsterdam
The Netherlands
Michael Karas
Johann Wolfgang Goethe University of Frankfurt
Institute of Pharmaceutical Chemistry, Biocenter
Max-von-Laue-Str. 9
60438 Frankfurt am Main
Germany
Markus Kostrzewa
Vice President – Clinical Mass Spectrometry
Bruker Daltonik GmbH
Fahrenheitstr. 4
28359 Bremen
Germany
Erika Lattová
Department of Chemistry
University of Manitoba
144 Dysart Road
Winnipeg, MB R3T 2N2
Canada
Fangbiao Li
Merck Research Laboratories
DMPK Bioanalytical Group
Mail Stop RY800B201
Rahway, NJ 07065
USA
Liang Li
University of Alberta
Department of Chemistry
Chemistry Centre W3-39
Edmonton, AB T6G 2G2
Canada
Peter B. O'Connor
University of Warwick
Department of Chemistry
Gibbet Hill Road
Coventry CV4 7AL
UK
Hélène Perreault
Department of Chemistry
University of Manitoba
144 Dysart Road
Winnipeg, MB R3T 2N2
Canada
Jasna Peter-Katalinic
Department of Biotechnology
University of Rijeka
Radmile Matejčić 2
51000 Rijeka
Croatia
Thang V. Pham
VU University Medical Center
VUmc-Cancer Center Amsterdam, Department of Medical Oncology
CCA 1-46, OncoProteomics Laboratory
De Boelelaan 1117
1081 HV Amsterdam
The Netherlands
Dijana Šagi
Sanofi-Aventis Deutchland GmbH
Industriepark Höchst, Geb. H773
65926 Frankfurt am Main
Germany
Jürgen Schiller
University of Leipzig
Institute of Medical Physics and Biophysics, Faculty of Medicine
Härtelstr. 16–18
04109 Leipzig
Germany
Gary Siuzdak
The Scripps Research Institute
Center for Metabolomics and Mass Spectrometry
Departments of Chemistry, Molecular and Computational Biology
BCC007
10550 North Torrey Pines Road
La Jolla, CA 92037
USA
Bernhard Spengler
Justus Liebig University Giessen
Institute of Inorganic and Analytical Chemistry
Schubertstr. 60, Bldg 16
35392 Giessen
Germany
Kerstin Strupat
Thermo Fisher Scientific
Life Science Mass Spectrometry
Hanna-Kunath-Str. 11
28199 Bremen
Germany
1
The MALDI Process and Method
Franz Hillenkamp, Thorsten W. Jaskolla, and Michael Karas
1.1 Introduction
Matrix-assisted laser desorption/ionization (MALDI) is one of the two “soft” ionization techniques besides electrospray ionization (ESI) which allow for the sensitive detection of large, nonvolatile and labile molecules by mass spectrometry. Over the past 27 years, MALDI has developed into an indispensable tool in analytical chemistry, and in analytical biochemistry in particular. In this chapter, the reader will be introduced to the technology as it stands now, and some of the underlying physical and chemical mechanisms as far as they have been investigated and clarified to date will be discussed.
Attention will also be focused on the central issues of MALDI, that are necessary for the user to understand for the efficient application of this technique. As an in-depth discussion of these topics is beyond the scope of this chapter, the reader is referred to recent reviews [1–4]. Details of the current state of instrumentation, including lasers and their coupling to mass spectrometers, will be presented in Chapter 2.
As with most new technologies, MALDI came as rather a surprise even to the experts in the field on the one hand, but also evolved from a diversity of prior art and knowledge on the other hand. The original notion had been that (bio)molecules with masses in excess of about 500–1000 Da could not be isolated out of their natural (e.g., aqueous) environment, and even less be charged for an analysis in the vacuum of a mass spectrometer without excessive and unspecific fragmentation. During the late 1960s, however, Beckey introduced field desorption (FD), the first technique to open a small road into the territory of mass spectrometry (MS) of bioorganic molecules [5]. Next came secondary ion mass spectrometry (SIMS), and in particular static SIMS, as introduced by A. Benninghoven in 1975 [6]. This development was taken a step further by M. Barber in 1981, with the bombardment of organic compounds dissolved in glycerol with high-energy atoms, which Barber coined fast atom bombardment (FAB). It was in this context, and in conjunction with the first attempts to desorb organic molecules with laser irradiation, that the concept of a “matrix” as a means of facilitating desorption and enhancing ion yield was born [7]. The principle of desorption by the bombardment of organic samples with the fission products of the 252Cf nuclear decay, later termed plasma desorption (PD), was first described by R. Macfarlane in 1974 [8]. Subsequently, the groups of Sundqvist and Roepstoff greatly improved the analytical potential of this technique by the addition of nitrocellulose, which not only cleaned up the sample but was also suspected of functioning as a signal-enhancing matrix [9].
The first attempts at using laser radiation to generate ions for a mass spectrometric analysis were reported only a few years after the invention of the laser [10, 11]. Vastola and Pirone had already demonstrated the possibility of recording the spectra of organic compounds with a time-of-flight (TOF) mass spectrometer. Subsequently, several groups continued to pursue this line of research, mainly R. Cotter at Johns Hopkins University in the USA and P. Kistemaker at the FOM Institute in Amsterdam, the Netherlands. Indeed, for a number of years the Amsterdam group held the high-mass record for a bioorganic analyte with a spectrum of underivatized digitonin at mass 1251 Da ([M + Na]+), desorbed with a CO2-laser at a wavelength of 10.6 μm in the far infrared (IR) [12].
Independently of, and parallel to, these groups, Hillenkamp and Kaufmann developed the laser microprobe mass analyzer (LAMMA) [13], the commercial version of which was marketed by Leybold Heraeus in Cologne, Germany and which is now on exhibition in the section on New Technologies of the Deutsches Museum in Munich, Germany. The instrument originally comprised a frequency-doubled ruby laser at a wavelength of 347 nm in the near ultraviolet (UV), and later a frequency-quadrupled Nd:YAG-laser at a wavelength of 266 nm in the far UV. The laser beam was focused to a spot of ≤1 μm in diameter to probe thin tissue sections for inorganic ions and trace elements such as Na, K, and Fe. The mass analyzer of the LAMMA instruments was also a TOF mass spectrometer, and was the first commercial instrument with an ion reflector, which had been invented a few years earlier by B.A. Mamyrin in Leningrad. The sensitivity-limiting “noise” of the LAMMA spectra were signals that were soon identified as coming from the organic polymer used to embed the tissue sections, as well as other organic tissue constituents. It was this background noise which triggered the search for a systematic analysis of organic samples and which eventually led to the discovery of the MALDI principle in 1984. The principle and its acronym were first described in 1985 [14], and the first spectrum of the nonvolatile bee venom mellitin, an oligopeptide at mass 2845 Da, in 1986 [15]. Spectra of proteins with masses exceeding 10 kDa and 100 kDa were reported in 1988 [16], and details presented at the International Mass Spectrometry Conference in Bordeaux in 1988, respectively.
Both, ESI and MALDI were developed independently but concurrently, and when their potential for the desorption of nonvolatile, fragile (bio)molecules was discovered, the scientific community was mostly impressed by the ability of these techniques to access the high mass range, particularly of proteins. However, FAB- and PD-MS had at that time already generated spectra of trypsin at mass 23 kDa and other high-mass proteins. What really made the difference in particular for the biologists was the stunning sensitivity which, for the first time, made MS compatible with sample preparation techniques used in these fields. For MALDI, the minimum amount of protein needed for a spectrum of high quality was reduced from 1 pmol in 1988 to a few femtomoles only about a year later. Today, in favorable cases, the level is now down in the low attomole range. Many other developments – both instrumental (see ) as well as specific sample preparation recipes and assays (see other chapters of the book) – took place during the following decade, and the joint impact of all of these together has today made MALDI-MS an indispensable tool not only in the life sciences but also in polymer analysis, food sciences, pharmaceutical drug discovery, or forensic jurisprudence.
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
Lesen Sie weiter in der vollständigen Ausgabe!
