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List of Contributors xxi
Preface xxix
Part I MALDI-TOF Mass Spectrometry 1
1 A Paradigm Shift from Research to Front?]Line Microbial Diagnostics in MALDI?]TOF and LC?]MS/MS: A Laboratory's Vision and Relentless Resolve to Help Develop and Implement This New Technology amidst Formidable Obstacles 3 Haroun N. Shah and Saheer E. Gharbia
2 Criteria for Development of MALDI?]TOF Mass Spectral Database 39 Markus Kostrzewa and Thomas Maier
3 Applications of MALDI?]TOF Mass Spectrometry in Clinical Diagnostic Microbiology 55 Onya Opota, Guy Prod'hom and Gilbert Greub
4 The Challenges of Identifying Mycobacterium to the Species Level using MALDI?]TOF MS 93
5 Transformation of Anaerobic Microbiology since the Arrival of MALDI?]TOF Mass Spectrometry 123 Elisabeth Nagy, Mariann Abrok, Edith Urban, A.C.M. Veloo, Arie Jan van Winkelhoff, Itaru Dekio, Saheer E. Gharbia and Haroun N. Shah
6 Differentiation of Closely Related Organisms using MALDI?]TOF MS 147 Mark A. Fisher
7 Identification of Species in Mixed Microbial Populations using MALDI?]TOF MS 167 Pierre Mahe, Maud Arsac, Nadine Perrot, Marie?]Helene Charles, Patrick Broyer, Jay Hyman, John Walsh, Sonia Chatellier, Victoria Girard, Alex van Belkum, and Jean?]Baptiste Veyrieras
8 Microbial DNA Analysis by MALDI?]TOF Mass Spectrometry 187
9 Impact of MALDI?]TOF MS in Clinical Mycology; Progress and Barriers in Diagnostics 211 Cledir R. Santos, Elaine Francisco, Mariana Mazza, Ana Carolina B. Padovan, Arnaldo Colombo and Nelson Lima
10 Development and Application of MALDI?]TOF for Detection of Resistance Mechanisms 231 Stefan Zimmermann and Irene Burckhardt
11 Discrimination of Burkholderia Species, Brucella Biovars, Francisella tularensis and Other Taxa at the Subspecies Level by MALDI?]TOF Mass Spectrometry 249 Axel Karger
12 MALDI?]TOF?]MS Based on Ribosomal Protein Coding in S10?]spc?]alpha Operons for Proteotyping 269 Hiroto Tamura
Part II Tandem MS/MS-Based Approaches to Microbial Characterization 311
13 Tandem Mass Spectrometry Analysis as an Approach to Delineate Genetically Related Taxa 313 Raju V. Misra, Tom Gaulton, Nadia Ahmod, Min Fang, Martin Hornshaw, Jenny Ho, Saheer E. Gharbia and Haroun N. Shah
14 Mapping of the Proteogenome of Clostridium difficile Isolates of Varying Virulence 379 Caroline H. Chilton, Saheer E. Gharbia, Raju V. Misra, Min Fang, Ian R. Poxton, Peter S. Borriello and Haroun N. Shah
15 Determination of Antimicrobial Resistance using Tandem Mass Spectrometry 399 Ajit J. Shah, Vlad Serafim, Zhen Xu, Hermine Mkrtchyan and Haroun N. Shah
16 Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic Characterization and Typing of Pathogenic Microorganisms 419 Roger Karlsson, Lucia Gonzales?]Siles, Fredrik Boulund, Asa Lindgren, Liselott Svensson?]Stadler, Anders Karlsson, Erik Kristiansson and Edward R.B. Moore
17 Proteogenomics of Pseudomonas aeruginosa in Cystic Fibrosis Infections 451 Liang Yang and Song Lin Chua
18 Top?]Down Proteomics in the Study of Microbial Pathogenicity 493 Joseph Gault, Egor Vorontsov, Mathieu Dupre, Valeria Calvaresi, Magalie Duchateau, Diogo B. Lima, Christian Malosse and Julia Chamot?]Rooke
19 Tandem Mass Spectrometry in Resolving Complex Gut Microbiota Functions 505 Carolin Kolmeder, Kaarina Lahteenmaki, Pirjo Wacklin, Annika Kotovuori, Ilja Ritamo, Jaana Matto, Willem M. de Vos, and Leena Valmu
20 Proteogenomics of Non?]model Microorganisms 529 Jean Armengaud
21A Analysis of MALDI?]TOF MS Spectra using the BioNumerics Software 539 Katleen Vranckx, Katrien De Bruyne and Bruno Pot
21B Subtyping of Staphylococcus spp. Based upon MALDI?]TOF MS Data Analysis 563 Zhen Xu, Ali Olkun, Katleen Vranckx, Hermine V. Mkrtchyan, Ajit J. Shah, Bruno Pot, Ronald R. Cutler and Haroun N. Shah
21C Elucidating the Intra?]Species Proteotypes of Pseudomonas aeruginosa from Cystic Fibrosis 579 Ali Olkun, Ajit J. Shah and Haroun N. Shah
References 588
Index 593
Mariann Ábrók Institute of Clinical Microbiology Faculty of Medicine University of Szeged Hungary Nadia Ahmod Proteomics Research Public Health England London UK David J. Allen Virology Public Health England London UK Jean Armengaud CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D Laboratory "Innovative Technologies for Detection and Diagnostics" Bagnols-sur-Cèze France Maud Arsac bioMérieux SA Marcy-l'Etoile France Peter S. Borriello Veterinary Medicines Directorate Surrey UK Fredrik Boulund Department of Mathematical Sciences Chalmers University of Technology Gothenburg Sweden Patrick Broyer bioMérieux SA Marcy-l'Etoile France Irene Burckhardt Division of Medical Microbiology and Hygiene, Department of Infectious Diseases University Hospital Heidelberg Germany Valeria Calvaresi Structural Mass Spectrometry and Proteomics Unit Institut Pasteur Paris, France Timothy Chambers Proteomics Research Public Health England London UK Julia Chamot-Rooke Structural Mass Spectrometry and Proteomics Unit Institut Pasteur Paris France Marie-Hélène Charles bioMérieux SA Marcy-l'Etoile France Sonia Chatellier bioMérieux SA La Balme-les-Grottes France Caroline H. Chilton Leeds Institute for Biomedical and Clinical Sciences University of Leeds UK Song Lin Chua Singapore Centre for Environmental Life Sciences Engineering (SCELSE) and Lee Kong Chian School of Medicine Nanyang Technological UniversitySingapore Arnaldo Colombo Department of Medicine Infectious Diseases Section Federal University of São Paulo (UNIFESP) SP Brazil Renata Culak Proteomics Research Public Health England London UK Ronald R. Cutler School of Biological and Chemical Sciences Queen Mary University of London UK Katrien De Bruyne Applied Maths NV Sint-Martens Latem Belgium Willem M. de Vos Faculty of Veterinary Medicine University of Helsinki Finland and Laboratory of Microbiology Wageningen University The Netherlands Itaru Dekio Medical Centre East Tokyo Women's Medical University Japan Magalie Duchateau Structural Mass Spectrometry and Proteomics Unit Institut Pasteur Paris France Mathieu Dupré Structural Mass Spectrometry and Proteomics Unit Institut Pasteur Paris France Min Fang Proteomics Research Public Health England London UK Mark A. Fisher University of Utah School of Medicine and Bacteriology and Antimicrobials ARUP Infectious Diseases Laboratory Salt Lake City, UT, USA Elaine Francisco Department of Medicine Infectious Diseases Section Federal University of São Paulo (UNIFESP) SP Brazil Joseph Gault Structural Mass Spectrometry and Proteomics Unit Institut Pasteur Paris France Tom Gaulton Proteomics Research Public Health England London UK Saheer E. Gharbia Genomic Research Unit Public Health England London UK Victoria Girard bioMérieux SA La Balme-les-Grottes France Lucia Gonzales-Siles Department of Infectious Diseases Institute of Biomedicine The Sahlgrenska Academy University of Gothenburg Sweden Gilbert Greub Institute of Microbiology, University Hospital Center, and University of Lausanne Switzerland Nicola Hennessy Genomic Research Unit Public Health England London UK Jenny Ho ThermoFisher Scientific Hemel Hempstead Hertfordshire UK Christiane Honisch Illumina, Inc. San Diego, CA USA Martin Hornshaw ThermoFisher Scientific Hemel Hempstead Hertfordshire UK Jay Hyman bioMérieux Inc Durham, NC USA Axel Karger Friedrich-Loeffler-Institut Federal Research Institute for Animal Health Greifswald - Insel Riems Germany Anders Karlsson Nanoxis Consulting AB Gothenburg Sweden Roger Karlsson Department of Clinical Microbiology Sahlgrenska University Hospital and Nanoxis Consulting AB Gothenburg Sweden Jae-Seok Kim Department of Laboratory Medicine Hallym University College of Medicine Seoul Korea Yangsun Kim ASTA Inc Gyeonggi-do Korea Carolin Kolmeder Faculty of Veterinary Medicine University of Helsinki Finland Markus Kostrzewa Bruker Daltonik GmbH Bremen Germany Annika Kotovuori ThermoFisher Scientific Vantaa Finland Erik Kristiansson Department of Mathematical Sciences Chalmers University of Technology Gothenburg Sweden Kaarina Lähteenmäki Finnish Red Cross Blood Service Helsinki Finland Diogo B. Lima Structural Mass Spectrometry and Proteomics Unit Institut Pasteur Paris France Nelson Lima CEB-Centre of Biological Engineering Micoteca da Universidade do Minho University of Minho Braga Portugal Åsa Lindgren Department of Clinical Microbiology Sahlgrenska University Hospital and Department of Infectious Diseases Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg Sweden Pierre Mahé bioMérieux SA Marcy-l'Etoile France Thomas Maier Bruker Daltonik GmbH Bremen Germany Christian Malosse Structural Mass Spectrometry and Proteomics Unit Institut Pasteur Paris France Jaana Mättö Finnish Red Cross Blood Service Helsinki Finland Mariana Mazza Department of Mycology INEI/Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán"-ANLIS. Ciudad Autónoma de Buenos Aires Argentina Raju V. Misra Genomic Research Unit Public Health England London UK Hermine V. Mkrtchyan School of Biological and Chemical Sciences Queen Mary University of London UK Edward R.B. Moore Department of Clinical Microbiology Sahlgrenska University Hospital and Department of Infectious Diseases Institute of Biomedicine The Sahlgrenska Academy University of Gothenburg Sweden Leonardo P. Munoz Department of Natural Sciences Middlesex University London, UK Elisabeth Nagy Institute of Clinical Microbiology Faculty of Medicine University of Szeged Hungary Ali Olkun Department of Natural Sciences Middlesex University London, UK Onya Opota Institute of Microbiology, University Hospital Center, and University of Lausanne Switzerland Ana Carolina B. Padovan Department of Medicine Infectious Diseases Section Federal University of São Paulo (UNIFESP) SP Brazil Nadine Perrot bioMérieux SA La Balme-les-Grottes France Bruno Pot Applied Maths NV Sint-Martens Latem Belgium Ian R. Poxton Department of Medical Microbiology University of Edinburgh UK Guy Prod'hom Institute of Microbiology, University Hospital Center, and University of Lausanne Switzerland Christopher Ring Department of Natural Sciences Middlesex University London, UK Ilja Ritamo ThermoFisher Scientific Vantaa Finland Graham Rose Genomic Research Unit Public Health England London UK Cledir R. Santos Department of Chemical Sciences and Natural Resources CIBAMA, BIOREN, University of La Frontera Temuco Chile Vlad Serafim Department of Natural Sciences Middlesex University London UK Ajit J. Shah Department of Natural Sciences Middlesex University London UK Haroun N. Shah Proteomics Research Public...
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