MALDI–TOF and Tandem MS for Clinical Microbiology

EDITORS Haroun N. Shah, Department of Natural Sciences, Middlesex University, London, UK Saheer E. Gharbia, Genomic Research, Public Health England, London, UK

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