MALDI-TOF and Tandem MS for Clinical Microbiology

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

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• List of Contributors xxiPreface xxixPart I MALDI-TOF Mass Spectrometry 11 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 3Haroun N. Shah and Saheer E. Gharbia2 Criteria for Development of MALDI]TOF Mass Spectral Database 39Markus Kostrzewa and Thomas Maier3 Applications of MALDI]TOF Mass Spectrometry in Clinical Diagnostic Microbiology 55Onya Opota, Guy Prod’hom and Gilbert Greub4 The Challenges of Identifying Mycobacterium to the Species Level using MALDI]TOF MS 935 Transformation of Anaerobic Microbiology since the Arrival of MALDI]TOF Mass Spectrometry 123Elisabeth Nagy, Mariann Abrok, Edith Urban, A.C.M. Veloo, Arie Jan van Winkelhoff, Itaru Dekio, Saheer E. Gharbia and Haroun N. Shah6 Differentiation of Closely Related Organisms using MALDI]TOF MS 147Mark A. Fisher7 Identification of Species in Mixed Microbial Populations using MALDI]TOF MS 167Pierre Mahe, Maud Arsac, Nadine Perrot, Marie]Helene Charles, Patrick Broyer, Jay Hyman, John Walsh, Sonia Chatellier, Victoria Girard, Alex van Belkum, and Jean]Baptiste Veyrieras8 Microbial DNA Analysis by MALDI]TOF Mass Spectrometry 1879 Impact of MALDI]TOF MS in Clinical Mycology; Progress and Barriers in Diagnostics 211Cledir R. Santos, Elaine Francisco, Mariana Mazza, Ana Carolina B. Padovan, Arnaldo Colombo and Nelson Lima10 Development and Application of MALDI]TOF for Detection of Resistance Mechanisms 231Stefan Zimmermann and Irene Burckhardt11 Discrimination of Burkholderia Species, Brucella Biovars, Francisella tularensis and Other Taxa at the Subspecies Level by MALDI]TOF Mass Spectrometry 249Axel Karger12 MALDI]TOF]MS Based on Ribosomal Protein Coding in S10]spc]alpha Operons for Proteotyping 269Hiroto TamuraPart II Tandem MS/MS-Based Approaches to Microbial Characterization 31113 Tandem Mass Spectrometry Analysis as an Approach to Delineate Genetically Related Taxa 313Raju V. Misra, Tom Gaulton, Nadia Ahmod, Min Fang, Martin Hornshaw, Jenny Ho, Saheer E. Gharbia and Haroun N. Shah14 Mapping of the Proteogenome of Clostridium difficile Isolates of Varying Virulence 379Caroline H. Chilton, Saheer E. Gharbia, Raju V. Misra, Min Fang, Ian R. Poxton, Peter S. Borriello and Haroun N. Shah15 Determination of Antimicrobial Resistance using Tandem MassSpectrometry 399Ajit J. Shah, Vlad Serafim, Zhen Xu, Hermine Mkrtchyan and Haroun N. Shah16 Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic Characterization and Typing of Pathogenic Microorganisms 419Roger Karlsson, Lucia Gonzales]Siles, Fredrik Boulund, Asa Lindgren, Liselott Svensson]Stadler, Anders Karlsson, Erik Kristiansson and Edward R.B. Moore17 Proteogenomics of Pseudomonas aeruginosa in Cystic Fibrosis Infections 451Liang Yang and Song Lin Chua18 Top]Down Proteomics in the Study of Microbial Pathogenicity 493Joseph Gault, Egor Vorontsov, Mathieu Dupre, Valeria Calvaresi, Magalie Duchateau, Diogo B. Lima, Christian Malosse and Julia Chamot]Rooke19 Tandem Mass Spectrometry in Resolving Complex Gut Microbiota Functions 505Carolin Kolmeder, Kaarina Lahteenmaki, Pirjo Wacklin, Annika Kotovuori, Ilja Ritamo, Jaana Matto, Willem M. de Vos, and Leena Valmu20 Proteogenomics of Non]model Microorganisms 529Jean Armengaud21A Analysis of MALDI]TOF MS Spectra using the BioNumerics Software 539Katleen Vranckx, Katrien De Bruyne and Bruno Pot21B Subtyping of Staphylococcus spp. Based upon MALDI]TOF MS Data Analysis 563Zhen Xu, Ali Olkun, Katleen Vranckx, Hermine V. Mkrtchyan, Ajit J. Shah, Bruno Pot, Ronald R. Cutler and Haroun N. Shah21C Elucidating the Intra]Species Proteotypes of Pseudomonas aeruginosa from Cystic Fibrosis 579Ali Olkun, Ajit J. Shah and Haroun N. ShahReferences 588Index 593