Mass Spectrometry for the Characterization of Microorganisms

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MASS SPECTROMETRY FOR CHARACTERIZATION OF MICROORGANISMS

Subject Index

Downloaded by STOCKHOLM UNIV on August 11, 2015 | http://pubs.acs.org Publication Date: November 30, 1993 | doi: 10.1021/bk-1994-0541.ix002

A Acinetobacter calcoaceticus, fast atom bombardment MS, 25i,26 Acute infections, use of lipid biomarkers for rapid diagnosis, 14 Alditol acetate(s), MS, 113-119 Alditol acetate method comparison to other procedures, 110 description and development, 109-110 procedure, 110-113 Algae, fast atom bombardment MS, 23 Anaerobic Gram-negative rods, fast atom bombardment MS, 28,29/ Analytical microbiology, development, 107 D-Arabinitol as Candida metabolite formulas, 135/ identification, 134-135 Arabinitol enantiomers, GC-MS quantifica tion techniques, 137

Β Bacteria fast atom bombardment MS, 20 identification, 125-126 identification and detection of carbohydrate markers, 107-128 structural components, 107 volatile detection by using membrane inlet MS, 101,103 Bacteria in complex matrices trace detection, 127-128 trace GC-MS analysis, 122-126 Bacteria in organic dust, chemical markers, 123-126/ Bacterial carbohydrates, 108 Bacterial cells, whole, analysis by GC-MS, 118,120-122 Bacterial chemotaxonomy, fast atom bom bardment MS of phospholipids, 18-33 Bacterial polar lipids, 20,24/ Biological agents, detection and identification by using analytical instrumentation, 62 Biological welfare agents, detection by using pyrolysis-GC-MS, 62-82 Biomarker, detection techniques, 9

Biomolecules, examples, 36 Bioremediation strategies, use of lipid bio markers for monitoring and prediction, 14

C Candidiasis, disseminated, See Disseminated candidiasis Capnocytophaga, fast atom bombardment MS, 28,29/ Capnophilic Gram-negative rods, fast atom bombardment MS, 28,29/ Carbohydrate markers for bacteria after derivatization and GC-MS alditol acetate method, 109-110 bacterial carbohydrates, 108 future directions, 125,127-128 MS of alditol acetates, 113-119 trace GC-MS analysis of bacteria in complex matrices, 122-126/ whole bacterial cell analysis, 118,120-122 Characterization of microorganisms, 1 Chemical welfare agents, detection and identification, 62-63 Chemosystematics, definition, 18 Chemotaxonomic markers complex polar lipids, 3-5 nuclease digests of tRNA, 3 protein sequences, 3 Chemotaxonomy, definition, 18 Citrobacterfreundii,fast atom bombardment MS, 25/,26 Clinical matrices, rapid identification of microbes, 8-14 Complex polar lipids, use as chemotaxonomic markers, 3-5 Culturing, strategy for microorganism characterization, 6 Curie-point pyrolysis analytical dimensions of information, 66-69 1-min generation of bacterial lipids, 74-79/ mislabeled microorganism, 69,71/ nucleic acid formation, 69,71-72/ procedure, 63-64 procedure using 2-m GC column, 65 reproducibility, 69,70/"

In Mass Spectrometry for the Characterization of Microorganisms; Fenselau, C.; ACS Symposium Series; American Chemical Society: Washington, DC, 1993.

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INDEX Curie-point pyrolysis—Continued restructured ion chromatographic patterns, 69,73/,74 Cyclopropyl fatty acids, biomarkers for meta bolic status of microbial consortia, 11

Environmental toxicity, use of lipid bio markers for assessment, 14 Ether lipids, microbial biomass measure ment, 9-10

F


D D/L arabinitol ratios, MS determination for diagnosis and monitoring of disseminated candidiasis, 132-144 Data analytical techniques for phospholipid profiling cluster analysis, 54,56-59/ library searching, 54 visual inspection of data, 54 Derivatization-supercritical fluid extraction, rapid analysis of lipid biomarkers, 12,13/ Desorption MS, description, 2 Directly combined LC-MS modified nucleoside determination, 151,153-157 procedure, 155-157/ Disseminated candidiasis blood culturing, 134 Candida organisms, 133 clinical manifestations, 133 definitive diagnosis, 134 description, 132 diagnosis and monitoring by MS determina tion of D/L arabinitol ratios, 134-144 epidemiology, 133 opportunistic infection, 132-133 serodiagnosis, 134 signs and symptoms, 134 treatment, 133-134 DNA, posttranscriptional modifications, 147

Ε Enterobacter cloacae, fast atom bombard ment MS, 25i-27/ Enterobacteria, fast atom bombardment MS, 23-25/ Environmental matrices, rapid identification of microbes, 8-14

Fast atom bombardment MS Acinetobacter calcoaceticus, 25r,26 algae, 23 anaerobic Gram-negative rods, 28,29/ bacteria, 20 Capnocytophaga, 28,29/ capnophilic Gram-negative rods, 28,29/ Gram-positive cocci, 28,30/ lipid A moiety of lipopolysaccharides, 174-176 microbial polar lipids, 23-32

Micrococcus, 28 nonfermenting Gram-negative rods, 25/,26 nonsporing Gram-positive rods, 28,31/ phosphatidylcholine, 20,21/ phosphatidylethanolamine, 21,22/ phosphatidylglycerol, 22,23/ phosphatidylserine, 23 polar lipids, 20-23/ Prevotella, 28,29/ Pseudomonas, 25/,26 sporing Gram-positive rods, 32

Staphylococcus, 28 Streptococcus, 28,30/" structural analysis of mycobacterial lipids, 224-225,228/ Fast atom bombardment MS of phospho lipids for bacterial chemotaxonomy bacteria, 20 future applications, 33 microbial polar lipids, 23-32 numerical data analysis, 32/,33 polar lipids, 20-23/ schematic representation, 18,19/ Fatty acyl groups, identification and location, 221,223-227 Filter paper sampling of whole blood and urine, GC-MS quantification techniques, 137-138 Fingerprinting, strategy for microorganism characterization, 6 Fungi, toxin production, 85


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G Gas chromatography-MS applications, 91-92 identification and detection of carbohydrate markers for bacteria, 107-128 Gas chromatographic-MS analysis of volatile metabolites for grain infection detection advantages, 86 application, 87,90 electron impact MS, 87,89,90/ experimental procedure, 86 odor volatiles, 87,88r total ion chromatogram, 87,89/ Gas chromatographic-MS quantification techniques arabinitol enantiomers, 137 filter paper sampling of whole blood and urine, 137-138 pentitols, 135-137 polyols, 136 Glycolipids of mycobacteria absolute configuration procedure, 214 alkylation procedure, 215 amino acid analytical procedure, 214 characteristics, 203-204 classes, 204,205/ composition determination procedure, 214 glycopeptidolipids, 210,212/,213 glycosyl linkage analytical procedure, 215 lipooligosaccharide antigens, 204,206-210 MS procedures, 216 NMR analytical procedure, 215-216 oligosaccharide hapten preparation procedure, 215 phenolic glycolipids, 210,211/ purification, 213-214 structural analysis, 216-228 Glycopeptidolipids of mycobacteria, characterization, 210,2121,213 Glycosyl residues absolute configuration elucidation, 217,219/ composition determination, 216-218/ sequence, 217,220/-222/ Grain infection by toxicogenous fungi species detection by GC-MS analysis of volatile metabolites, 85-90

Grain infection by toxicogenous fungi species—Continued detection methods, 85-86 Gram-negative bacteria, MS analysis of lipid A, 173-183 Gram-positive cocci, fast atom bombardment MS, 28,30/

H Haemophilus species, health consequences, 185 Harvested cereals, fungi and bacterial infections, 85 High-performance liquid chromatography (HPLC)-MS, use for nucleoside identification, 147 HIV-1 vims characterization of processed G A G proteins, 159-171 structural organization, 159-161/

L Laser desorption MS analysis, lipid A moiety of lipopolysaccharides, 174,176-178/ Lipid(s), functions, 36-37 Lipid A moiety of lipopolysaccharides analytical methods, 173-174 fast atom bombardment MS analysis, 174-176 health effects, 173 identifications, 182-183 laser desorption MS analysis, 174,176-178/ plasma desorption MS analysis, 178-182 stmcture, 173,175/ Lipid biomarker(s) applications, 9 microbial biomass measurement, 9-10 microbial community stmcture measurement, 10-11 rapid analysis, 12,13/ Lipid biomarker analysis, advantages of rapid methods, 8 Lipooligosaccharide(s), structure, 186,188-189/ Lipooligosaccharide antigens of Mycobacterium spp., characterization, 204,206-210


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INDEX Lipooligosaccharide(s) in pathogenic Haemophilus and Neisseria species using MS techniques lipooligosaccharide preparation and isolation, 186 liquid secondary ion MS free oligosaccharides, 191-194/ hydrazone oligosaccharides, 193,195-197/ procedure, 187 molecular weight analysis, 187,191 O-deacetylated lipooligosaccharide preparation and analysis, 186 oligosaccharide fraction preparation and purification, 186 oligosaccharide separation and derivatization, 187,190/ structure determination, 191 tandem MS of free and derivatized oligosaccharides, 197-200/ tandem MS procedure, 187 Lipopolysaccharides, structural regions, 173 Liquid layer, unstirred, transport, 95 Liquid secondary ion MS, identification and characterization of lipooligosaccharides in pathogenic Haemophilus and Neisseria species, 185-200

M Mass spectral analysis of lipid A of Gramnegative bacteria fast atom bombardment MS, 174-176 identifications, 182-183 laser desorption MS, 174,176-178/ plasma desorption, 178-182 Mass spectrometric determination of D/L arabinitol ratios for diagnosis and monitoring of disseminated candidiasis advantages of GC-MS, 138 D-arabinitol as Candida metabolite, 134,135/ candidiasis, 132-134 D/L ratios, 138-139 diagnostic sensitivity and specificity, 142r enantiomer separation procedure, 138,141/ endogenous total arabinitol and D/Lratios, 140U41/ filter sampling procedure, 139 GC-MS quantification techniques, 135-138

Mass spectrometric determination of D/L arabinitol ratios for diagnosis and monitoring of disseminated candidiasis— Continued

monitoring of D/L arabinitol ratios, 142-144 rationale for using D/L arabinitol ratios, 139 Mass spectrometry, identification and characterization of lipooligosaccharides in pathogenic Haemophilus and Neisseria species, 185-200 Mass spectrometry for microorganism characterization advantages and disadvantages, 1-2 chemotaxonomic markers, 3-5 strategies, 6 techniques, 2-3 Membrane inlet(s) design and application, 92,93/95-97 instrumentation, 97 techniques, 97-98 transport through polymer membranes, 92,94-95 transport through unstirred liquid layer, 95 transport through vacuum tubes, 95 Membrane inlet MS, applications, 91 Membrane inlet MS for volatile metabolite detection advantages, 92 bacteria, 101,103 construction of membrane inlets, 92-98 protozoa, 99,101,102/ yeasts, 98-100/ Membrane responsetime,calculation, 94-95 Metabolic status of microbial consortia, 11 Microbes analytical techniques, 107-108 rapid identification, 8-14 Microbial biomass measurement ether lipids, 9-10 polar lipid fatty acids, 9 sterols, 9 Microbial characterization by phospholipid profiling culturing effect, 51,53 data analysis, 53-60 data analytical techniques, 54,56-59/ environmental effects on phospholipid contents, 45-53 experimental objectives, 37 growth media effect, 48-51



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Microbial characterization by phospholipid profiling—Continued growth temperature effect, 45,46/,48 growth time effect, 45,47/,48 phospholipid data space, 39,40/" phospholipid dissociation under low-energy conditions, 37,39/ potential information from phospholipid profile, 53-55/ profiling scheme, 40-43/ sample history effect, 51,52/" sensitivity, 42,44/45 structures of glycerophospholipids, 37,38/ unexplored-underdeveloped territory, 56,60 Microbial community structure measurement community stmcture by fingerprint analysis, 11 specific organism identification, 10-11 Microbial lipids, use as biomarker, 8 Microbial polar lipids, fast atom bombard ment MS, 23-32 Micrococcus, fast atom bombardment MS, 28 Microorganisms characterization by using MS, 2-6 ideal analytical method, 1-2 importance of identification, 1 quartz tube pyrolysis, 75-76,80-81/ RNA modification, 147-157 volatile detection using membrane inlet MS, 91-103 MIDI system, rapid analysis of lipid biomarkers, 12 M N strain of HTV-1, characterization of processed GAG proteins, 159-171 Morganella morganii, fast atom bombard ment MS, 25f,26 Muramic acid, alditol acetate procedure, 109 Mycobacteria glycolipids, 204-228 reasons for interest, 203 Mycobacterial lipids, structural analysis, 216-228

Ν Neisseria species, health consequences, 185 Nonfatty acyl groups, identification and location, 221,223-227 Nonfermenting Gram-negative rods, fast atom bombardment MS, 25i,26

Nonsporing Gram-positive rods, fast atom bombardment MS, 28,31/ Nuclease digests of tRNA, use as phyloge netic markers, 3 Nucleic acids, posttranscriptional modifica tions, 147 Nucleosides, thermospray MS, 155,156/

Organic dust, chemical markers for bacteria, 123-126/ Oxidative pyrolysis, definition, 63

Pentitols, GC-MS quantification techniques, 135-137 Peptidoglycan, processing, 122-123 Phenolic glycolipids of mycobacteria, charac terization, 210,21 It Phosphatidylcholine, fast atom bombardment MS, 20,21* Phosphatidylethanolamine, fast atom bom bardment MS, 21,22i Phosphatidylglycerol, fast atom bombardment MS, 22,23i Phosphatidylserine, fast atom bombardment MS, 23 Phospholipid(s), fast atom bombardment MS, 18-33 Phospholipid profiling, microbial character ization, 36-60 Phylogenetic significance of modified nucleosides in tRNA domains of living organisms, 148,151,152/ modified nucleoside(s) as markers of domain, 151,152f modified nucleoside occurrence in primary domains, 151 Plasma desorption MS analysis, lipid A moiety of lipopolysaccharides, 178-182 Plesiomonas shigelloides, fast atom bom bardment MS, 25i,26 Polar lipid(s), fast atom bombardment MS, 20-23f Polar lipid fatty acids, microbial biomass measurement, 9


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INDEX Ροΐν-β-hydroxyalkanoates, biomarkers for metabolic status of microbial consortia, 11 Polymer membranes, transport, 92,94-95 Polyols, GC-MS quantification techniques, 136 Porous membranes, flow, 94 Prevotella, fast atom bombardment MS, 28,29/ Processed GAG proteins from highly replicating HIV-1MN bond cleavages in amide backbone of peptides, 160,162,163/ characterization procedure, 160,162 locations, 160,161/ molecular weights, 162-167 partial reversed-phase HPLC of viruses, 160,161/ protein maps, 164,169/ protein sequences, 164,168/170-171/ Profiling, phospholipid, microbial characterization, 36-60 Protein sequences, use as chemotaxonomic markers, 3 Proteus, fast atom bombardment MS, 25i-27/ Protozoa, volatile detection by using mem brane inlet MS, 99,101,102/ Pseudomonas, fast atom bombardment MS, 25f,26 Pyrolysis, definition, 63 Pyrolysis-GC-MS for biological warfare agent detection analytes, 65-66 Curie-point pyrolytic procedure, 63-64,66-79 Curie-point pyrolytic procedure with 2-m GC column, 65 future work, 62 quartz tube pyrolytic procedure, 64-65 quartz tube pyrolysis, 75-76,80-81/

Q Quartz tube pyrolysis microorganisms, 75-76,80-81/ procedure, 64-65

R Rapid analysis of lipid biomarkers applications, 14 derivatization-supercritical fluid extraction, 12,13/ MIDI system, 12 Rapid identification of microbes from clinical and environmental matrices by characterization of signature lipids applications, 14 rapid analytical techniques, 12,13/ signature lipid biomarkers, 9-12 Respiratory quinones, biomarkers for meta bolic status of microbial consortia, 11 Reversed-phase high-performance liquid chromatography, process for modified nucleoside determination, 153,154/ Ribonucleic acid modification in microorganisms modified nucleoside determination by directly combined LC-MS, 151,153-157 phylogenetic significance of modified nucleosides, 148,151,152/r tRNA stmcture, 148-150/ Ribosomal RNA, posttranscriptional modifications, 147

S Separation MS, description, 2 Serratia, fast atom bombardment MS, 25f,26 Specific organisms, identification, 10-11 Sporing Gram-positive rods, fast atom bombardment MS, 32 Staphylococcus, fast atom bombardment MS, 28 Sterols, microbial biomass measurement, 10 Streptococcus, fast atom bombardment MS, 28,30/ Structural analysis of mycobacterial lipids fast atom bombardment MS, 224-225,228/ fatty and nonfatty acyl group identification and location, 221,223-227 glycosyl composition determination, 216-218/ glycosyl residue absolute configuration elucidation, 217,219/ glycosyl residue sequence, 217,220/-222/


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Structure elucidation, strategy for microor ganism characterization, 6 Supercritical fluid extraction, rapid analysis of lipid biomarkers, 12

Transfer RNA digests, preparation, 153 Triglycerides, biomarkers for metabolic status of microbial consortia, 12

U Unstirred liquid layer, transport, 95 Tandem MS description, 2-3 identification and characterization of lipooligosaccharides in pathogenic Downloaded by STOCKHOLM UNIV on August 11, 2015 | http://pubs.acs.org Publication Date: November 30, 1993 | doi: 10.1021/bk-1994-0541.ix002

Haemophilus and Neisseria species,

185-200 Thermospray MS, nucleosides, 155,156/ Trace GC-MS analysis of bacteria in complex matrices bacterial debris processing, 122-123 chemical markers for bacteria in organic dust, 123-126/ Trans monounsaturated fatty acids, biomarkers for metabolic status of microbial consortia, 11 Transfer RNA modified nucleoside determination by directly combined LC-MS, 151,153-157 modified nucleoside occurrence, 148,15(y modified nucleoside role, 148 phylogenetic significance of modified nucleosides, 148,151,152/r posttranscriptional modifications, 148

V Vacuum tubes, transport, 95 Viral proteins, reasons for study, 159-160 Volatile metabolitesfrommicroorganisms, detection using membrane inlet MS, 91-103

W Whole bacterial cells, analysis by GC-MS, 118,120-122

Y Yeasts, volatile detection by using mem brane inlet MS, 98-100/

Production: Donna Lucas Indexing: Deborah Κ Steiner Acquisition: Rhonda Bitterli Cover design: Amy Meyer Phifer Printed and bound by Maple Press, York, PA In Mass Spectrometry for the Characterization of Microorganisms; Fenselau, C.; ACS Symposium Series; American Chemical Society: Washington, DC, 1993.

Mass Spectrometry for the Characterization of Microorganisms

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