Direct mass spectrometric analysis of in situ thermally hydrolyzed and methylated lipids from whole bacterial cells

Identification of bacteria by fatty acid profiling with direct analysis in real time mass spectrometry

RATIONALE

Bacterial fatty acid profiling is a well-established technique for bacterial identification. Current methods involving esterification and gas chromatography/mass spectrometry (GC/MS) or matrix-assisted laser desorption/ionization (MALDI) analysis are effective, but there are potential benefits to be gained by investigating ambient ionization methods that can provide rapid analysis without derivatization or additional sample handling.

METHODS

Lipid extracts from colonies of five Gram-positive and five Gram-negative pathogenic bacteria were analyzed by Direct Analysis in Real Time (DART) ionization coupled with a time-of-flight mass spectrometer. Fatty acid profiles were obtained from the negative-ion DART mass spectra without additional derivatization or sample preparation.

RESULTS

Fatty acid profiles obtained from the deprotonated molecules [M - H](-) were found to be highly species-specific and reproducible. Leave-one-out cross validation (LOOCV) for principal component analysis (PCA) showed 100% correct classification accuracy.

CONCLUSIONS

The results of this preliminary feasibility study show good precision and accuracy, and the fatty acid patterns are clearly distinctive for each of the ten species examined. The speed and ease of analysis and the high classification accuracy for this initial study indicate that DART is an effective method for bacterial fatty acid profiling.

Strain-level bacterial identification by CeO2-catalyzed MALDI-TOF MS fatty acid analysis and comparison to commercial protein-based methods

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid approach for clinical bacterial identification. However, current protein-based commercial bacterial ID methods fall short when differentiating closely related species/strains. To address this shortcoming, we employed CeO2-catalyzed fragmentation of lipids to produce fatty acids using the energy inherent to the MALDI laser as a novel alternative to protein profiling. Fatty acid profiles collected from Enterobacteriaceae, Acinetobacter, and Listeria using CeO2-catalyzed metal oxide laser ionization (MOLI MS), processed by principal component analysis, and validated by leave-one-out cross-validation (CV), showed 100% correct classification at the species level and 98% at the strain level. In comparison, protein profile data from the same bacteria yielded 32%, 54% and 67% mean species-level accuracy using two MALDI-TOF MS platforms, respectively. In addition, several pathogens were misidentified by protein profiling as non-pathogens and vice versa. These results suggest novel CeO2-catalyzed lipid fragmentation readily produced (i) taxonomically tractable fatty acid profiles by MOLI MS, (ii) highly accurate bacterial classification and (iii) consistent strain-level ID for bacteria that were routinely misidentified by protein-based methods.

Rapid discrimination of bacteria by paper spray mass spectrometry

Paper spray mass spectrometry ambient ionization is utilized for rapid discrimination of bacteria without sample preparation. Bacterial colonies were smeared onto filter paper precut to a sharp point, then wetted with solvent and held at a high potential. Charged droplets released by field emission were sucked into the mass spectrometer inlet and mass spectra were recorded. Sixteen different species representing eight different genera from Gram-positive and Gram-negative bacteria were investigated. Phospholipids were the predominant species observed in the mass spectra in both the negative and positive ion modes. Multivariate data analysis based on principal component analysis, followed by linear discriminant analysis, allowed bacterial discrimination. The lipid information in the negative ion mass spectra proved useful for species level differentiation of the investigated Gram-positive bacteria. Gram-negative bacteria were differentiated at the species level by using a numerical data fusion strategy of positive and negative ion mass spectra.

Modified MALDI MS fatty acid profiling for bacterial identification

Bacterial fatty acid profiling is a well-established technique for bacterial identification. Ten bacteria were analyzed using both positive- and negative-ion modes with a modified matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) approach using CaO as a matrix replacement (metal oxide laser ionization MS (MOLI MS)). The results show that reproducible lipid cleavage similar to thermal in situ tetramethyl ammonium hydroxide saponification/derivatization had occurred. Principal component analysis showed that replicates from each organism grouped in a unique space. Cross validation (CV) of spectra from both ionization modes resulted in greater than 94% validation of the data. When CV results were compared for the two ionization modes, negative-ion data produced a superior outcome. MOLI MS provides clinicians a rapid, reproducible and cost-effective bacterial diagnostic tool.

Mass spectrometry characterization of the thermal decomposition/digestion (TDD) at cysteine in peptides and proteins in the condensed phase

We report on the characterization by mass spectrometry (MS) of a rapid, reagentless and site-specific cleavage at the N-terminus of the amino acid cysteine (C) in peptides and proteins induced by the thermal decomposition at 220-250 °C for 10 s in solid samples. This thermally induced cleavage at C occurs under the same conditions and simultaneously to our previously reported thermally induced site-specific cleavage at the C-terminus of aspartic acid (D) (Zhang, S.; Basile, F. J. Proteome Res. 2007, 6, (5), 1700-1704). The C cleavage proceeds through cleavage of the nitrogen and α-carbon bond (N-terminus) of cysteine and produces modifications at the cleavage site with an amidation (-1 Da) of the N-terminal thermal decomposition product and a -32 Da mass change of the C-terminal thermal decomposition product, the latter yielding either an alanine or β-alanine residue at the N-terminus site. These modifications were confirmed by off-line thermal decomposition electrospray ionization (ESI)-MS, tandem MS (MS/MS) analyses and accurate mass measurements of standard peptides. Molecular oxygen was found to be required for the thermal decomposition and cleavage at C as it induced an initial cysteine thiol side chain oxidation to sulfinic acid. Similar to the thermally induced D cleavage, missed cleavages at C were also observed. The combined thermally induced digestion process at D and C, termed thermal decomposition/digestion (TDD), was observed on several model proteins tested under ambient conditions and the site-specificity of the method confirmed by MS/MS.

Desorption electrospray ionization imaging mass spectrometry of lipids in rat spinal cord

Imaging mass spectrometry allows for the direct investigation of tissue samples to identify specific biological compounds and determine their spatial distributions. Desorption electrospray ionization (DESI) mass spectrometry has been used for the imaging and analysis of rat spinal cord cross sections. Glycerophospholipids and sphingolipids, as well as fatty acids, were detected in both the negative and positive ion modes and identified through tandem mass spectrometry (MS/MS) product ion scans using collision-induced dissociation and accurate mass measurements. Differences in the relative abundances of lipids and free fatty acids were present between white and gray matter areas in both the negative and positive ion modes. DESI-MS images of the corresponding ions allow the determination of their spatial distributions within a cross section of the rat spinal cord, by scanning the DESI probe across the entire sample surface. Glycerophospholipids and sphingolipids were mostly detected in the white matter, while the free fatty acids were present in the gray matter. These results show parallels with reported distributions of lipids in studies of rat brain. This suggests that the spatial intensity distribution reflects relative concentration differences of the lipid and fatty acid compounds in the spinal cord tissue. The "butterfly" shape of the gray matter in the spinal cord cross section was resolved in the corresponding ion images, indicating that a lateral resolution of better than 200 mum was achieved. The selected ion images of lipids are directly correlated with anatomic features on the spinal cord corresponding to the white and the gray matter.

Screening phosphatidylcholine biomarkers in mouse liver extracts from a hypercholesterolemia study using ESI-MS and chemometrics

When fed a high-fat, high-cholesterol diet (HFD), homozygous LDL receptor knockout mice exhibit extremely high levels of plasma cholesterol that are expected to influence liver metabolism. One step in the investigation of potential hepatic alterations was the analysis of organic extracts of livers from these and control mice by electrospray mass spectrometry (ESI-MS). Chemometrics (bioinformatics) analysis shows that the sample spectra cluster into two groups: one from mice with plasma cholesterol levels in excess of 900 mg dL(-1) and one from animals with cholesterol levels of 60-250 mg dL(-1). The loadings plot of the first PC in the principal-components analysis (PCA) reveals the chemical basis for clustering, i.e., biomarkers present at different concentrations in the different groups. The exact masses of the key peaks in this loadings plot indicate these species are phosphatidylcholines (PtdChos). This assignment is confirmed by tandem MS. Partial least-squares (PLS) with variable selection shows that the spectra are well correlated with plasma total cholesterol, HDL cholesterol, and triglyceride (TG) levels.

Recent Advances in Real-time Mass Spectrometry Detection of Bacteria

The analysis of bio-aerosols poses a technology challenge, particularly when sampling and analysis are done in situ. Mass spectrometry laboratory technology has been modified to achieve quick bacteria typing of aerosols in the field. Initially, aerosol material was collected and subjected off-line to minimum sample treatment and mass spectrometry analysis. More recently, sampling and analysis were combined in a single process for the real-time analysis of bio-aerosols in the field. This chapter discusses the development of technology for the mass spectrometry of bio-aerosols, with a focus on bacteria aerosols. Merits and drawbacks of the various technologies and their typing signatures are discussed. The chapter concludes with a brief view of future developments in bio-aerosol mass spectrometry.

Desorption electrospray ionization mass spectrometry of intact bacteria

Desorption electrospray ionization (DESI) mass spectrometry (MS) was used to differentiate seven bacteria species on the basis of their measured DESI-mass spectral profile. Both gram-positive and gram-negative bacteria were tested and included Escherichia coli, Staphyloccocus aureus, Enterococcus sp., Bordetella bronchiseptica, Bacillus thuringiensis, Bacillus subtilis and Salmonella typhimurium. Distinct DESI-mass spectra, in the mass range of 50-500 u, were obtained from whole bacteria in either positive or negative ion modes in less than 2 mins analysis time. Positive ion DESI-mass spectral fingerprints were compared using principal components analysis (PCA) to investigate reproducibility for the intraday and the day-to-day measurements and the method selectivity to differentiate the bacteria studied. Detailed study of variances in the assay revealed that a large contribution to the DESI-mass spectral fingerprint variation was the growth media preparation procedure. Specifically, experiments conducted with the growth media prepared using the same batch yielded highly reproducible DESI-mass spectra, both in intraday and in day-to-day analyses (i.e. one batch of growth media used over a 3-day period versus a new batch every day over the same 3-day period). Conclusions are drawn from our findings in terms of strategies for rapid biodetection with DESI-MS.

Mass spectrometry-based metabolomics

This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics. Metabolomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. These numerous analytes have very diverse physico-chemical properties and occur at different abundance levels. Consequently, comprehensive metabolomics investigations are primarily a challenge for analytical chemistry and specifically mass spectrometry has vast potential as a tool for this type of investigation. Metabolomics require special approaches for sample preparation, separation, and mass spectrometric analysis. Current examples of those approaches are described in this review. It primarily focuses on metabolic fingerprinting, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes. To perform this complex task, data analysis tools, metabolite libraries, and databases are required. Therefore, recent advances in metabolomics bioinformatics are also discussed.

Identification of Arcobacter species using phospholipid and total fatty acid profiles

High-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) were used to analyze the phospholipids and fatty acids of four Arcobacter species (becoming routinely isolated from a wide variety of food sources, especially of animal origin) to provide information for the identification within these species. Phospholipid differences were observed in the HPLC profiles. GC-MS analysis provided a complete fatty acid composition for each arcobacter that after pattern recognition analysis allows taxonomic classification of each species.

Characterizing the Phospholipid Profiles in Mammalian Tissues by MALDI FTMS

Discussed here is an analytical method for profiling lipids and phospholipids directly from mammalian tissues excised from Mus musculus (house mouse). Biochemical analysis was accomplished through the use of matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry, where whole tissue sections of mouse brain, heart, and liver were investigated. Lipid and phospholipid ions create complex MALDI mass spectra containing multiple ions with different m/z values corresponding to the same fundamental chemical species. When a computational sorting approach is used to group these ions, the standard deviation for observed relative chemical abundance can be reduced to 6.02%. Relative standard deviations of 10% are commonly accepted for standard chromatographic phospholipid analyses. Average mass measurement accuracy for 232 spectra representing three tissue types from 12 specimens was calculated to be 0.0053 Da. Further it is observed, that the data and the analysis between all the animals have near-identical phospholipid contents in their brain, heart, and liver tissues, respectively. In addition to the need to accurately measure relative abundances of phospholipid species, it is essential to have adequate mass resolution for complete and accurate overall analysis. It is reasonable to make mass composition assignments with spectral resolving power greater than 8000. However, results from the present study reveal 14 instances (C12 carbon isotope) of multiple m/z ions having the same nominal value that require greater resolution in order that overlap will not occur. Spectra measured here have an average resolving power of 12 000. It is established that high mass resolution and mass accuracy coupled with MALDI ionization provide for rapid and accurate phospholipid analysis of mammalian tissue sections.

Off-line direct deposition gas chromatography/surface-enhanced Raman scattering and the ramifications for on-line measurements

Surface-enhanced Raman spectra (SERS) of molecules separated by gas chromatography (GC) were measured off-line by condensing the analyte on a moving, liquid-nitrogen-cooled ZnSe window on which a 5 nm layer of silver had been formed by physical vapor deposition. After the components that eluted from the chromatograph had been deposited, the substrate was allowed to warm up to room temperature and transferred to the focus of a Raman microspectrometer where the spectrum of each component was measured. Band intensities in the spectrum of 3 ng of caffeine prepared in this way were approximately the same as in the spectrum of bulk caffeine. By making some logical assumptions, it was shown that identifiable GC/SERS spectra of 30 pg of many molecules could be measured over a 300 cm(-1) region in real-time and that if an optimized substrate were used the minimum identifiable quantity could be reduced to 1 pg or less.

A comprehensive and comparative analysis for MALDI FTMS lipid and phospholipid profiles from biological samples

Described here is a computationally automated method for translating complex accurate mass spectra into biologically relevant and meaningful data. Rapid profiling of detailed high resolution mass spectra resulting from direct analysis of whole cells and tissues by matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) is discussed. Lipid and phospholipid ions create complex spectra containing multiple m/z values corresponding to the same fundamental chemical species. A computational approach is employed to sort ions, with mass to charge ratios lower than m/z 1000, into groups of similar lipid and phospholipid compositions for comprehensive and rapid analysis. By sorting or binning ions in this manner, variations in the degree of cation exchange can be avoided, thus increasing the comparability of the data. The result is displayed as a histogram that is easily interpretable and comparable with similar analyses and is particularly useful for direct comparison of similar tissues. Spectra of leaves from a healthy Prunus persica (peach) tree are compared with those from leaves infected by the fungus Taphrina deformans. Although the infection can be seen as a difference in leaf structure and by visual inspection of the mass spectra, the method described here details the chemical difference in phospholipid compositions and their relative abundances.

Molecular characterisation of Xanthomonas strains isolated from aroids in Mauritius

Mauritius is one of the largest world producers of Anthurium cut flowers but outbreaks of bacterial blight have never been reported on the island. This work was about the characterisation and identification of bacterial strains isolated from Anthurium andreanum, Dieffenbachia maculata and Aglaonema simplex in Mauritius. Fifteen strains, that showed the morphological properties of Xanthomonas on conventional media, were tested on two semi-selective media (Esculin-trehalose and cellobiose-starch). ELISA tests using a panel of monoclonal antibodies were carried out and three out of 15 strains reacted with a Xanthomonas-specific monoclonal antibody (MAb XII). Analysis using four sets of ribosomal primers revealed that the same three Mauritius strains shared conserved PCR products with reference xanthomonads including virulent strains of Xanthomonas axonopodis pv. dieffenbachiae (Xad). BIOLOG tests and the Sherlock Microbial Identification system (MIDI) identified these three new strains at the species level as X. axonopodis. The complementary tests that were carried out clearly confirmed that the three strains are xanthomonads and, moreover, a DNA probe which showed specificity to Xad strains suggested that the three Mauritius strains are non-virulent forms of the pathogen causing Anthurium blight.

Use of fatty acid profiles to identify food-borne bacterial pathogens and aerobic endospore-forming bacilli

Capillary gas chromatography (GC) with flame ionization detection was used to determine the cellular fatty acid profiles of various food-borne microbial pathogens and to compare the fatty acid profiles of spores and vegetative cells of the same endospore-forming bacilli. Fifteen bacteria, representing eight genera (Staphylococcus, Listeria, Bacillus, Yersinia, Salmonella, Shigella, Escherichia, and Vibrio) and 11 species were used to compare the extracted fatty acid methyl esters (FAMEs). Endospore-forming bacilli were processed to obtain pure spores and whole cell FAMEs for GC analysis. A data set for each bacterial agent was prepared using fatty acid profiles from five replicates prepared on different days. The results showed that these fatty acid intensity profiles were unique for each of the 11 species and that they could be used as a fingerprint for the organisms. The cellular fatty acid profiles for Bacillus anthracis and Bacillus cereus show that there are two branched chain fatty acids, iso 17:1 omega10c and 17:1 anteiso, which are unique in these species. Iso 17:1 omega10c is present in B. cereus vegetative cells and spores but is not observed in B. anthracis. The 17:1 anteiso fatty acid is present in B. anthracis cells but not in B. cereus cells. Fatty acids 16:0 2OH and 17:0 iso 3OH are present in B. anthracis and B. cereus spores but not in the vegetative cells. In summary, analysis of FAMEs from bacteria and spores can provide a sensitive procedure for the identification of food-borne pathogens.

Characterization of non-discriminating tetramethylammonium hydroxide-induced thermochemolysis–capillary gas chromatography–mass spectrometry as a method for profiling fatty acids in bacterial biomasses

Thermochemolysis using tetramethylammonium hydroxide (TMAH) as a method for profiling fatty acids (FAs) as methyl esters (FAMEs) was studied with respect to discrimination of bacterial fatty acid patterns in Gram-negative Pseudomonas putida in comparison with patterns obtained by classical preparation schemes (pressurized solvent extraction, alkaline saponification). A new, non-discriminating pyrolysis approach was used in these experiments. In this method, pyrolysis is carried out inside a deactivated stainless steel capillary constituting a part of the column train. This approach made it possible to distinguish analyte discrimination brought about by (i) the pyrolyzer set-up in conventional pyrolysis and (ii) chemical thermochemolysis reaction itself. Our results showed no significant discrimination for saturated, monounsaturated and cyclopropane FAs when using thermochemolysis temperatures up to 550 degrees C with the non-discriminating, capacitive-discharged based approach. Likewise, the cis/trans ratio of monounsaturated FAs was preserved. This is in sharp contrast to conventional pyrolysis systems (both Curie-point or flash pyrolyzers) using much longer thermochemolysis times. When using these systems, artificial monounsaturated FAMEs were formed during heat treatment resulting in biased species identification/classification. Hydroxy-FAs, chiefly bound covalently in lipopolysaccharides, could be almost quantitatively liberated by TMAH using non-discriminating pyrolysis (beyond 90%), whereas the recoveries were lower with conventional approaches. The new method makes it possible to profile fatty acids in very small amounts of both solid and liquid samples without significant sample preparation. This was exemplified by the results of TMAH-thermochemolysis of a fermentation broth taken from an in situ bioremediation reactor to monitor enhanced natural attenuation processes, and tomato roots which were subjected to cellulolytic bacteria attacks (Streptomyces), resulting in adsorption of these carboxymethyl-cellulose decomposing bacteria onto the root.

Chemometric Studies for the Characterization and Differentiation of Microorganisms Using in Situ Derivatization and Thermal Desorption Ion Mobility Spectrometry

Whole-cell bacteria were characterized and differentiated by thermal desorption ion mobility spectrometry and chemometric modeling. Principal component analysis was used to evaluate the differences in the ion mobility spectra of whole-cell bacteria and the fatty acid methyl esters (FAMEs) generated in situ after derivatization of the bacterial lipids. Alternating least squares served to extract bacterial peaks from the complex ion mobility spectra of intact microorganisms and, therefore, facilitated the characterization of bacterial strains, species, and Gram type. In situ thermal hydrolysis/methylation with tetramethylammonium hydroxide was necessary for the differentiation of Escherichia coli strains, which otherwise could not be distinguished by spectra acquired with the ITEMISER ion mobility spectrometer. The addition of the methylating agent had no effect on Gram-positive bacteria, and therefore, they could not be differentiated by genera. The classification of E. coli strains was possible by analysis of the IMS spectra from the FAMEs generated in situ. By using the fuzzy multivariate rule-building expert system and cross-validation, a correct classification rate of 96% (22 out of 23 spectra) was obtained. Chemometric modeling on bacterial ion mobility spectra coupled to thermal hydrolysis/methylation proved a simple, rapid (2 min/sample), inexpensive, and sensitive technique to characterize and differentiate intact microorganisms. The ITEMISER ion mobility spectrometer could detect as few as 4 x 10(6) cells/sample.

Reagentless detection and classification of individual bioaerosol particles in seconds

The rapid chemical analysis of individual cells is an analytical capability that will profoundly impact many fields including bioaerosol detection for biodefense and cellular diagnostics for clinical medicine. This article describes a mass spectrometry-based analytical technique for the real-time and reagentless characterization of individual airborne cells without sample preparation. We characterize the mass spectral signature of individual Bacillus spores and demonstrate the ability to distinguish two Bacillus spore species, B. thuringiensis and B.atrophaeus, from one another very accurately and from the other biological and nonbiological background materials tested with no false positives at a sensitivity of 92%. This example demonstrates that the chemical differences between these two Bacillus spore species are consistently and easily detected within single cells in seconds.

Microfabricated Differential Mobility Spectrometry with Pyrolysis Gas Chromatography for Chemical Characterization of Bacteria

A microfabricated drift tube for differential mobility spectrometry (DMS) was used with pyrolysis-gas chromatography (py-GC) to chemically characterize bacteria through three-dimensional plots of ion intensity, compensation voltage from differential mobility spectra, and chromatographic retention time. The DMS analyzer provided chemical information for positive and negative ions simultaneously from chemical reactions between pyrolysis products in the GC effluent and reactant ions of H+(H2O)n and O2-(H2O)n in air at ambient pressure. Authentic standards for chemicals formed in the pyrolysis of bacteria showed favorable matches with plots from py-GC/DMS analysis and were supported by py-GC/MS results. These and other yet-unidentified constituents provided a means to distinguish Escherichia coli from Micrococcus luteus. A Gram-positive spore former (Bacillus megaterium) was distinguished by an abundant peak for crotonic acid evident in positive and negative ions and not observed with M. luteus. In contrast, plots from py-GC/DMS of lipid A and lipoteichoic acid showed poor matches to plots for a Gram-negative (E. coli) bacterium and a Gram-positive (M. luteus) bacterium and the differences were attributed to differences in genus sources of the biopolymers. A significant percentage of the chemical information available in py-GC/DMS is unidentified, and the analytical utility must be established. Precision in the chemical measurement was determined as +/- 0.2 V, 10% relative standard deviation (RSD), and +/- 0.05 min for compensation voltage, peak intensity, and retention time, respectively. The minimum number of total bacteria (cell forming units) detected was 6000 though detection limits and resolution could be varied by the magnitude of the separation voltage in the differential mobility spectrometer.

Solid-phase microextraction, gas chromatography, and mass spectrometry coupled with discriminant factor analysis and multilayer perceptron neural network for detection of Escherichia coli

This study was performed to investigate the ability of using discriminant factor analysis (DFA) and an artificial neural network (ANN) to identify and quantify the number of Escherichia coli (ATCC 25922) in nutrient media from data generated by analysis of E. coli volatile metabolic compounds using solid-phase microextraction (SPME) coupled with gas chromatography (GC) and mass spectrometry (MS). E. coli was grown in super broth and incubated at 37 degrees C for 2 to 12 h. Numbers of E. coli were followed using a colony counting method. An SPME device was used to collect the volatiles from the headspace above the samples, and the volatiles were identified using GC-MS. DFA was used to classify the samples from different incubation times. From DFA, it was possible to differentiate super broth from media containing E. coli when cell numbers were 10(5) CFU or more. The potential to predict the number of E. coli from the SPME-GC-MS data was investigated using a multilayer perceptron (MLP) neural network with back propagation training. The MLP comprised an input layer, one hidden layer, and an output layer, with a hyperbolic tangent sigmoidal transfer function in the hidden layer and a linear transfer function in the output layer. Good prediction was found as measured by a regression coefficient (R2 = 0.996) between actual and predicted data.

Identification of foodborne bacteria by infrared spectroscopy using cellular fatty acid methyl esters

Identification of bacterial species by profiling fatty acid methyl esters (FAMEs) has commonly been carried out by using a 20-min capillary gas chromatographic procedure followed by library matching of FAME profiles using commercial MIDI databases and proprietary pattern recognition software. Fast GC (5 min) FAME procedures and mass spectrometric methodologies that require no lipid separation have also been reported. In this study, bacterial identification based on the rapid (2 min) infrared measurement of FAME mixtures was demonstrated. The microorganisms investigated included Gram positive bacteria Staphylococcus aureus, Listeria monocytogenes, Bacillus anthracis, and Bacillus cereus, and Gram negative bacteria from the family Enterobacteriacae: Yersinia enterocolitica, Salmonella typhimurium, Shigella sonnei, and Escherichia coli (four strains of E. coli), and non-Enterobacteriacae: Vibrio cholerae, Vibrio vulnificus, and Vibrio parahemolyticus. Foodborne bacterial mixtures of FAMEs were measured by using an attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopic procedure and discriminated by multivariate analysis. Results showed that the Enterobacteriacae could be discriminated from the vibrios. The identification was at the level of species (for the Bacillus and Vibrio genera) or strains (for the E. coli species). A series of bacterial FAME test samples were prepared and analyzed for accuracy of identification, and all were correctly identified. Our results suggest that this infrared strategy could be used to identify foodborne pathogens.

Detection of fatty acids from intact microorganisms by molecular beam static secondary ion mass spectrometry

We report the use of a surface analysis approach, static secondary ion mass spectrometry (SIMS) equipped with a molecular (ReO(4)(-)) ion primary beam, to analyze the surface of intact microbial cells. SIMS spectra of 28 microorganisms were compared to fatty acid profiles determined by gas chromatographic analysis of transesterfied fatty acids extracted from the same organisms. The results indicate that surface bombardment using the molecular primary beam cleaved the ester linkage characteristic of bacteria at the glycerophosphate backbone of the phospholipid components of the cell membrane. This cleavage enables direct detection of the fatty acid conjugate base of intact microorganisms by static SIMS. The limit of detection for this approach is approximately 10(7) bacterial cells/cm(2). Multivariate statistical methods were applied in a graded approach to the SIMS microbial data. The results showed that the full data set could initially be statistically grouped based upon major differences in biochemical composition of the cell wall. The gram-positive bacteria were further statistically analyzed, followed by final analysis of a specific bacterial genus that was successfully grouped by species. Additionally, the use of SIMS to detect microbes on mineral surfaces is demonstrated by an analysis of Shewanella oneidensis on crushed hematite. The results of this study provide evidence for the potential of static SIMS to rapidly detect bacterial species based on ion fragments originating from cell membrane lipids directly from sample surfaces.

Investigation of MALDI-TOF and FT-MS techniques for analysis of Escherichia coli whole cells

Recently, it has been demonstrated that bacteria can be characterized using whole cells and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). However, identification of specific bacterial proteins usually requires analysis of cellular fractions or purified extracts. Here, the first application of Fourier transform mass spectrometry (FTMS) to analysis of bacterial proteins directly from whole cells is reported. It is shown that accurate mass MALDI-FTMS can be used to characterize specific ribosomal proteins directly from Escherichia coli cells. High-accuracy mass measurements and high-resolution isotope profile data confirm posttranslational modifications proposed previously on the basis of low-resolution mass measurements. Seven ribosomal proteins from E. coli whole cells were observed with errors of less than 27 ppm. This was accomplished directly from whole cells without fractionation, concentration, or overt overexpression of characteristic cellular proteins. MALDI-FTMS also provided information regarding E. coli lipids in the low-mass region. Although ions with m/z values below 1000 have been observed by FTMS of whole cells, this represents the first report of detection of ions in the 5000 to 10,000 m/z range by MALDI-FTMS using whole cells.

Rapid sample processing and fast gas chromatography for identification of bacteria by fatty acid analysis

A commercially available system for microbial identification by fatty acid analysis (Microbial Identification System (MIS), MIDI, Newark, DE, USA) requires a four-step sample derivatization procedure in screw-cap test tubes. By using glass tubes in a 96-well format with multichannel pipetting, the time required for sample preparation can be greatly reduced. The standard gas chromatography column, 25 m long by 0.20 mm ID, is replaced with a 10 m long by 0.10 mm ID column, reducing the gas chromatography run time to one third of the standard time. Either or both of these procedures can be easily implemented in any laboratory using the MIDI system, resulting in faster identifications and higher sample throughput.

Rapid analysis of intact phospholipids from whole bacterial cells by matrix-assisted laser desorption/ionization mass spectrometry combined with on-probe sample pretreatment

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), utilizing an on-probe sample pretreatment, was applied to the rapid and direct detection of intact phospholipids from whole bacterial cells. The sample preparation procedure involved depositing growing bacterial colonies from culture dishes directly onto the MALDI probe followed by treatment of the sample spot with a 3 micro L aliquot of an aqueous 0.05 M solution of sodium iodide prior to the addition of a 2,5-dihydroxybenzoic acid (DHB) matrix solution (ca. 8 mg dissolved in 70% acetonitrile/30% H(2)O containing 0.1% of trifluoroacetic acid). The MALDI spectra obtained from whole bacteria cells showed a series of ions generated from bacterial phospholipids, such as phosphatidylethanol-amines (PEs) and phosphatidylglycerols (PGs), which were clearly observed as well-resolved peaks. The ranges of the observed total carbon numbers in two acyl groups for PEs and PGs (30-36 and 33-36, respectively) were in good agreement with those reported previously. Furthermore, the distinct discrimination of four species of the Enterobacteriaceae family cultured identically was achieved by using principal components analysis (PCA) conducted on the relative peak intensities of phospholipids observed from the MALDI spectra.

Validation using sensitivity and target transform factor analyses of neural network models for classifying bacteria from mass spectra

Temperature constrained cascade correlation networks (TCCCNs) are computational neural networks that configure their own architecture, train rapidly, and give reproducible prediction results. TCCCN classification models were built using the Latin-partition method for five classes of pathogenic bacteria. Neural networks are problematic in that the relationships among the inputs (i.e., mass spectra) and the outputs (i.e., the bacterial identities) are not apparent. In this study, neural network models were constructed that successfully classified the targeted bacteria and the classification model was validated using sensitivity and target transformation factor analysis (TTFA). Without validation of the classification model, it is impossible to ascertain whether the bacteria are classified by peaks in the mass spectrum that have no causal relationships with the bacteria, but instead randomly correlate with the bacterial classes. Multiple single output network models did not offer any benefits when compared to single network models that had multiple outputs. A multiple output TCCCN model achieved classification accuracies of 96 +/- 2% and exhibited improved performance over multiple single output TCCCN models. Chemical ionization mass spectra were obtained from in situ thermal hydrolysis methylation of freeze-dried bacteria. Mass spectral peaks that pertain to the neural network classification model of the pathogenic bacterial classes were obtained by sensitivity analysis. A significant number of mass spectral peaks that had high sensitivity corresponded to known biomarkers, which is the first time that the significant peaks used by a neural network model to classify mass spectra have been divulged. Furthermore, TTFA furnishes a useful visual target as to which peaks in the mass spectrum correlate with the bacterial identities.

Rapid detection of taxonomically important fatty acid methyl ester and steroid biomarkers using in situ thermal hydrolysis/methylation mass spectrometry (THM-MS): implications for bioaerosol detection

Implications for the rapid interrogation of biological materials collected from the atmosphere using a simple, one step, sample preparation technique was explored. For this purpose, various samples of whole bacteria, fungi, pollen, media contaminated with viruses, and proteins were treated with an aliquot of methanolic tetramethylammonium hydroxide prior to thermal introduction into the ion source of a triple quadrupole mass spectrometer. Molecular and fragment ions, consistent with fatty acid methyl esters (FAMEs) and steroids (non-methylated and methylated), generated during electron ionization (70 eV) of the volatile hydrolysates were subsequently detected. The varying distributions and relative intensities of these ions were used to discriminate between the different biological samples. More specifically, it was found that polyunsaturated FAMEs and steroids could be used to differentiate eukaryotic cells from prokaryotic cells since the latter do not generally synthesize either of these lipid membrane constituents. Further discrimination of the different eukaryotic samples was made based on the detection of ergosterol for fungi, cholesterol for the viral media, and C18:3Me for pollen. Multivariate statistical analysis was employed to evaluate and compare the large set of mass spectra generated during the study and to build a trained model for predicting the class membership of test samples entered as unknowns. Of 132 different samples subjected to the model as unknowns, 131 were correctly classified into their proper biological categories. Moreover, 29 out of 30 bacteria test samples representing five species of pathogenic bacteria were correctly classified at the species level.

Correlating cell cycle with metabolism in single cells: combination of image and metabolic cytometry

BACKGROUND

We coin two terms: First, chemical cytometry describes the use of high-sensitivity chemical analysis techniques to study single cells. Second, metabolic cytometry is a form of chemical cytometry that monitors a cascade of biosynthetic and biodegradation products generated in a single cell. In this paper, we describe the combination of metabolic cytometry with image cytometry to correlate oligosaccharide metabolic activity with cell cycle. We use this technique to measure DNA ploidy, the uptake of a fluorescent disaccharide, and the amount of metabolic products in a single cell.

METHODS

A colon adenocarcinoma cell line (HT29) was incubated with a fluorescent disaccharide, which was taken up by the cells and converted into a series of biosynthetic and biodegradation products. The cells were also treated with YOYO-3 and Hoechst 33342. The YOYO-3 signal was used as a live-dead assay, while the Hoechst 33342 signal was used to estimate the ploidy of live cells by fluorescence image cytometry. After ploidy analysis, a cell was injected into a fused-silica capillary, where the cell was lysed. Fluorescent metabolic products were then separated by capillary electrophoresis and detected by laser-induced fluorescence.

RESULTS

Substrate uptake measured with metabolic cytometry gave rise to results similar to those measured by use of laser scanning confocal microscopy. The DNA ploidy histogram obtained with our simple image cytometry technique was similar to that obtained using flow cytometry. The cells in the G(1) phase did not show any biosynthetic activity in respect to the substrate. Several groups of cells with unique biosynthetic patterns were distinguished within G(2)/M cells.

CONCLUSIONS

This is the first report that combined metabolic and image cytometry to correlate formation of metabolic products with cell cycle. A complete enzymatic cascade is monitored on a cell-by-cell basis and correlated with cell cycle.

Direct analysis and identification of Helicobacter and Campylobacter species by MALDI-TOF mass spectrometry

Campylobacter jejuni, Campylobacter fetus, and Campylobacter coli were compared with Helicobacter pylori and Helicobacter mustelae by direct analysis of individual cultured colonies in 50% methanol-water with a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS). H. pylori and Campylobacter species from blood agar culture produced unique, complex spectra with over 25 different ions in mass/charge (m/z) range from 2,000 to 62,000. A biomarker for H. pylori was centered around m/z 58,268, and H. mustelae was distinguished from H. pylori by its ions at m/z 49,608 and 57,231. Campylobacters could be distinguished from Helicobacters by their lack of ions around m/z 58,000 and 61,000 as well as distinguishing biomarkers of lower m/z: 10,074 and 25,478 for C. coli; m/z 10,285 and 12,901 for C. jejuni; m/z 10,726 and 11,289 for C. fetus. MALDI-TOF MS is a rapid and direct method for detection of these potentially pathogenic bacteria from culture.

The effects of electron and chemical ionization modes on the MS profiling of whole bacteria

Free fatty acid profiling of whole bacteria [Francisella tularensis, Brucella melitensis, Yersinia pestis, Bacillus anthracis (vegetative and sporulated), and Bacillus cereus] was carried out with direct probe mass spectrometry under 70-eV electron ionization (EI) and isobutane chemical ionization in both the positive (CI+) and negative modes (CI-). Electron ionization produced spectra that contained molecular ions and fragment ions from various free fatty acids. Spectra acquired with isobutane chemical ionization in the positive mode yielded molecular ions of free fatty acids as well as ions from other bacterial compounds not observed under EI conditions. Spectra obtained with negative chemical ionization did not contain as much taxonomic information as EI or CI+; however, some taxonomically significant compounds such as dipicolinic acid and poly(3-hydroxybutyrate) did produce negative ions. All ionization modes yielded spectra that could separate the bacteria by Gram-type when observed with principle components analysis (PCA). Chemical ionization in the positive ion mode produced the greatest amount of differentiation between the four genera of bacteria when the spectra where examined by PCA.

Investigation of cell culture media infected with viruses by pyrolysis mass spectrometry: implications for bioaerosol detection

Mass spectrometry coupled with a pyrolysis inlet system was used to investigate media from cell cultures infected with viruses. Cell culture media is an intricate mixture of numerous chemical constituents and cells that collectively produce complicated mass spectra. Cholesterol and free fatty acids were identified and attributed to lipid sources in the media (blood serum supplement and plasma membranes of host cells). These lipid moieties could be utilized as signature markers for rapidly detecting the cell culture media. Viruses are intracellular parasites and are dependent upon host cells in order to exist. Therefore, it is highly probable that significant quantities of media needed to grow and maintain viable host cells would be present if a viral agent were disseminated as an aerosol into the environment. Cholesterol was also detected from a purified virus sample, further substantiating its use as a target compound for detection. Implications of this research for detection of viral bioaerosols, using a field-portable pyrolysis mass spectrometer, is described.

Differentiation of microorganisms based on pyrolysis-ion trap mass spectrometry using chemical ionization

The ability to differentiate microorganisms using pyrolysision trap mass spectrometry was demonstrated for five Gram-negative disease-causing organisms: Brucella melitensis, Brucella suis, Vibrio cholera, Yersinia pestis, and Francisella tularensis. Bacterial profiles were generated for gamma-irradiated bacterial samples using pyrolytic methylation and compared for electron ionization and chemical ionization using several liquid reagents with increasing proton affinities. Electron ionization combined with pyrolysis caused extensive fragmentation, resulting in a high abundance of lower mass ions and diminishing the diagnostic value of the technique for compound identification and bacterial profiling. Chemical ionization reduced the amount of fragmentation due to ionization while enhancing the molecular ion region of the fatty acids. As the proton affinity of the reagent increased, the protonated molecular ions of the fatty acids became the predominant ions observed in the mass spectrum. As a result, chemical ionization was shown to be more effective than electron ionization in bacterial profiling. Whereas the bacteria could be distinguished at the Genera level using electron ionization, further differentiation to the subspecies level was possible using chemical ionization. The greatest separation among the five test organisms, in terms of Euclidean distances, was obtained using ethanol as the chemical ionization reagent and using pooled masses representing specific fatty acid biomarkers rather than total ion profiles.

A comparison of matrix-assisted laser desorption/ionization time-of-flight and liquid chromatography electrospray ionization mass spectrometry methods for the analysis of crude tarantula venoms in the Pterinochilus group

The search for novel pharmacological tools in spider venoms involves the need for precise and reproducible species identification methods. As an addition to morphological analysis, we have developed venom fingerprinting by reversed-phase chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) as an efficient and precise venom identification tool. In order to compare the possible use of liquid chromatography electrospray ionization mass spectrometry (LC/ESI-MS) as an additional venom characterization tool, we have applied both methodologies to the study of several tarantula venom samples in the Pterinochilus murinus group. These species possess highly active venoms yet their taxonomy remains difficult. We demonstrate that both methodologies can be successfully applied to tarantula venom characterization. MALDI-TOFMS and ESI-MS gave similar overall profiles and allowed fine discrimination of samples. At least one venom sample was proven to belong to a completely different venom group. Coupling of ESI-MS with HPLC separation afforded a new dimension in venom analysis, with clear discrimination between components of similar Mr and gave a finer picture of venom composition, number of molecular species and molecular weight distribution.

Direct mass spectrometric analysis of Bacillus spores

Spores from the Bacillus species, B. cereus, B. anthracis, B. thuringensis, B. lichenformis, B. globigi, and B. subtilis, were examined by direct probe mass spectrometry using electron ionization (EI) and positive and negative chemical ionization (CI). Molecular ions from free fatty acids and nucleic acids were observed in the 70eV spectra as were fragments from glycerides. Spectra obtained with isobutane positive chemical ionization (CI(+)) were dominated by ions associated with pyranose compounds such as N-acetylglucosamine (NAG). Unlike the positive ion spectra, the negative ion spectra of the spores were very simple and contained few peaks. The M(-.) ion from dipicolinic acid (DPA) was the base peak in the negative ion spectra of all spore species except those from B. lichenformis. The negative ion of DPA produced such a strong signal that 10(8) colony forming units (CFUs) of B. cereus spores could be detected directly in 0.5 g of ground rice. Principal component analysis (PCA) of the spectra revealed that only CI(+) spectra contained differences that could be used to identify the spectra by species. Differentiation of the CI(+) spectra by PCA was attributed to variances in the peaks associated with the bacterial polymer poly(3-hydroxybutyrate) (PHB) and NAG. Similar differences in PHB and NAG peaks were detected in the CI(+) spectra of a suite of vegetative Bacillus stains grown with various media.