Computer-based linear regression analysis of desorption mass spectra of microorganisms

Characterization of microbial mixtures by mass spectrometry

MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.

Current developments to use linear MALDI-TOF spectra for the identification and typing of bacteria and the characterization of other cells/organisms related to infectious diseases

Within the past few years identification of bacteria by MALDI-TOF MS has become a standard technique in bacteriological laboratories for good reasons. MALDI-TOF MS identification is rapid, robust, automatable, and the per-sample costs are low. Yet, the spectra are very informative and the reliable identification of bacterial species is usually possible. Recently, new MS-based approaches for the identification of bacteria are emerging that are based on the detailed analysis of the bacterial proteome by high-resolution MS. These "proteotyping" approaches are highly discriminative and outperform MALDI-TOF MS-based identification in terms of specificity, but require a laborious proteomic workflow and far more expertise and sophisticated instrumentation than identification on basis of MALDI-TOF MS spectra, which can be obtained with relative simple and uncostly linear MALDI-TOF mass spectrometers. Thus MALDI-TOF MS identification of bacteria remains an attractive option for routine diagnostics. Additionally, MALDI-TOF MS identification protocols have been extended and improved in many respects making linear MALDI-TOF MS a versatile tool that can be useful beyond the identification of a bacterial species, e.g. for the characterization of leucocytes and arthropod vectors of infectious diseases. This review focuses on such improvements and extensions of the typical MALDI-TOF MS workflow in the field of infectious diseases.

Rapid characterization of microorganisms by mass spectrometry--what can be learned and how?

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method--everything has a mass--and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Metabolomics as a potential new approach for investigating human reproductive disorders

Metabolomics has been emerging for several years as a global chemical phenotyping approach offering fascinating descriptive capabilities for addressing life complexity. It facilitates the understanding of the mechanisms of biological and biochemical processes in complex systems and promises new insights into specific research questions. The objective of this study was to use for the first time a metabolomic approach based on liquid chromatography high resolution mass spectrometry for characterizing an alteration of the testicular function, namely impaired semen quality. Metabolomic fingerprints were generated from serum samples collected from Danish young men presenting low, intermediate, or high sperm concentrations. Serum metabolic profiles were found to be significantly different among the three groups of volunteers. The developed methodology permitted to correlate the studied clinical parameter (i.e., sperm concentration) with the metabolite profiles generated. Peptides related to the Protein Complement C3f were identified as putative markers associated with this clinical parameter. The biological interpretation and further robustness linked to this observation remain to be further investigated, in particular to address the inter- and intraindividual variabilities.

Species determination and characterization of developmental stages of ticks by whole-animal matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of crude bacterial samples has been introduced as a very cost-efficient and rapid, yet highly informative tool to identify and classify bacteria. The potential of this approach to characterize whole animals, so far preferentially insects, is only evolving. Here, a simple protocol was developed to perform MALDI-MS analysis on extracts from whole ticks of 7 species and 4 developmental stages. Using commercially available software designed for the identification of bacteria, a reference database of spectra was constructed that allowed the species determination of ticks using larvae, nymphs, or adult individuals as starting material. Cluster analysis on the basis of MALDI mass spectra indicated that the primary determinant for the mass spectra was the species, followed by the developmental stages, which formed distinct clusters within the given species. With certain limitations, species identification was also possible using body parts and engorged animals. Spectra of developing Ixodes ricinus eggs showed dramatic changes with time, suggesting that, beyond its usefulness for species determination, MALDI-typing may have applications in developmental biology.

MALDI-ToF mass spectrometry-multivariate data analysis as a tool for classification of reactivation and non-culturable states of bacteria

Some bacterial life states are only difficult to describe and to detect because they are on the border of active metabolism. A prominent example is the so-called viable but non-culturable state, which is mainly characterized by the inability of bacteria to grow on synthetic media. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF/MS) in combination with multivariate data analysis represents a powerful tool for mass-spectrometric pattern recognition of biological samples. This method is already used for differentiation of bacterial strains. In this study we present a rapid readout method based on MALDI-ToF/MS in combination with principal component analysis to classify the bacterial non-culturable state using Enterococcus faecalis as a model organism. By applying this technique to samples of different physiological states, distinct clusters were calculated and all mass spectra were classified correctly into groups of similar type concerning their physiological state.

Determination of serotypes of Shiga toxin-producing Escherichia coli isolates by intact cell matrix-assisted laser desorption ionization-time of flight mass spectrometry

Shiga toxin-producing Escherichia coli (STEC) isolates representing the serotypes O165:H25, O26:H11/H32, and O156:H25 were analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectra of whole cells, a procedure also known as intact cell mass spectrometry (ICMS or IC-MALDI MS) or MALDI-typing. We demonstrate that within the given species the three serotypes can be well discriminated by ICMS. Conditions for the construction of serotype-specific prototypic mass spectra were systematically optimized by filtering out masses that do not contribute to the discrimination of the serotypes. Binary distances between prototypic spectra and sample spectra were used to determine serotypes of unknown samples. With parameters optimized, only 0.7% of the assignments were incorrect compared to 31% when distances were calculated from alignments of unfiltered mass spectra. Within the different serotypes, clusters of genetically related E. coli most probably originating from single clones could be distinguished by restriction fragment length polymorphism analysis. Since ICMS did not reproduce these clusters, we conclude that the power of ICMS is just sufficient to discriminate E. coli serotypes under certain conditions but fails for the differentiation of E. coli below this level.

Laser desorption-atmospheric pressure chemical ionization mass spectrometry for the analysis of peptides from aqueous solutions

A recently reported ionization method, comprising an infrared (IR) laser pulse to desorb (LD) analyte species, followed by atmospheric pressure chemical ionization (APCI) with a corona discharge (LD-APCI) to effect ionization of the desorbed neutral analyte molecules, is described for the direct analysis of aqueous peptide solutions. The source employs a heated capillary atmospheric pressure (AP) inlet coupled to a quadrupole ion trap mass spectrometer and allows sampling under normal ambient air conditions. By use of the corona discharge, signals of the atmospheric pressure infrared matrix-assisted laser desorption/ionization (AP-IR-MALDI)-generated analyte protonated molecule were enhanced by factors as large as 1400. In addition, the acid modifier trifluoroacetic acid (TFA) was found to improve the AP-IR-MALDI-generated signal by a factor of approximately 10, whereas the LD-APCI generated signal yielded a 100-fold increase. In this study, the use of the corona discharge is described to enhance the analyte signal generated via AP-IR-MALDI and, as a tool, to probe the gas-phase neutral molecule population generated by the MALDI process. Finally, through the decoupling of desorption from ionization, implications regarding the application of LD-APCI for the direct analysis of numerous new analyte containing matrixes (e.g., polyacrylamide gel electrophoresis (PAGE), tissue, etc.) are discussed.

Analyzing the physiological signature of anabolic steroids in cattle urine using pyrolysis/metastable atom bombardment mass spectrometry and pattern recognition

Pyrolysis coupled to metastable atom bombardment (MAB) and time-of-flight mass spectrometry (TOFMS) is used for generating mass spectra from bovine urine samples obtained from cattle treated with anabolic steroids. These spectra constitute fingerprints, which can be discriminated by multivariate statistical analysis. Four main conclusions can be drawn from this work: (i) The use of different metastable gases, such as Xe*, Kr*, or N2*, as an energy-tunable ionization beamline allows control of the internal energy and the dissociation processes of the produced odd electron molecular ions, thus giving rise to complementary mass spectra fingerprints. (ii) A variable transformation depending on the biofluid matrix suitably contracts the frequency distribution of the generated data for low m/z ratios holding information related to endogenous metabolites encountered in urine. (iii) Coupling variable selection to statistical pattern recognition methods results in low error rates (< 1%) for predicting MAB mass fingerprints, especially using lineardiscriminant analysis (LDA). (iv) LDA discriminates controls from treated animals and also correlates to quantitative physiological responses induced by anabolic steroids. This work shows that Py-MAB-TOFMS could be a suitable method for complementary monitoring anabolic use in sports, medicine, and cattle breeding, as well as monitoring many other long-lasting although weak physiological disruptions.

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.

Characterization of intact microorganisms by MALDI mass spectrometry

The application of MALDI mass spectrometry to desorb protein biomarkers from intact viruses, bacteria, fungus, and spores is the focus of this review. Instrumentation, sample collection, sample preparation, and algorithms for data analysis are summarized. Optimally these analyses should be carried out in less than five minutes. Successful applications are discussed from biotechnology, cell biology, and the pharmaceutical industry.

Corona plasma discharge for rapid analysis of microorganisms by mass spectrometry

Corona plasma discharge provides a rapid and reliable tool for release of biomarkers from gram negative and positive bacteria, spores and viruses for characterization by mass spectrometry.

Viral characterization by direct analysis of capsid proteins

Matrix-assisted laser desorption/ionization mass spectrometry has enabled viral coat proteins to be characterized directly from the virus. This analysis, demonstrated here with tobacco mosaic virus U2, a bacteriophage MS2, and equine encephalitis TRD, is achieved with a combination of organic acid, UV-absorbing matrix, and high-energy desorption with a nitrogen laser. The molecular weights of these proteins are determined with sufficient accuracy to allow differentiation among viral species and strains. The abundant hydrophobic MS2 coat protein was analyzed in aliquots of culture medium and of the tobacco mosaic virus coat protein in infected leaves. This method provides rapid detection of coat protein in the low-femtomole range, as estimated by titering plaque-forming units of MS2.

Microorganism gram-type differentiation based on pyrolysis-mass spectrometry of bacterial Fatty Acid methyl ester extracts

Curie-point pyrolysis (Py)-mass spectrometry has been used to differentiate 19 microorganisms by Gram type on the basis of the methyl esters of their fatty acid distribution. The mass spectra of gram-negative microorganisms were characterized by the presence of palmitoleic acid (C(inf16:1)) and oleic acid (C(inf18:1)), as well as a higher abundance of palmitic acid (C(inf16:0)) than pentadecanoic acid (C(inf15:0)). For gram-positive microorganisms, a signal of branched C(inf15:0) (isoC(inf15:0) and/or anteisoC(inf15:0)) more intense than that of palmitic acid was observed in the mass spectra. Principal components analysis of these mass spectral data segregated the microorganisms investigated in this study into three discrete clusters that correlated to their gram reactions and pathogenicities. Further tandem mass spectrometric analysis demonstrated that the nature of the C(inf15:0) fatty acid isomer (branched or normal) present in the mass spectrum of each microorganism was important for achieving the classification into three clusters.

Analysis of polar lipids from some representative enterobacteria, Plesiomonas and Acinetobacter by fast atom bombardment-mass spectrometry

Fast atom bombardment-mass spectrometry (FAB-MS) was used to analyse lipid extracts of bacteria to assess its usefulness for analysing anionic phospholipids of potential chemotaxonomic value. The following micro-organisms were tested: Acinetobacter calcoaceticus, Acinetobacter sp., Citrobacter freundii, Enterobacter cloacae (2 strains), Escherichia coli (3 strains), Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, Morganella morganii, Plesiomonas shigelloides, Proteus mirabilis (3 strains), Serratia liquefaciens and Serratia marcescens. Negative-ion spectra provide data for twenty-seven major carboxylate anions (m/z 209-325) and for thirty-seven major phospholipid anions (m/z 645-774). Generally, the largest carboxylate peaks were due to 16:1, 16:0, cyc17 and 18:1 while the largest phospholipid anion peaks were due to PE(32:1), PE(33:1), PE(34:1), PE(34:2), PG(30:2), PG(31:2), PG(32:2), PG(34:1) and PS(33:0). However, quantitative differences were observed. For example, Acinetobacter lacked PE (33:1) but had exceptionally high peaks at m/z 748, PS(33:0), and m/z 281, octadecanoate. Unknown 'carboxylate' peaks were detected at m/z 254, 256, 261, 268, 282 and 301. In some cases, unknown peaks appeared to constitute possible homologous series being separated by delta m/z of 14(identical to methylene). For chemotaxonomic purposes, the complexity of the data required numerical analysis. Using the Pearson coefficient of linear correlation, as a measure of association, it was possible to compare all strains analysed. Typical results for strain comparisons were as follows: Ent. cloacae vs Ent. cloacae, r = 0.90 (Ent. cloacae vs Ac. calcoaceticus, r = 0.46). Thus FAB-MS represents an excellent means of obtaining large quantities of data on polar lipids of a range of bacterial isolates, which may be suitable for chemotaxonomic purposes.

Fast atom bombardment-mass spectrometry for bacterial chemotaxonomy: influence of culture age, growth temperature, gaseous environment and extraction technique

Extracted phospholipids of Escherichia coli, Proteus mirabilis and Enterobacter cloacae were examined by fast atom bombardment-mass spectrometry which yielded major peaks between m/z 225 and 761. The result of extracting freeze-dried or 'wet' cells showed that freeze-drying may be omitted although weighing of dried cells offers a useful means of standardizing the extraction procedure. Anaerobic growth quantitatively altered the chemical finger-print as a result of increase in ratio of saturated: unsaturated carboxylic acids. Growth temperature also affected profiles over the temperature range 24-45 degrees C. A less drastic influence on mass spectra was culture age, over the range 16-48 h. Comparison of spectra was possible with Pearson's coefficient of linear correlation which yielded the following values: wet and lyophilized cells, r = 0.97; aerobic and anaerobic growth, r = 0.82; 24 degrees C and 45 degrees C, r = 0.76; 16 h and 48 h, r = 0.95. These results show that although quantitative differences do occur between spectra for the same organism prepared in different ways, they are less than interspecies variation, e.g. with E. coli and P. mirabilis, r = 0.46. Any differences which are due preparation method can be overcome by standardization of technique.

Desorption of ions from rat membranes: selectivity of different ionization techniques

Complex lipid biomarkers, including phosphatidylcholines, cerebrosides and sulfatides, are shown to be desorbed intact from rat brain myelin and rat liver microsomes by liquid secondary ion mass spectrometry, by plasma desorption and by laser desorption. Different polar lipids are favored by the different desorption techniques and as negative or positive ions. These selectivities support current theories about ionization for the different techniques.