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Maldi Mass Spectrometry May Enhance Counter-terrorism Efforts
January 23, 2002Various Approaches Under Investigation to Determine Efficacy and Benefits
The application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to discern protein biomarkers from intact viruses, bacteria, fungus, and spores as a means of identifying and classifying them will likely have a significant impact on the biotechnology, biology, and pharmaceutical industries in the near future. A study published in the February 2002 issue of Mass Spectrometry Reviews, which reports on the application, significance and procedural aspects of this method, suggests that it can have dramatic implications for air, water, and food safety. In light of recent events, it promises to play a critical role in counter-bioterrorism efforts that have assumed central importance in modern society.
Current mass spectrometry, intended to distinguish among the 200-6,000 molecular species in bacteria, is grounded in the capability to detect a broad m/z range of biomarker ions that are unique and representative of individual microorganisms. This procedure dates back to 1975, when it was demonstrated that individual mass spectra could be obtained for different species of bacteria. The desorption/ionization techniques, which emerged in the 1980s, were proven effective in generating molecular biomarker ions from microorganisms for identification purposes. MALDI, introduced in 1996, provided spectra of protein biomarkers. With current technological capabilities, proteins provide the best biomarkers plausable in an analysis that excludes extraction, separation, or amplification, because they contribute 50% of the dry weight of a vegetative bacterium, in comparison with lipids (the prior focus of mass spectrometry techniques), which comprise merely 5-8% of dry weight. Although DNA is the most unique biomarker for each kind of bacterium, there is only one copy per cell without amplification, which makes analysis difficult.
In a recent report, researchers Catherine Fenselau and Plamen Demirev reviewed a sequence of prior studies discussing MALDI mass spectrometry procedures and interpreting their efficacy. According to previous observations, MALDI mass spectrometry of bacteria and viruses does not appear to require a lysis step. However, fungal cells, spores, and single-celled parasites do seem to require lysis - exposure of the sample in the sample holder to a strong organic acid, for instance - to obtain a MALDI spectrum.
Prior studies have also indicated that combining MALDI with time-of-flight (TOF) mass analysis enhances the technique`s detection function, as TOF instruments provide rapid analysis, tandem mass spectrometry, and miniaturization. When combined, the two methods perpetuate easy desorbtion and analysis of positive as well as negative ions in the samples, which improves identification precision and specificity. Most MALDI TOF instruments used in microorganism characterization are equipped with an ultra-violet (UV) nitrogen laser. However, infrared (IR) lasers are also capable of generating phospholipi and lipopeptide biomarker ion profiles. When compared to UV MALDI, IR MALDI mass spectra displayed a larger number and a higher m/z range for biomarker peaks detected above m/z 4,000.
Sample collection and sample preparation are integral steps in performing mass spectrometry. The simplest and most easily replicated method of sample collection is the removal of a single colony from a bacteria strand grown in a Petri dish. Once deposited directly into the sample plate and saturated in matrix, the sample undergoes MALDI analysis, which, if successful, allowing a fairly reproducible MALDI spectra to be obtained. Sample preparation is critical to the sensitivity, reproducibility, and mass accuracy of the MALDI technique, as well as to the nature of the biomarkers detected. Prior studies have demonstrated that adding methanol, for instance, improves the sample stability before MALDI analysis. Several physical methods have been applied to improve biomarker signals as well. In addition, sample-to-matrix ration and the amount of material on the holder appear to also affect the quality of the MALDI spectra.
Several studies cited in the report have determined that between 5,000 and 1,0000 intact cells deposited on the sample holder are sufficient to obtain a biomarker signal with a sufficient signal-noise ratio. Intact proteins are species readily desorbed from cells and detected in MALDI spectra above 4,000 Da and most proteins with bacterial genomes fall in the range 4,000-15,000 Da. Various algorithms have been engineered to match spectra (signatures), in order to classify microorganisms. Generally, the reference library of algorithms is constructed by extracting the essential biomarkers from a large number of spectra from the same analyte under various conditions. The biomarkers are described by their m/z values, intensity, related standard deviations, and frequency of their occurrence in the replicate spectra. The peak position and the number of matched peaks between the fingerprint spectrum and an unknown are then compared for identification purposes.
Because characterizing microorganisms with MALDI spectra has been based on determining and comparing the biomarker mass values observed for organisms, the comparisons are heavily based on the ability to reproduce the observed m/z values, rather than on the peak intensity. However, Drs. Fenselau and Demirev point out that "the reproducibility of spectra of the complex biochemical mixtures that compose the thick and irregular bacterial samples is problematic," adding that "this has been the major difficulty in compiling reliable fingerprint libraries and in applying spectrum-comparison algorithms."
Recently, a novel bioinformatics-based approach proposes the characterization of microorganisms based on matching protein molecular masses in the spectrum with protein molecular masses predicted from sequenced genomes. Its application is limited to microorganisms whose genomes are sequenced, but the number of such genomes in the public domains is growing rapidly. This approach interprets the biomarker spectrum rather than matching or correlating it, which provides newfound flexibility to MALDI, because even when different proteins are observed, they can be related back to and identified with an individual organism. This approach also accommodates mutations.
Various mass spectral strategies are currently being explored for identification and analysis of airborne and waterborne microorganisms, with added urgency spurred by mounting anxiety about the unpredictable threat of bio-terrorism. The researchers cite a study in 1999, in which researchers described an algorithm for identifying potential biological threat agents. The measured spectrum was compared to a library of stored mass spectra of threat agents, in analogy to an approach initially developed for comparisons of FAB spectra of phospholipid biomarkers. Several other studies have investigated the combined application of bioaffinity surfaces with MALDI mass spectrometry to microorganisms in wastewater or urine, allowing the sample to be cleansed of salts and contaminants. Upon exposure of the affinity complex to acid, the antigen is released for direct MALDI analysis. In another study, aerosols, containing bacterial vegetative cells and spores, were sampled in an ion trap mass spectrometer through an atmospheric pressure inlet system, and the microorganisms were detected in real time, by tandem mass spectrometry in the ion trap.
Tandem mass spectrometry involves the analysis of proteolytic peptides from their proteins or sequence tags. Search algorithms for identification can be based on a set of peptide molecular masses, and/or a sequence tag obtained from a proteolytic peptide or intact protein. When fully developed, this approach will enable the characterization of microorganisms in mixtures and will enhance the value of lipopeptides and glycolipids as biomarkers.
The implications of these advances in mass spectrometry for various facets of life are many-fold. These techniques (capabilities) can be integral and invaluable to counter-terrorism efforts as well to the general promotion of air, water, drug, etc. safety. They can be used to screen for bacterial contaminants, as well as applied for rapid analysis of culture from food, the development of agents to combat drug-resistant strands of bacteria and viruses, and rapid medical diagnostics, which are especially essential in crisis circumstances.
"Speed, sensitivity, tolerance to contaminants, and screening capability are improved by automation in this physicochemical method that is complementary to biochemical and morphological methods," comment the authors. "The approaches discussed here are receiving intense attention in pharmaceutical companies and governmental regulatory agencies, and increased utility is anticipated," they conclude.
MALDI-TOF Mass Spectrometry Is a Versatile and Effective Technique for Identifying Biomarker Proteins and Bacteria in Order to Classify Microorganisms
Advances in Cell Preparation and Data Interpretation Required to Reach Maximum Potential Efficacy of the Technique
Matrix-assisted laser desorption-ionization (MALDI) time of flight mass spectrometry (TOF/MS) has proven to be an effective tool for bacterial identification and characterization. Prior published literature is reviewed by Jackson Lay, Jr., in a report published in the February 2002 issue of Mass Spectrometry Reviews. The report indicates that MALDI-TOF/MS may revolutionize various aspects of bacterial characterization. For instance, MALDI-TOF/MS can increase the speed and specificity of identifying bacteria that cause human disease and can be used for rapidly characterizing chemical changes associated with their biochemical life cycles. However, the author indicates that development of protocols that do not require preliminary culture steps to expand the number of bacteria for analysis and more suitable methods for data interpretation would advance MALDI-TOF/MS beyond its current limitations.
Mass spectrometry for the characterization of bacteria dates back to 1975 and is based on the detection of a broad m/z range of biomarker ions that are theoretically unique to and representative of a microorganism. The desorption-ionization techniques that emerged in the 1980s proved more effective in generating small molecule biomarker ions from microorganisms. Subsequently MALDI provided mass spectra of proteins and was combined with TOF mass analysis to yield a powerful new bio-analytical tool. MALDI-TOF/MS is based on simple technology, yet it provides high sensitivity and specificity, and is compatible with rapid (usually 5 minutes) analysis. MALDI can be implemented in a tandem mass spectrometry configuration and is suitable for miniaturization.
For analysis of bacteria, MALDI-TOF/MS traditionally has used complex, time consuming purification procedures to isolate specific proteins from bacteria before analysis. New methods using whole and disrupted cells have been recently investigated in order to bypass isolation procedures. Recent applications include identification of unknown proteins, such as toxins and strain-specific markers, characterization of RNA and double- and single-stranded DNA, proteins and associations between proteins, bacterial metabolism, and the range of protein expression profiles of disease-causing organisms, and, finally, proteomics (the process and tools used to study a proteome, which is the combination of all of the proteins that have been expressed by a genome at any given time in a cell, tissue, fluid, spore, culture, etc.)
In the current report, Dr. Lay reviews published MALDI-TOF/MS studies to assess MALDI-TOF/MS' utility for bacterial analysis. The report discusses the technique`s efficacy with regard to bacterial systemic classification and proteomics, protein identification, and bacterial metabolism, and evaluates the novel methods developed for preparation of cells for mass spectrometry.
One of the major applications of MALDI-TOF/MS has been in the identification of naturally occurring and recombinant proteins in bacteria. Prior studies have demonstrated that MALDI-TOF/MS is capable of identifying previously unknown bacterial proteins. Dr. Lay notes a study of poorly defined bacteria, Spiroplasma melliferum, in which MALDI-TOF/MS coupled with amino acid analysis identified 9 of 12 isolated proteins. The technique is sufficiently sensitive and specific to allow detection of modifications to known proteins, as demonstrated by a particular referenced study, in which three different species of the same protein (PfRd) were gleaned in the analysis. Time-dependence studies of recombinant proteins are feasible because MALDI-TOF/MS analysis can take only 10 minutes to accomplish based on direct analysis of untreated cells. This has proven beneficial in investigating bacterial biochemical responses to external environmental changes.
According to the report, prior studies have also demonstrated that MALDI-TOF/MS may be an invaluable tool in proteomics when used in conjunction with existing genomic data. In one study, MALDI-TOF/MS was critical to the identification of 152 proteins from the bacteria Helicobacter pylori, including 9 known disease-producing factors, and 28 antibody-producing substances. When coupled with methods that increase the number of protein fractions collected, such as high performance liquid chromatography (HPLC), MALDI-TOF/MS is even more effective and insightful. The combined analysis of several simple membrane separated fractions was able to detect over 300 peaks in the 2-19 kDa mass range for a sample of E. coli, representing, according to Dr. Lay, "an order of magnitude increase over the number of components observed by direct MALDI analysis of the same proteins in the mixture".
Additionally, some studies have demonstrated that MALDI-TOF/MS can be extended to bacterial taxonomic identification by generating characteristic spectra and biomarker profiles from bacteria samples. Multiple studies have been performed with MALDI-TOF/MS to identify bacteria at the species level, by distinguishing among specific biomarkers. Other studies have differentiated bacterial strains on the basis of subtle differences in the spectra between bacteria species.
However, data reproducibility and subsequent development of solid and reliable spectra libraries, remains difficult. It appears that minor variations in the preparations sample, matrix, protein extraction, and bacterial samples may dramatically effect the spectral pattern gleaned and the detection of certain ions, including major high-mass ions. Moreover, there is still some disagreement regarding the optimal matrix and the matrix characteristics that may alter the observed spectra.
Various studies have investigated strategies for improving the speed and quality of analysis by reducing the number of steps in sample preparation. The "whole cell" approach has been evaluated as an alternative to the more traditional but time consuming and complex protein isolation and purification protocols. Some of the approaches researched include: preparing bacteria samples in a matrix such as ferulic acid, or sinapinic, air-drying them, and introducing them directly into the mass spectrometer; using affinity surfaces to isolate specific bacteria; or simply collecting bacteria from contaminated media, such as water or a lettuce leaf, and introducing them directly into the mass spectrometer. Although these methods of "whole cell" analysis detect only a fraction of bacterial proteins present and, hence, are not useful for protein identification and proteomics, they are sufficient to generate strain-specific spectra and identify highly preserved biomarker proteins. Most importantly, this approach is quite fast.
"The rapidity of the MALDI method, the sometimes single-strain specificity of organisms that have human health effects, and the absence of methods for rapidly differentiating among similar strains, together, provide a compelling basis for the development of rapid methods for strain-specific taxonomic identification of bacteria," comments Dr. Lay. He concludes that "MALDI seems uniquely suited to the task of rapidly characterizing intact organisms, based on the rapid detection of a unique bacterial fingerprint at the genus, species, strain, and even substrain level."
John Wiley & Sons
In a recent report, researchers Catherine Fenselau and Plamen Demirev reviewed a sequence of prior studies discussing MALDI mass spectrometry procedures and interpreting their efficacy. According to previous observations, MALDI mass spectrometry of bacteria and viruses does not appear to require a lysis step. However, fungal cells, spores, and single-celled parasites do seem to require lysis - exposure of the sample in the sample holder to a strong organic acid, for instance - to obtain a MALDI spectrum.
Prior studies have also indicated that combining MALDI with time-of-flight (TOF) mass analysis enhances the technique`s detection function, as TOF instruments provide rapid analysis, tandem mass spectrometry, and miniaturization. When combined, the two methods perpetuate easy desorbtion and analysis of positive as well as negative ions in the samples, which improves identification precision and specificity. Most MALDI TOF instruments used in microorganism characterization are equipped with an ultra-violet (UV) nitrogen laser. However, infrared (IR) lasers are also capable of generating phospholipi and lipopeptide biomarker ion profiles. When compared to UV MALDI, IR MALDI mass spectra displayed a larger number and a higher m/z range for biomarker peaks detected above m/z 4,000.
Sample collection and sample preparation are integral steps in performing mass spectrometry. The simplest and most easily replicated method of sample collection is the removal of a single colony from a bacteria strand grown in a Petri dish. Once deposited directly into the sample plate and saturated in matrix, the sample undergoes MALDI analysis, which, if successful, allowing a fairly reproducible MALDI spectra to be obtained. Sample preparation is critical to the sensitivity, reproducibility, and mass accuracy of the MALDI technique, as well as to the nature of the biomarkers detected. Prior studies have demonstrated that adding methanol, for instance, improves the sample stability before MALDI analysis. Several physical methods have been applied to improve biomarker signals as well. In addition, sample-to-matrix ration and the amount of material on the holder appear to also affect the quality of the MALDI spectra.
Several studies cited in the report have determined that between 5,000 and 1,0000 intact cells deposited on the sample holder are sufficient to obtain a biomarker signal with a sufficient signal-noise ratio. Intact proteins are species readily desorbed from cells and detected in MALDI spectra above 4,000 Da and most proteins with bacterial genomes fall in the range 4,000-15,000 Da. Various algorithms have been engineered to match spectra (signatures), in order to classify microorganisms. Generally, the reference library of algorithms is constructed by extracting the essential biomarkers from a large number of spectra from the same analyte under various conditions. The biomarkers are described by their m/z values, intensity, related standard deviations, and frequency of their occurrence in the replicate spectra. The peak position and the number of matched peaks between the fingerprint spectrum and an unknown are then compared for identification purposes.
Because characterizing microorganisms with MALDI spectra has been based on determining and comparing the biomarker mass values observed for organisms, the comparisons are heavily based on the ability to reproduce the observed m/z values, rather than on the peak intensity. However, Drs. Fenselau and Demirev point out that "the reproducibility of spectra of the complex biochemical mixtures that compose the thick and irregular bacterial samples is problematic," adding that "this has been the major difficulty in compiling reliable fingerprint libraries and in applying spectrum-comparison algorithms."
Recently, a novel bioinformatics-based approach proposes the characterization of microorganisms based on matching protein molecular masses in the spectrum with protein molecular masses predicted from sequenced genomes. Its application is limited to microorganisms whose genomes are sequenced, but the number of such genomes in the public domains is growing rapidly. This approach interprets the biomarker spectrum rather than matching or correlating it, which provides newfound flexibility to MALDI, because even when different proteins are observed, they can be related back to and identified with an individual organism. This approach also accommodates mutations.
Various mass spectral strategies are currently being explored for identification and analysis of airborne and waterborne microorganisms, with added urgency spurred by mounting anxiety about the unpredictable threat of bio-terrorism. The researchers cite a study in 1999, in which researchers described an algorithm for identifying potential biological threat agents. The measured spectrum was compared to a library of stored mass spectra of threat agents, in analogy to an approach initially developed for comparisons of FAB spectra of phospholipid biomarkers. Several other studies have investigated the combined application of bioaffinity surfaces with MALDI mass spectrometry to microorganisms in wastewater or urine, allowing the sample to be cleansed of salts and contaminants. Upon exposure of the affinity complex to acid, the antigen is released for direct MALDI analysis. In another study, aerosols, containing bacterial vegetative cells and spores, were sampled in an ion trap mass spectrometer through an atmospheric pressure inlet system, and the microorganisms were detected in real time, by tandem mass spectrometry in the ion trap.
Tandem mass spectrometry involves the analysis of proteolytic peptides from their proteins or sequence tags. Search algorithms for identification can be based on a set of peptide molecular masses, and/or a sequence tag obtained from a proteolytic peptide or intact protein. When fully developed, this approach will enable the characterization of microorganisms in mixtures and will enhance the value of lipopeptides and glycolipids as biomarkers.
The implications of these advances in mass spectrometry for various facets of life are many-fold. These techniques (capabilities) can be integral and invaluable to counter-terrorism efforts as well to the general promotion of air, water, drug, etc. safety. They can be used to screen for bacterial contaminants, as well as applied for rapid analysis of culture from food, the development of agents to combat drug-resistant strands of bacteria and viruses, and rapid medical diagnostics, which are especially essential in crisis circumstances.
"Speed, sensitivity, tolerance to contaminants, and screening capability are improved by automation in this physicochemical method that is complementary to biochemical and morphological methods," comment the authors. "The approaches discussed here are receiving intense attention in pharmaceutical companies and governmental regulatory agencies, and increased utility is anticipated," they conclude.
MALDI-TOF Mass Spectrometry Is a Versatile and Effective Technique for Identifying Biomarker Proteins and Bacteria in Order to Classify Microorganisms
Advances in Cell Preparation and Data Interpretation Required to Reach Maximum Potential Efficacy of the Technique
Matrix-assisted laser desorption-ionization (MALDI) time of flight mass spectrometry (TOF/MS) has proven to be an effective tool for bacterial identification and characterization. Prior published literature is reviewed by Jackson Lay, Jr., in a report published in the February 2002 issue of Mass Spectrometry Reviews. The report indicates that MALDI-TOF/MS may revolutionize various aspects of bacterial characterization. For instance, MALDI-TOF/MS can increase the speed and specificity of identifying bacteria that cause human disease and can be used for rapidly characterizing chemical changes associated with their biochemical life cycles. However, the author indicates that development of protocols that do not require preliminary culture steps to expand the number of bacteria for analysis and more suitable methods for data interpretation would advance MALDI-TOF/MS beyond its current limitations.
Mass spectrometry for the characterization of bacteria dates back to 1975 and is based on the detection of a broad m/z range of biomarker ions that are theoretically unique to and representative of a microorganism. The desorption-ionization techniques that emerged in the 1980s proved more effective in generating small molecule biomarker ions from microorganisms. Subsequently MALDI provided mass spectra of proteins and was combined with TOF mass analysis to yield a powerful new bio-analytical tool. MALDI-TOF/MS is based on simple technology, yet it provides high sensitivity and specificity, and is compatible with rapid (usually 5 minutes) analysis. MALDI can be implemented in a tandem mass spectrometry configuration and is suitable for miniaturization.
For analysis of bacteria, MALDI-TOF/MS traditionally has used complex, time consuming purification procedures to isolate specific proteins from bacteria before analysis. New methods using whole and disrupted cells have been recently investigated in order to bypass isolation procedures. Recent applications include identification of unknown proteins, such as toxins and strain-specific markers, characterization of RNA and double- and single-stranded DNA, proteins and associations between proteins, bacterial metabolism, and the range of protein expression profiles of disease-causing organisms, and, finally, proteomics (the process and tools used to study a proteome, which is the combination of all of the proteins that have been expressed by a genome at any given time in a cell, tissue, fluid, spore, culture, etc.)
In the current report, Dr. Lay reviews published MALDI-TOF/MS studies to assess MALDI-TOF/MS' utility for bacterial analysis. The report discusses the technique`s efficacy with regard to bacterial systemic classification and proteomics, protein identification, and bacterial metabolism, and evaluates the novel methods developed for preparation of cells for mass spectrometry.
One of the major applications of MALDI-TOF/MS has been in the identification of naturally occurring and recombinant proteins in bacteria. Prior studies have demonstrated that MALDI-TOF/MS is capable of identifying previously unknown bacterial proteins. Dr. Lay notes a study of poorly defined bacteria, Spiroplasma melliferum, in which MALDI-TOF/MS coupled with amino acid analysis identified 9 of 12 isolated proteins. The technique is sufficiently sensitive and specific to allow detection of modifications to known proteins, as demonstrated by a particular referenced study, in which three different species of the same protein (PfRd) were gleaned in the analysis. Time-dependence studies of recombinant proteins are feasible because MALDI-TOF/MS analysis can take only 10 minutes to accomplish based on direct analysis of untreated cells. This has proven beneficial in investigating bacterial biochemical responses to external environmental changes.
According to the report, prior studies have also demonstrated that MALDI-TOF/MS may be an invaluable tool in proteomics when used in conjunction with existing genomic data. In one study, MALDI-TOF/MS was critical to the identification of 152 proteins from the bacteria Helicobacter pylori, including 9 known disease-producing factors, and 28 antibody-producing substances. When coupled with methods that increase the number of protein fractions collected, such as high performance liquid chromatography (HPLC), MALDI-TOF/MS is even more effective and insightful. The combined analysis of several simple membrane separated fractions was able to detect over 300 peaks in the 2-19 kDa mass range for a sample of E. coli, representing, according to Dr. Lay, "an order of magnitude increase over the number of components observed by direct MALDI analysis of the same proteins in the mixture".
Additionally, some studies have demonstrated that MALDI-TOF/MS can be extended to bacterial taxonomic identification by generating characteristic spectra and biomarker profiles from bacteria samples. Multiple studies have been performed with MALDI-TOF/MS to identify bacteria at the species level, by distinguishing among specific biomarkers. Other studies have differentiated bacterial strains on the basis of subtle differences in the spectra between bacteria species.
However, data reproducibility and subsequent development of solid and reliable spectra libraries, remains difficult. It appears that minor variations in the preparations sample, matrix, protein extraction, and bacterial samples may dramatically effect the spectral pattern gleaned and the detection of certain ions, including major high-mass ions. Moreover, there is still some disagreement regarding the optimal matrix and the matrix characteristics that may alter the observed spectra.
Various studies have investigated strategies for improving the speed and quality of analysis by reducing the number of steps in sample preparation. The "whole cell" approach has been evaluated as an alternative to the more traditional but time consuming and complex protein isolation and purification protocols. Some of the approaches researched include: preparing bacteria samples in a matrix such as ferulic acid, or sinapinic, air-drying them, and introducing them directly into the mass spectrometer; using affinity surfaces to isolate specific bacteria; or simply collecting bacteria from contaminated media, such as water or a lettuce leaf, and introducing them directly into the mass spectrometer. Although these methods of "whole cell" analysis detect only a fraction of bacterial proteins present and, hence, are not useful for protein identification and proteomics, they are sufficient to generate strain-specific spectra and identify highly preserved biomarker proteins. Most importantly, this approach is quite fast.
"The rapidity of the MALDI method, the sometimes single-strain specificity of organisms that have human health effects, and the absence of methods for rapidly differentiating among similar strains, together, provide a compelling basis for the development of rapid methods for strain-specific taxonomic identification of bacteria," comments Dr. Lay. He concludes that "MALDI seems uniquely suited to the task of rapidly characterizing intact organisms, based on the rapid detection of a unique bacterial fingerprint at the genus, species, strain, and even substrain level."
John Wiley & Sons
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