Rapid identification of environmental bacterial strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In recent years, various mass spectrometry procedures have been developed for bacterial identification. The accuracy and speed with which data can be obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) could make this a powerful tool for environmental monitoring. However, minor variations in the sample preparation can influence the mass spectra significantly. Therefore, the first objectives of this study were the adjustment and the optimization of experimental parameters allowing a rapid identification of whole bacterial cells without laborious sample preparation. The tested experimental parameters were matrix, extraction solvent, salt content, deposition method, culture medium and incubation time. This standardized protocol was applied to identify reference and environmental bacterial strains of Escherichia coli, Salmonella and Acinetobacter. The environmental bacterial strains were isolated from sewage sludge using an original microextraction procedure based on repeated sonications and enzymatic treatments. The bacterial identification was realized by the observation of the respective genus-, species- and strain-specific biomarkers. This bacterial taxonomy could be completed within one hour, with minimal sample preparation, provided that sufficient bacteria had been collected prior to MALDI-TOF analysis.     

Rapid identification of microorganisms by mass spectrometry: improved performance by incorporation of in-house spectral data into a commercial database

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used as a microbial diagnostic method for species identification of pathogens. However, MALDI-TOF identification of bacteria at the species level remains unsatisfactory, with the major problem being an incomplete database that still needs refinement and expansion. Augmentation of the original MALDI BioTyper 2.0 (Bruker) database by incorporating mass spectra obtained in-house from clinical isolates may increase the identification rate at the species level. We conducted a prospective study to assess whether the augmented database can improve the performance of MALDI-TOF MS for routine identification of species. Cluster analyses revealed distinct differences in MS spectral profiles of clinical isolates obtained in our hospital and those of ATCC strains in the Bruker database. In the first part of the study, which was performed over 3 weeks, 259 bacterial isolates were subjected to analysis by MALDI-TOF MS, and MS spectra of 229 successfully identified isolates (49 species) were incorporated into the original database to give the augmented Bruker-Chiba database. In a second separate analysis, the concordance of identification of 498 clinical isolates of the 49 species with conventional methods was 87.1% (434/498) with the commercial Bruker database and 98.0% (488/498) using the Bruker-Chiba database. These results indicate that refinement of a commercial database can be achieved relatively easy and effectively by incorporating MS spectra of clinical isolates obtained in a clinical laboratory.     

SpectraBank: an open access tool for rapid microbial identification by MALDI-TOF MS fingerprinting

MALDI-TOF MS has proved to be an accurate, rapid, and cost-effective technique for microbial identification in which the spectral fingerprint of an unknown strain can be compared to a database of spectra from reference strains. Most of the existing databases are private and often costly to access, and little spectral information is shared among researchers. The objective of the present communication is to introduce the SpectraBank database (http://www.spectrabank.org), which provides open access MALDI-TOF mass spectra from a variety of microorganisms. This work aims to familiarize readers with the SpectraBank database, from the sample preparation, data collection, and data analysis to how the spectral reference data can be used for microbial species identification. The database currently includes more than 200 MALDI-TOF MS spectra from more than 70 bacterial species and links to the freely available web-based application SPECLUST (http://bioinfo.thep.lu.se/speclust.html) to allow comparisons of the obtained peak mass lists and evaluate phyloproteomic relationships. The SpectraBank database is intended to be expanded by the addition of new spectra from microbial strains, obtained in our laboratory and by other researchers.     

Strain and phase identification of the U.S. category B agent Coxiella burnetii by matrix assisted laser desorption/ionization time-of-flight mass spectrometry and multivariate pattern recognition

Accurate bacterial identification is important in diagnosing disease and in microbial forensics. Coxiella burnetii, a highly infective microorganism causative of the human disease Q fever, is now considered a U.S. category B potential bioterrorism agent. We report here an approach for the confirmatory identification of C. burnetii at the strain level which involves the combined use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and supervised pattern recognition via Partial Least Squares-Discriminant Analysis (PLS-DA). C. burnetii isolates investigated in this study included the following prototype strains from different geographical and/or historical origins and with different antigenic properties: Nine Mile I, Australian QD, M44, KAV, PAV, Henzerling, and Ohio. After culture and purification following standard protocols, linear MALDI-TOF mass spectra of pure bacterial cultures were acquired in positive ion mode. Mass spectral data were normalized, baseline-corrected, denoised, binarized and modeled by PLS-DA under crossvalidation conditions. Robustness with respect to uncontrolled variations in the sample preparation and MALDI analysis protocol was assessed by repeating the experiment on five different days spanning a period of 6 months. The method was validated by the prediction of unknown C. burnetii samples in an independent test set with 100% sensitivity and specificity for five out of six strain classes.     

Automated mass analysis of low-molecular-mass bacterial proteome by liquid chromatography-electrospray ionization mass spectrometry

Due to the presence of a large number of proteins in cell extracts, ion chromatograms of cell extracts obtained by electrospray ionization mass spectrometry (ESI-MS) can be quite complicated. It is found that the elevated baseline in an ion chromatogram contains many protein signals. One deficiency of current commercially available LC-ESI-MS data interpretation software is found to be the lack of functional operation that allows automated mass spectral integration and interpretation over signals hidden in the baseline. This current limitation can be overcome by a technique that involves the introduction of artificial pulses to an ion chromatogram by removing the solvent mixer in the HPLC pump. These artificial pulses are treated as chromatographic peaks by the software, thereby allowing automated spectral integration over the duration of a pulse. The reliability of mass analysis from the integrated spectra is shown to be dependent on spectral interpretation parameters such as mass spectral baseline threshold. The application of this method is demonstrated for rapid detection and mass analysis of low-molecular-mass proteins from cell extracts of Escherichia coli or Bacillus globigii.     

Environmental semivolatiles and nonvolatiles analysis by hyphenated spectral techniques

Environmental sample extracts contain a variety of volatile and nonvolatile organic compounds exhibiting a range of polarities and concentrations. Although gas chromatography/mass spectrometry (GC/MS) is the method of choice thus far for such analyses, this technique used alone cannot adequately characterize the volatiles in such samples and is not amenable to environmental nonvolatiles. A more complete characterization of environmental and hazardous waste samples is required to assess the dangers posed to the nation's groundwater by hazardous waste dumps. Online spectral confirmation by directly linked GC/Fourier transform infrared (FTIR)/MS is shown to provide useful structural information on environmental volatiles in hazardous wastes, even when the analyte's spectrum is not in either spectral database. This information can lead to biological-hazard estimation. The diffuse reflectance Fourier transform infrared (DRIFT) technique, used in conjunction with thermospray MS or fast atom bombardment (FAB) MS, provides confirmed identifications or confirmed compound class assignments of organic nonvolatiles in solid wastes. This is believed to be the first report of spectral confirmation (identification or functionality) of organic volatiles and nonvolatiles in environmental samples.     

A new matching algorithm for high resolution mass spectra

We present a new matching algorithm designed to compare high-resolution spectra. Whereas existing methods are bound to compare fixed intervals of ion masses, the accurate mass spectrum (AMS) distance method presented here is independent of any alignment. Based on the Jeffreys-Matusitas (JM) distance, a difference between observed peaks across pairs of spectra can be calculated, and used to find a unique correspondence between the peaks. The method takes into account that there may be differences in resolution of the spectra. The algorithm is used for indexing in a database containing 80 accurate mass spectra from an analysis of extracts of 80 isolates representing the nine closely related species in the Penicillium series Viridicata. Using this algorithm we can obtain a retrieval performance of approximately 97-98% that is comparable with the best of the existing methods (e.g., the dot-product distance). Furthermore, the presented method is independent of any variable alignment procedures or binning.     

Quality evaluation of tandem mass spectral libraries

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including “tandem-in-time” instruments; this is due to the coverage of a large range of different collision energy settings—including the very low range—which is an outstanding characteristics of the MSforID library.     

Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification

Flow-injection electrospray ionization mass spectrometry (FI-ESI-MS) of unfractionated cell-free extracts obtained from bacterial cells suspended in a solvent mixture was investigated as a rapid analytical method for reproducible, high-throughput bacterial identification. Five bacterial strains (two Escherichia coli, two Bacillus spp. and one Brevibacillus laterosporus) were studied in this investigation. Axenically grown bacterial cells were suspended in an acidic organic solvent and the cell-free extract was sequentially injected into a solvent flow stream that was sprayed into the ionization chamber of the ESI-MS. The spectra produced contained reproducible information, which was useful for discriminating between the bacteria. Tandem mass spectrometry was used to characterize further the peaks, and at least three classes of macromolecules, namely phospholipids, glycolipids, and proteins, were found to contribute most to the spectral information. Bacterial extracts stored under different conditions gave very similar mass spectra for each of the five bacterial strains, indicating that the extracts were stable even at room temperature for up to 24 h, with no loss of information content, which has obvious implications for automated high-throughput analysis. An analysis of the components of the extracting solvent mixture and their effects on the spectral information showed that acetonitrile contributes most significantly to the extraction process and hence to the information content of the spectra.     

Two-dimensional LC-MS analysis of components in Swertia franchetiana Smith

An off-line 2-D-LC approach was developed for the separation and identification of components in extracts of Swertia franchetiana Smith, which is a traditional Chinese medicine. An octadecylsilica column was used for further separation of fractions from a cyano column with UV and MS detection. In this method, a longer column was used in the second dimension to improve the separation ability, and "on-column focusing" was adopted to reduce sample loss and pollution on concentrating the fractions from the first dimension. More than 118 and 575 components were detected in the chloroform and n-butanol extracts by this method, respectively. In contrast, only 20 and 95 peaks were detected by the one-dimensional method. Most of the additionally detected compounds were of low-abundance components. Many compounds can be preliminarily identified according to their UV and mass spectra in the two-dimensional method. The obtained results not only demonstrated the powerful resolution of 2-D-LC, but also led to in-depth comprehension of the UV and mass spectra of complex samples.     

Strip-based regression: A method to obtain comprehensive co-polymer architectures from matrix-assisted laser desorption ionisation-mass spectrometry data

A method aimed to obtain the relative abundances of all molecular species in highly overlapped mass spectra is presented. Its performance is demonstrated with an example of matrix-assisted laser desorption ionization (MALDI) spectra obtained from a polysterene-co-polyisoprene sample, retrieving the full co-polymer architecture. The method is based on a multiple regression operation, applied locally at consecutive regions. The method is designed in such a way that it is not necessary to locate regions in the spectrum that are not influenced by adjacent ones. This increases its applicability, since the method is able to tackle the analysis of highly complex spectra, tending to minimise the need of user intervention. The method allows to correct for non-idealities (such as wrong calibration) or to adjust the variations of spectral resolution with mass. Additionally, the algorithm calculates the precision of the computation in a straightforward way.     

Software-based mass spectral enhancement to remove interferences from spectra of unknowns

Gas chromatography-mass spectrometry data from the analysis of complex environmental samples were converted into ASCII text and imported into a personal computer spreadsheet. A macro was written to perform mass spectral enhancement by statistical and mathematical procedures to separate the spectra of compounds of interest from interfering mass spectral responses, such as those of broadly eluting hydrocarbons. The extracted mass spectra were compared to reference spectra, with the result that usually 80–90% of the ions common to those in the reference spectra were successfully extracted by using this method. This procedure improved mass spectral quality and the ability of the data system to perform successful library searches. The fitted quality parameters showed systematic improvements after the data were subjected to the spectral enhancement procedures. These procedures could help to identify unknowns by separating their spectra from other signals, such as those of background aliphatic hydrocarbons.     

The use of MS classifiers and structure generation to assist in the identification of unknowns in effect-directed analysis

Structure generation and mass spectral classifiers have been incorporated into a new method to gain further information from low-resolution GC-MS spectra and subsequently assist in the identification of toxic compounds isolated using effect-directed fractionation. The method has been developed for the case where little analytical information other than the mass spectrum is available, common, for example, in effect-directed analysis (EDA), where further interpretation of the mass spectra is necessary to gain additional information about unknown peaks in the chromatogram. Structure generation from a molecular formula alone rapidly leads to enormous numbers of structures; hence reduction of these numbers is necessary to focus identification or confirmation efforts. The mass spectral classifiers and structure generation procedure in the program MOLGEN-MS was enhanced by including additional classifier information available from the NIST05 database and incorporation of post-generation ‘filtering criteria’. The presented method can reduce the number of possible structures matching a spectrum by several orders of magnitude, creating much more manageable data sets and increasing the chance of identification. Examples are presented to show how the method can be used to provide ‘lines of evidence’ for the identity of an unknown compound. This method is an alternative to library search of mass spectra and is especially valuable for unknowns where no clear library match is available.     

Evaluation of the sensitivity of the ‘Wiley registry of tandem mass spectral data,MSforID’ with MS/MS data of the ‘NIST/NIH/EPA mass spectral library’

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the ‘NIST/NIH/EPA Mass Spectral Library’ (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross‐validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.     

Bacterial analysis by MALDI-TOF mass spectrometry: An inter-laboratory comparison

Bacterial analysis by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry has been demonstrated in numerous laboratories, and a few attempts have been made to compare results from different laboratories on the same organism. It has been difficult to understand the causes behind the observed differences between laboratories when different instruments, matrices, solvents, etc. are used. In order to establish this technique as a useful tool for bacterial identification, additional efforts in standardizing the methods by which MALDI mass spectra are obtained and comparisons of spectra from different instruments with different operators are needed. Presented here is an extension of our previous single-laboratory reproducibility study with three different laboratories in a controlled experiment with aliquots of the same bacterial culture, matrix stock solution, and calibrant standards. Using automated spectral collection of whole-cell bacteria and automated data processing and analysis algorithms, fingerprints from three different laboratories were constructed and compared. Nine of the ions appeared reproducibly within all three laboratories, with additional unique ions observed within each of the laboratories. An initial evaluation of the ability to use a fingerprint generated within one laboratory for bacterial identification of a sample from another laboratory is presented, and strategies for improving identification rates between laboratories is discussed.     

Atmospheric pressure chemical ionisation liquid chromatography/mass spectrometry of the ultraviolet screening pigment scytonemin: characteristic fragmentations

Atmospheric pressure chemical ionisation reversed-phase high-performance liquid chromatography/multistage mass spectrometry has been used to study the mass spectral fragmentation of the cyanobacterial sheath pigment scytonemin and its reduced counterpart. The two pigments exhibit characteristic fragment ions in their MS2 and MS3 spectra that are of value in confirming the identification of the structures in extracts from natural environments.     

A “Low-Molecular” Approach to the Identification of Microorganisms by MALDI Mass Spectrometry

A new approach to the identification of microorganisms is presented. It includes the transformation of their MALDI mass spectra aimed at reducing mass scale by one order of magnitude and the use of standard software for building mass spectral libraries of low-molecular compounds and library searches. A library of 728 transformed (“rescaled”) mass spectra of 182 strains for some Streptococcus species was built. With this library, the rate of true microorganism identification was estimated by cross-comparison between library mass spectra (internal validation of the approach). The true identification rate was 84% for three Streptococcus species, which corresponds to the average trueness of species identification by MALDI as found in the literature. The proposed approach to identification can be considered as a method of choice for solving identification problems under consideration.     

Spectral and non-spectral interferences in inductively coupled plasma mass-spectrometry

Inductively coupled plasma mass spectrometry of environmental and biological samples is often hampered by spectral and non-spectral interferences. Spectral interferences, caused by the limited resolution of the quadrupole mass spectrometer, can be eliminated in a variety of ways. For their identification inspection of a signal versus carrier gas flowrate is useful. Anion exchange allows the removal of most S and Cl containing compounds, which are at the origin of the majority of spectral interferences. Matrix modification, for example the addition of ethanol and subsequent optimization of the gas flow rates in a number of cases enables the reduction of the interferences to insignificant values. Often a mathematical correction based on isotopic signal ratios can be applied. Non-spectral interferences can be divided in reversible, that is occurring while the sample is being measured, and irreversible matrix effects, that is clogging of the nebulizer and sampling orifices or deposition on the torch or in the ion lens stack. The errors associated with non-spectral interferences can be eliminated by appropriate calibration procedures, adapted sample preparation or limitation of the amount of sample delivered to nebulizer, plasma and sampling devices, for example by the application of flow injection. Applications of all the elimination procedures are described for the analysis of sea-water, estuarine water, soil and sewage extracts, percolate water, urine, serum and wine.     

Reconstruction of mass spectra of components of unknown mixtures based on factor analysis

A method is described for the spectral resolution of combined gas chromatographic—mass spectrometric data. Factor analysis is applied to the identification of a second species in a single gas chromatographic peak. A plot can be constructed from the region of the non-negative values of spectral lines in the factor space. Feasible locations for the spectra of these constituents in the plot can be identified and give recognizable spectra of the separated constituents.     

Efficient method to locate double bond positions in conjugated trienes

The double bond positions of 11 conjugated trienes were unambiguously located through a simple derivatization method amenable to nanogram-scale analyses. The trienes were reacted with the powerful dienophile 4-methyl-1,2,4-triazoline-3,5-dione (MTAD), and the mass spectra of the resulting cycloadducts exhibited large diagnostic fragments which allowed the unequivocal location of the double bonds in the parent triene in most cases. Catalytic hydrogenation of the cycloadducts produced saturated compounds with characteristic mass spectral fragments from which the positions of the trienes in the parent compounds could be readily confirmed. Application of the method was demonstrated by the microscale identification of two conjugated triene and one conjugated diene components from extracts of the sex pheromone gland of the saturniid moth Automeris cecrops pamina.