Analysis of microbial mixtures by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Many different laboratories are currently developing mass-spectrometric techniques to analyze and identify microorganisms. However, minimal work has been done with mixtures of bacteria. To demonstrate that microbial mixtures could be analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), mixed bacterial cultures were analyzed in a double-blind fashion. Nine different bacterial species currently in our MALDI-MS fingerprint library were used to generate 50 different simulated mixed bacterial cultures similar to that done for an initial blind study previously reported (Jarman, K. H.; Cebula, S. T.; Saenz, A. J.; Petersen, C. E.; Valentine, N. B.; Kingsley, M. T.; Wahl, K. L. Anal. Chem. 2000, 72, 1217-1223). The samples were analyzed by MALDI-MS with automated data extraction and analysis algorithms developed in our laboratory. The components present in the sample were identified correctly to the species level in all but one of the samples. However, correctly eliminating closely related organisms was challenging for the current algorithms, especially in differentiating Serratia marcescens, Escherichia coli, and Yersinia enterocolitica, which have some similarities in their MALDI-MS fingerprints. Efforts to improve the specificity of the algorithms are in progress.     

Gender identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A rapid, simple, and reliable gender determination of human DNA samples was successfully obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Detection sensitivity reached 0.01 ng or less for DNA samples.     

Anionic adducts of oligosaccharides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The formation and decomposition (postsource decay, PSD) of anionic adducts in negative ion matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry have been studied. Chloride, a small inorganic anion, has been found to form stable anionic adducts with a variety of neutral oligosaccharides that can survive the MALDI process to give readily identifiable signals (with characteristic isotope patterns) allowing subpicomole detection in the best cases. The matrixes that can aid the formation of chloride adducts of oligosaccharides have gas-phase acidities lower than or close to that of HCl (1373 kJ/mol). In PSD experiments, precursor chloride adducts of oligosaccharides yield fragment ions that retain the charge on the sugar molecule rather than solely forming Cl-, and these fragments can provide structurally informative product ions. In negative ion MALDI, highly acidic oligosaccharides do not form adducts with chloride anions, but mildly acidic saccharides (e.g., containing a carboxylic acid group) form both deprotonated molecules and chloride adducts, and each may provide structural information concerning the oligosaccharide upon decomposition.     

Proteomic profiling of intact mycobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Current methods for the identification of mycobacteria in culture are time-consuming, requiring as long as 12 weeks for positive identification. One potential approach to rapid mycobacterial identification is to utilize proteomic profiling of cultures by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In this report, we have applied MALDI-TOF MS to proteomic profiling of cultured microorganisms representing six species of the genus Mycobacterium. We find that analysis of acetonitrile/trifluoroacetic acid cellular extracts produces data similar to that of the analysis of deposited whole cells, while minimizing human contact with the microorganisms and rendering them nonviable. A matrix composition of alpha-cyano-4-hydroxycinnamic acid with fructose yields highly reproducible MALDI-TOF spectra. Statistical analysis of MALDI-TOF MS data allows differentiation of each individual mycobacterial species on the basis of unique mass fingerprints. The methodology allows identification of a number of unique (potentially diagnostic) biomarkers as targets for protein identification by MS/MS experiments. In addition, we observe a number of signals common to all mycobacterial species studied by MALDI-TOF MS, which may be genus-specific biomarkers. The potentially genus-specific biomarkers occur at low mass (<2 kDa) and are likely to be lipids and cell wall components such as mycolic acids. This study demonstrates the potential for mass spectrometry-based identification/classification of mycobacteria.     

High-throughput quantitative analysis of total N-glycans by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Accurate and reproducible quantification of glycans from protein drugs has become an important issue for quality control of therapeutic proteins in biopharmaceutical and biotechnology industries. Mass spectrometry is a promising tool for both qualitative and quantitative analysis of glycans owing to mass accuracy, efficiency, and reproducibility, but it has been of limited success in quantitative analysis for sialylated glycans in a high-throughput manner. Here, we present a solid-phase permethylation-based total N-glycan quantitative method that includes N-glycan releasing, purification, and derivatization on a 96-well plate platform. The solid-phase neutralization enabled us to perform reliable absolute quantification of the acidic N-glycans as well as neutral N-glycans from model glycoproteins (i.e., chicken ovalbumin and porcine thyroglobulin) by only using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Furthermore, low-abundance sialylated N-glycans from human serum prostate specific antigen (PSA), an extremely valuable prostate cancer marker, were initially quantified, and their chemical compositions were proposed. Taken together, these results demonstrate that our all-inclusive glycan preparation method based on a 96-well plate platform may contribute to the precise and reliable qualitative and quantitative analysis of glycans.     

Quantitative analysis of synthetic polymers using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Quantitative analyses of synthetic polymers were accomplished using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). Many factors have hindered the development of quantitative measurement of polymers via MALDI TOF MS, e.g., laser power, matrix, cation salt, and cocrystallization. By probing the optimal conditions, two sets of polymers were studied. Fair repeatability of the samples ensures acceptable results. In set 1, two poly(ethylene glycols) with different end groups showed equal desorption/ionization efficiencies. Two synthetic polymers in set 2 with different chemical properties resulted in different MALDI responses. Good linearity was achieved by plotting the relationship between the sample concentration ratio and the total signal intensity ratio in both sets.     

Identification of phosphorylation sites in N-linked glycans by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Glycan phosphorylation is a significant feature of complex carbohydrate chemistry and glycobiology. For example, N-linked glycans containing mannose-6-phosphate (Man-6-P) residues play a key role as targeting signals for the transport of proteins from the Golgi apparatus to lysosomes. Structural information on Man-6-P glycans involved in transport of proteins is usually obtained using nuclear magnetic resonance (NMR) spectroscopy. However, an alternative and simple method with comparable accuracy is desirable because large amounts of samples and special techniques are required for structural analysis using NMR. Recently, postsource decay (PSD) fragment spectra obtained by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) have provided critical information on complex carbohydrates. Since few Man-6-P-containing glycans are commercially available, very little information has been collected on the mass spectrometry of phosphorylated glycans. In this report, four kinds of phosphorylated glycans labeled with 2-aminopyridine (PA) were purified from yeast mannan, and their PSD spectra were measured in the positive ion mode. The phospho-6-O-mannose monoester linkages (PO3H-Man) in glycans are stable, although cleavage of the mannose-1-phosphate linkage (Man-alpha-1-PO3H) occurs readily. Fragment ions indicated the presence of the alpha-1,3-branching chain of an N-linked high-mannose-type glycan, and characteristic fragmentation patterns were observed for phosphorylated glycans. On the basis of the MALDI-PSD spectra, we deduced fragmentation rules for phosphorylated N-glycans that will be valuable for distinguishing the position of phosphorylation.     

Analysis of whole bacterial cells by flow field-flow fractionation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The purpose of this study is to develop a novel bacterial analysis method by coupling the flow field-flow fractionation (flow FFF) separation technique with detection by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The composition of carrier liquid used for flow FFF was selected based on retention of bacterial cells and compatibility with the MALDI process. The coupling of flow FFF and MALDI-TOF MS was demonstrated for P. putida and E. coli. Fractions of the whole cells were collected after separation by FFF and further analyzed by MALDI-MS. Each fraction, collected over different time intervals, corresponded to different sizes and possibly different growth stages of bacteria. The bacterial analysis by flow FFF/MALDI-TOF MS was completed within 1 h with only preliminary optimization of the process.     

Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry

A novel ionization source for biological mass spectrometry is described that combines atmospheric pressure (AP) ionization and matrix-assisted laser desorption/ionization (MALDI). The transfer of the ions from the atmospheric pressure ionization region to the high vacuum is pneumatically assisted (PA) by a stream of nitrogen, hence the acronym PA-AP MALDI. PA-AP MALDI is readily interchangeable with electrospray ionization on an orthogonal acceleration time-of-flight (oaTOF) mass spectrometer. Sample preparation is identical to that for conventional vacuum MALDI and uses the same matrix compounds, such as alpha-cyano-4-hydroxycinnamic acid. The performance of this ion source on the oaTOF mass spectrometer is compared with that of conventional vacuum MALDI-TOF for the analysis of peptides. PA-AP MALDI can detect low femtomole amounts of peptides in mixtures with good signal-to-noise ratio and with less discrimination for the detection of individual peptides in a protein digest. Peptide ions produced by this method generally exhibit no metastable fragmentation, whereas an oligosaccharide ionized by PA-AP MALDI shows several structurally diagnostic fragment ions. Total sample consumption is higher for PA-AP MALDI than for vacuum MALDI, as the transfer of ions into the vacuum system is relatively inefficient. This ionization method is able to produce protonated molecular ions for small proteins such as insulin, but these tend to form clusters with the matrix material. Limitations of the oaTOF mass spectrometer for singly charged high-mass ions make it difficult to evaluate the ionization of larger proteins.     

Using electrospray-assisted laser desorption/ionization mass spectrometry to characterize organic compounds separated on thin-layer chromatography plates

Electrospray-assisted laser desorption/ionization (ELDI), an ionization method that combines laser desorption and electrospray ionization (ESI), can be used under ambient conditions to characterize organic compounds (including FD&C dyes, amines, extracts of a drug tablet) separated in the central track on a thin-layer chromatography (TLC) plate coated with either reversed-phase C18 particles or normal-phase silica gel. After drying, the TLC plate was placed on an acrylic sample holder set in front of the sampling skimmer of an ion trap mass analyzer. The chemicals at the center of the TLC plate were analyzed by pushing the sample holder into the path of a laser beam with a syringe pump. The molecules in the sample spot were desorbed by continuously irradiating the surface of the TLC plate with a pulsed nitrogen laser. Then, the desorbed sample molecules entered an ESI plume where they were ionized through the reactions with the charged species (including protons, hydronium ions and their cluster ions, solvent ions, and charged droplets) generated by electrospraying a methanol/water solution. MS/MS analyses were also performed to further characterize the analytes. The detection limit of TLC/ELDI/MS is approximately 10(-6) M. This was evaluated by using FD&C red dye as the standard. A linear relationship was found for the calibration curve with the concentration of FD&C red dye ranged from 10(-3) to 10(-6) M.     

Chemical cleavage sequencing of DNA using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

In this paper, we report for the first time use of laser desorption mass spectrometry for measurement of chemical cleavage sequencing products of DNA. In this method, the target DNA was labeled with biotin and subjected to chemical modification and cleavage according to the Maxam-Gilbert sequencing protocol. The biotin-containing fragments were captured by streptavidin-coated magnetic beads and separated from the other fragments. The captured fragments were released by hot ammonia treatment, and the released fragments were analyzed by mass spectrometry. Potential applications of this method in resolving sequence ambiguities and sequencing repeat sequences as well as in the analysis of DNA-protein interactions are discussed.     

End-group analysis of blue light-emitting polymers using matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry

An analytical method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been applied to provide information on the structure of a copolymer, e.g., repeat unit and end group. Seven conjugated polymers, which have been demonstrated as the active component in blue light-emitting diodes, were synthesized through Suzuki polycondensation reaction in the presence of Pd(PPh3)4 catalyst. Their molecular weights were obtained using gel permeation chromatography analysis. MALDI-TOF MS was used to investigate the structure information in detail. The proposed end-group structures were confirmed by the identity between the observed and the simulated isotopic distribution of each polymer. The results demonstrate that these synthetic polymers possess various end groups and even contain macrocycles. The catalyst Pd(PPh3)4 was found to introduce phenyl end groups via aryl-aryl exchange between the catalytic palladium intermediate and the triphenylphosphine ligand. All these results are based on the analysis of the mass spectrum data, which suggests that MALDI-TOF MS is an extraordinarily strong tool in synthetic polymer structure analysis.     

Direct determination of the peptide content in microspheres by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A quantitative determination of peptides incorporated into poly(d,l-lactide-co-glycolide) microspheres by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was accomplished in a single step without pretreatment for extracting the peptide from the microsphere. The conventional extraction methods often underestimate the actual amount of peptide because of incomplete extraction from the microspheres or loss during the procedures. In this study, the microspheres dissolved in acetonitrile containing 0.1% trifluoroacetic acid were mixed with matrix solution containing the internal standard, and the peptide content was directly determined by MALDI-TOF MS. The drug content values determined by MALDI-TOF MS in both the leuprolide- and salmon calcitonin-incorporated microspheres were closer to the theoretical contents than those determined by the conventional extraction method. This method using MALDI-TOF MS could be a good alternative to time-consuming and less-accurate conventional methods.     

Carbon nanotubes as assisted matrix for laser desorption/ionization time-of-flight mass spectrometry

Analysis of low molecular weight compounds with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been developed by using carbon nanotubes obtained from coal by arc discharge as the matrix. The carbon nanotube matrix functions as substrate to trap analytes of peptides, organic compounds, and beta-cyclodextrin deposited on its surface. It has been found that carbon nanotubes can transfer energy to the analyte under laser irradiation, which makes analytes well desorbed/ionized, and the interference of intrinsic matrix ions can be eliminated. At the same time, the fragmentation of the analyte can be avoided. A good sensitivity and excellent reproducibility of the spectrum signals are achieved. It is believed that this work not only will open a new field for applications of carbon nanotubes, but also will offer a new technique for high-speed analysis of low molecular weight compounds in areas such as metabolism research and characterization of natural products.     

Sample deposition device for off-line combination of supercritical fluid chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A new sample deposition device for off-line SFC-MALDI combination of supercritical fluid chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was assembled. This device was successfully applied to the detailed characterization of synthetic silicone oils. SFC was used to separate samples of silicone oils on micropacked capillary columns and to determine their molecular mass distribution. The separated fractions for the identification studies were obtained from SFC runs at defined time intervals. Using the constructed deposition device, these fractions were sprayed directly from the restrictor on the target probe covered with a proper matrix. MALDI-TOF MS was used for the identification of individual oligomers in the separated fractions and also in the unfractionated sample. The determined molecular mass distributions based on supercritical fluid chromatography with flame ionization detector, MALDI-TOF MS, and combined SFC-MALDI measurements were compared and the results were in a good agreement. The sample deposition device is based on a common plotter unit, complemented by a microcontroller PIC16C84. The unit is connected by an RS-232 interface to a PC with the main control software running under MS Windows. The new sample deposition device made the off-line combination SFC-MALDI simpler, faster, and more sensitive.     

Hollow-fiber flow field-flow fractionation for whole bacteria analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

This work proposes for the first time the use of hollow-fiber flow field-flow fractionation (HF FlFFF) for improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOFMS) of whole bacteria. HF FlFFF has proved to be able to prepurify or fractionate different species of whole bacteria. Sample preparation by HF FlFFF gives improved spectra quality because noncellular components possibly present in the sample can be separated from the cells. When a mixture of two bacteria (Bacillus subtilis and Escherichia coli) is fractionated through HF FlFFF, MALDI/TOFMS analysis of each separated bacterial species preserves the most characteristic ion signals of the species without the presence of characteristic signals of the other species. The main advantages of HF FlFFF for MALDI/TOFMS analysis of whole bacteria are miniaturization, simplicity, and low cost of the fractionator components. This low cost makes disposable usage of the fractionator possible, thus eliminating the risk of run-to-run contamination of spectra due to sample carryover. The low fractionator volume yields bacterial fractionation on the order of a few minutes, which is comparable to MALDI/TOFMS analysis time. The small fractionation volume makes sample dilution low enough so that additional sample concentration steps are not strictly required to preserve MALDI/TOFMS detection.     

Single cell matrix-assisted laser desorption/ionization mass spectrometry imaging

Application of mass spectrometry imaging (MS imaging) analysis to single cells was so far restricted either by spatial resolution in the case of matrix-assisted laser desorption/ionization (MALDI) or by mass resolution/mass range in the case of secondary ion mass spectrometry (SIMS). In this study we demonstrate for the first time the combination of high spatial resolution (7 μm pixel), high mass accuracy (<3 ppm rms), and high mass resolution (R = 100?000 at m/z = 200) in the same MS imaging measurement of single cells. HeLa cells were grown directly on indium tin oxide (ITO) coated glass slides. A dedicated sample preparation protocol was developed including fixation with glutaraldehyde and matrix coating with a pneumatic spraying device. Mass spectrometry imaging measurements with 7 μm pixel size were performed with a high resolution atmospheric-pressure matrix-assisted laser desorption/ionization (AP-MALDI) imaging source attached to an Exactive Orbitrap mass spectrometer. Selected ion images were generated with a bin width of Δm/z = ±0.005. Selected ion images and optical fluorescence images of HeLa cells showed excellent correlation. Examples demonstrate that a lower mass resolution and a lower spatial resolution would result in a significant loss of information. High mass accuracy measurements of better than 3 ppm (root-mean-square) under imaging conditions provide confident identification of imaged compounds. Numerous compounds including small metabolites such as adenine, guanine, and cholesterol as well as different lipid classes such as phosphatidylcholine, sphingomyelin, diglycerides, and triglycerides were detected and identified based on a mass spectrum acquired from an individual spot of 7 μm in diameter. These measurements provide molecularly specific images of larger metabolites (phospholipids) in native single cells. The developed method can be used for a wide range of detailed investigations of metabolic changes in single cells.     

Molecular profiling of native and matrix-coated tissue slices from rat brain by infrared and ultraviolet laser desorption/ionization orthogonal time-of-flight mass spectrometry

Phospho- and glycolipids contained in the plasma membrane of neuronal tissue were profiled by direct infrared laser desorption/ionization orthogonal time-of-flight mass spectrometry (IR-LDI-o-TOF-MS), performed on cryosected native slices generated from rat brain. About 100 different detected lipid species are putatively assigned based on their molecular weight. Spraying of potassium acetate onto the slices was found to facilitate data interpretation in positive ion mode by reducing residual sodium adduct ion intensities. Coating the slices with matrix and using an ultraviolet laser for UV-MALDI-o-TOF-MS extends the analysis to peptides and small proteins but induces analyte diffusion. Peptides and partially cleaved proteins derived from proteolytic digests were recorded after incubation of native sections with trypsin and subsequent coating of the slices with MALDI matrix.     

Coupling thin-layer chromatography with vibrational cooling matrix-assisted laser desorption/ionization Fourier transform mass spectrometry for the analysis of ganglioside mixtures

Thin-layer chromatography (TLC), which is widely used for separation of glycolipids, oligosaccharides, lipids, and compounds of environmental and pharmaceutical interest, can be readily coupled to matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometers, but this arrangement usually compromises mass spectral resolution due to the irregularity of the TLC surface. However, TLC can be coupled to an external ion source MALDI-Fourier transform (FT) MS instrument without compromising mass accuracy and resolution of the spectra. Furthermore, when the FTMS has a vibrationally cooled MALDI ion source, fragile glycolipids can be desorbed from TLC plates without fragmentation, even to the point that desorption of intact molecules from "hot"matrixes such as alpha-cyano-4-hydroxycinnamic acid is possible. In this work, whole brain gangliosides are separated using TLC; the TLC plates are attached directly to the MALDI target, where the gangliosides are desorbed, ionized, and detected in the FTMS with >70 000 resolving power.     

Detection and quantification of neurotensin in human brain tissue by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A method was developed for mass spectrometric detection of neurotensin (NT)-like immunoreactivity and quantification of NT in human brain tissue. The method is based on immunoprecipitation followed by analysis using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The identity of the major component of the immunoprecipitates as neurotensin was confirmed by fragment ion analysis on an electrospray ionization quadrupole time-of-flight instrument. MALDI-TOF-MS quantification of NT was achieved using stable-isotope-labeled NT as the internal standard, yielding an error of less than 5%. The method allowed detection of low-femtomole amounts of NT, staring from low-milligram amounts of lyophilized brain tissue. In addition to NT, several other peptides were detected in the purified samples, most of which, according to their molecular masses, corresponded to fragments of NT. The method is demonstrated with quantification of NT from human hypothalamus tissue, and a comparison is made with results obtained from competitive radioimmunoassay.