High-accuracy molecular mass determination of proteins using matrix-assisted laser desorption mass spectrometry

A method for obtaining protein molecular masses with an accuracy of approximately +/- 0.01% by matrix-assisted laser desorption using an internal calibrant is described. The technique allows accurate mass determinations of protein sample sizes as small as 1 pmol. High concentrations of organic and inorganic contaminants (e.g. 1 M urea) do not strongly affect either the signal intensity or the mass assignment. The ability to assign an accurate molecular mass to a protein is contingent on the observation of clearly resolved protonated molecule ions in the mass spectrum.     

Targeted analyte detection by standard addition improves detection limits in matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) has proven an effective tool for fast and accurate determination of many molecules. However, the detector sensitivity and chemical noise compromise the detection of many invaluable low-abundance molecules from biological and clinical samples. To challenge this limitation, we developed a targeted analyte detection (TAD) technique. In TAD, the target analyte is selectively elevated by spiking a known amount of that analyte into the sample, thereby raising its concentration above the noise level, where we take advantage of the improved sensitivity to detect the presence of the endogenous analyte in the sample. We assessed TAD on three peptides in simple and complex background solutions with various exogenous analyte concentrations in two MALDI matrices. TAD successfully improved the limit of detection (LOD) of target analytes when the target peptides were added to the sample in a concentration close to optimum concentration. The optimum exogenous concentration was estimated through a quantitative method to be approximately equal to the original LOD for each target. Also, we showed that TAD could achieve LOD improvements on an average of 3-fold in a simple and 2-fold in a complex sample. TAD provides a straightforward assay to improve the LOD of generic target analytes without the need for costly hardware modifications.     

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.     

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.     

An algorithm for automated bacterial identification using matrix-assisted laser desorption/ionization mass spectrometry

An algorithm for bacterial identification using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is being developed. This mass spectral fingerprint comparison algorithm is fully automated and statistically based, providing objective analysis of samples to be identified. Based on extraction of reference fingerprint ions from test spectra, this approach should lend itself well to real-world applications where samples are likely to be impure. This algorithm is illustrated using a blind study. In the study, MALDI-MS fingerprints for Bacillus atrophaeus ATCC 49337, Bacillus cereus ATCC 14579T, Escherichia coli ATCC 33694, Pantoea agglomerans ATCC 33243, and Pseudomonas putida F1 are collected and form a reference library. The identification of test samples containing one or more reference bacteria, potentially mixed with one species not in the library (Shewanella alga BrY), is performed by comparison to the reference library with a calculated degree of association. Out of 60 samples, no false positives are present, and the correct identification rate is 75%. Missed identifications are largely due to a weak B. cereus signal in the bacterial mixtures. Potential modifications to the algorithm are presented and result in a higher than 90% correct identification rate for the blind study data, suggesting that this approach has the potential for reliable and accurate automated data analysis of MALDI-MS.     

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.     

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.     

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.     

Detection of oligosaccharides labeled with cyanine dyes using matrix-assisted laser desorption/ionization mass spectrometry

The sensitivity of oligosaccharides in mass spectrometry lags far behind that of peptides. This is a critical factor in realizing the high-throughput analysis of posttranslational modifications in proteomics. We here described that hydrazide derivatives of cyanine dyes (Cy3, Cy5) with a positive charge made excellent labeling reagents for the detection of oligosaccharides by matrix-assisted laser desorption/ionization mass spectrometry. Cy3-labeled standard N-glycan could be detected at 200 amol on the MALDI target plate in reflectron mode without any purification procedures after the labeling reaction, which may meet the level of sensitivity required in proteome research. Despite the general recognition that the production of signals of oligosaccharides under MALDI conditions would be highly dependent on the matrix, most of the known N-glycans from chicken ovalbumin could be detected upon Cye derivatization nearly independent of the kind of matrix tested (e.g., nor-harman, 2,5-dihydroxybenzoic acid and alpha-cyano-4-hydroxycinnamic acid) without spoiling the signal strength. Postsource decay afforded simple spectra mainly consisting of Y-type fragment ions, thus simplifying the sequence analysis. In-source decay afforded a similar fragmentation pattern only when acidic matrixes were used. In addition, this derivatization technique was successfully applied to the profiling of N-glycans of gel-separated glycoproteins.     

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.     

Atmospheric pressure matrix-assisted laser desorption/ionization in transmission geometry

In both atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI) and vacuum MALDI, the laser typically illuminates the analyte on the front side of an opaque surface (reflection geometry). Another configuration consisting of laser illumination through the sample backside (transmission geometry) has been used in conventional MALDI; however, its use and the number of reports in the literature are limited. The viability of transmission geometry with AP MALDI is demonstrated here. Such a geometry is simple to implement, eliminates the restriction for a metallic sample holder, and allows for the potential analysis of samples on their native transparent surfaces, e.g., cells or tissue sections on slides.     

Affinity capture and detection of immunoglobulin E in human serum using an aptamer-modified surface in matrix-assisted laser desorption/ionization mass spectrometry

Capture and detection of immunoglobulin E (IgE) in simple solution and in human serum using an aptamer-modified probe surface for affinity matrix-assisted laser desorption/ionization mass spectroscopy detection is reported. Detectable signals were obtained for 1 amol of IgE applied either in a single, 1microL application of 1 pM IgE or after 10 successive, 1-microL applications of 100 fM IgE. In both cases, the surface was rinsed after each application of IgE to remove sample concomitants including salts and free or nonspecifically associated proteins. Detection of native IgE, which is the least abundant of the serum immunoglobulins and occurs at subnanomolar levels, in human serum was demonstrated and interference from the high-abundance immunoglobulins and albumin was investigated. The aptamer-modified surface showed high selectivity toward immunoglobulins in serum, with no significant interference from serum albumin. Addition of IgE to the serum suppressed the signals from the other immunoglobulins, confirming the expected selectivity of the aptamer surface toward IgE. Dilution of the serum increased the selectivity toward IgE; the protein was detected without interference in a 10,000-fold dilution of the serum, which is consistent with detection of IgE at amol (pM) levels in standard solutions.     

Internal energy of ions generated by matrix-assisted laser desorption/ionization

To provide an objective measure of the correlation between the internal energy content of ions generated by matrix-assisted laser desorption/ionization (MALDI) and the matrix properties, a series of well-characterized benzyl-substituted benzylpyridinium salts were used as thermometer molecules (TMs). To determine the internal energy variations of analyte ions, the survival yields of TM molecular ions were measured in three different matrixes, alpha-cyano-4-hydroxycinnamic acid (CHCA), 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid, SA), and 2,5-dihydroxybenzoic acid (DHB). Statistical analysis of extensive survival yield data indicated that there were discernible differences among the studied matrixes. The experimental survival yields of the TM ions were used to calculate the unimolecular decomposition rate coefficient. Corresponding theoretical reaction rate coefficients were calculated based on the Rice-Ramsperger-Kassel-Marcus (RRKM) theory for different internal energies of the TMs. The internal energies of the ions were obtained by projecting the experimental rate coefficient values onto the theoretical curves obtained by the RRKM calculations. Molecular ions of the analytes showed decreasing survival yields and consequently increasing internal energies in the three matrixes in the following order: CHCA, SA, and DHB with "cold", "intermediate", and "hot" characteristics, respectively. Qualitatively, this could be interpreted as a significant departure from earlier observations suggesting an opposite trend. The classification as hot and cold matrixes should be further qualified by accounting for the influence of laser pulse energy and the nature of the analyte. Higher laser pulse energy led to an elevated level of energy transferred to the analyte, which in turn resulted in a diminished survival yield of the analyte molecular ion. It is quite possible that the assignment of hot and cold reverses as the analyte or the laser energy changes. These findings can help predict the outcome of postsource decay experiments and clarify the concept of hot and cold matrixes in MALDI mass spectrometry.     

Differentiation of Aeromonas isolated from drinking water distribution systems using matrix-assisted laser desorption/ionization-mass spectrometry

The genus Aeromonas is one of several medically significant genera that have gained prominence due to their evolving taxonomy and controversial role in human diseases. In this study, matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was used to analyze the whole cells of both reference strains and unknown Aeromonas isolates obtained from water distribution systems. A library of over 45 unique m/z signatures was created from 40 strains that are representative of the 17 recognized species of Aeromonas, as well as 3 reference strains from genus Vibrio and 2 reference strains from Plesiomonas shigelloides. The library was used to help speciate 52 isolates of Aeromonas. The environmental isolates were broken up into 2 blind studies. Group 1 contained isolates that had a recognizable phenotypic profile and group 2 contained isolates that had an atypical phenotypic profile. MALDI-MS analysis of the water isolates in group 1 matched the phenotypic identification in all cases. In group 2, the MALDI-MS-based determination confirmed the identity of 18 of the 27 isolates. These results demonstrate that MALDI-MS analysis can rapidly and accurately classify species of the genus Aeromonas, making it a powerful tool especially suited for environmental monitoring and detection of microbial hazards in drinking water.     

Automation of data collection for matrix-assisted laser desorption/ionization mass spectrometry using a correlative analysis algorithm

Automation of data collection in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry using a correlative analysis algorithm is demonstrated. This algorithm was employed to compensate for mass spectral jittering in MALDI data collection (e.g., peak shifts along the m/z axis, signal intensity deviations, etc.). Several important parameters for performing correlative analysis, such as the minimum correlation coefficient to be used and number of mass spectra to acquire prior to correlation, have been investigated and optimized. In addition, the correlation algorithm improved mass resolution of low- and high-molecular-weight compounds by as much as a factor of 4. Signal reproducibility in MALDI quantitative analysis also is improved when correlation is employed for data collection. This data collection algorithm can be used in conjunction with other instrumental optimization programs to allow for fully automated MALDI analysis, which is required for the routine applications carried out in many analytical laboratories.     

Improving spot homogeneity by using polymer substrates in matrix-assisted laser desorption/ionization mass spectrometry of oligonucleotides

We describe a method for improving the homogeneity of MALDI samples prepared for analysis of small, single-stranded oligonucleotides using the widely used DNA matrix system, 3-hydroxypicolinic acid/picolinic acid/ ammonium citrate. This matrix system typically produces large crystals around the rim of the dried sample and requires tedious searching of this rim with the laser. However, when a substrate is prepared using both Nafion and a hydrophilic, high-molecular-weight polymer, such as linear polyacrylamide, linear poly(ethylene oxide), or methyl cellulose, oligonucleotide-doped matrix crystals tend to be smaller and more uniformly distributed across the entire spot, thus decreasing the time that is required for locating a usable signal. In addition to MALDI characterization of the spatial distribution of "sweet spots," fluorescence microscopy allows for imaging dye-labeled DNA in dried MALDI spots. The mechanism of enhanced uniformity may involve increased viscosity in the MALDI sample droplet due to partial solubilization of the substrate by the MALDI sample solvent as well as partitioning of the matrix or DNA between the solvent and the undissolved portion of the polymer substrate.     

Reproducibility of temperature-selected mass spectra in matrix-assisted laser desorption ionization of peptides

Matrix-assisted laser desorption ionization of peptides was investigated using α-cyano-4-hydroxycinnamic acid as the matrix. In each experiment, a set of mass spectra was collected by repetitive irradiation of a spot on a sample. Even though shot-to-shot variation in spectral pattern was significant, it was reproducible for different spots and samples. Each spectrum was tagged with the temperature in the early plume (T(early)) estimated through kinetic analysis of the peptide ion survival probability. T(early) decreased as the shot continued because the thermal conduction got more efficient as the sample got thinner. From each spectral set collected under various experimental conditions, a spectrum tagged with a particular T(early) was selected. Then, patterns of the spectra thus selected were the same. The reaction quotient for the matrix-to-peptide proton transfer determined at a specified T(early) was independent of the sample composition, indicating quasi-thermal equilibrium for this reaction. Furthermore, the van't Hoff plots were linear, also indicating quasi-thermal equilibrium. This, together with the thermal kinetics for the fragmentation of peptide and matrix ions, is responsible for the reproducibility of the mass spectral pattern at a specified T(early).     

Quantitative analysis of cyanobacterial toxins by matrix-assisted laser desorption ionization mass spectrometry

Microcystins (MCs) are a growing problem in drinking water supplies worldwide. Common analytical techniques used to determine MC concentrations have several shortcomings, including extensive sample handling and lengthy analysis times. A simple, rapid method for quantitation of MCs by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is presented. Four potential internal standards were tested, including an 15N-labeled MC. For MC-LR in mixed standard solutions, a linear range of 0.11-5.0 microM (R2 = 0.98) was achieved, with a method detection limit (MDL) of 0.015 microM. Matrix effects due to extracted cell components decreased the MC-LR linear range slightly to 0.19-5.0 microM (R2 = 0.99), with MDL = 0.058 microM. Extensive analysis of possible internal standards indicates that nodularin was preferred over [15N]10-microcystin-YR or angiotensin I. The ionization efficiency and analyte-analyte suppression for four MCs of varying polarity are presented; the three polar congeners exhibited good ionization efficiency and acceptable levels of analyte-analyte suppression. These results indicate that MALDI-TOF MS represents a viable alternative for the quantitative measurement of MCs in field samples.     

Detection of Staphylococcus aureus using 15N-labeled bacteriophage amplification coupled with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry

A novel approach to rapid bacterial detection using an isotopically labeled (15)N bacteriophage and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is introduced. Current phage amplification detection (PAD) via mass spectrometric analysis is limited because host bacteria must be inoculated with low phage titers in such a way that initial infecting phage concentrations must be below the detection limit of the instrument, thus lengthening incubation times. Additionally, PAD techniques cannot distinguish inoculate input phage from output phage which can increase the possibility of false positive results. Here, we report a rapid and accurate PAD approach for identification of Staphylococcus aureus via detection of bacteriophage capsid proteins. This approach uses both a wild-type (14)N and a (15)N-isotopically labeled S. aureus-specific bacteriophage. High (15)N phage titers, above our instrument's detection limits, were used to inoculate S. aureus. MALDI-TOF MS detection of the (14)N progeny capsid proteins in the phage-amplified culture indicated the presence of the host bacteria. Successful phage amplification was observed after 90 min of incubation. The amplification was observed by both MALDI-TOF MS analysis and by standard plaque assay measurements. This method overcomes current limitations by improving analysis times while increasing selectivity when compared to previously reported PAD methodologies.     

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.