Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.     

AZ-1518 Photoresist analysis with synchrotron radiation using high-resolution time-of-flight mass spectrometry

With the aim of identifying molecular modifications among photoresists unexposed and previously exposed to the ultraviolet light the photon stimulated ion desorption (PSID) technique was employed in the study of the AZ-1518 photoresist. Data acquisition was performed at the Brazilian Synchrotron Light Source (LNLS), during a single-bunch operation mode of the storage ring and using high-resolution time-of-flight mass spectrometry (TOF-MS) for ion analysis. PSID mass spectra on both photoresists (unexposed and exposed) were obtained following the S K-shell photoexcitation and desorption ion yield curves have been determined for the main fragments as a function of the photon energy. The AZ-1518 photoresists presented different PSID spectra, showing characteristic fragments. Most of the analyzed ions showed larger relative yields for the exposed photoresist. Fragments related to the photochemical decomposition of the photoresist could be clearly identified. These results showed that the PSID technique is adequate to investigate structural changes in molecular level in unexposed and exposed photoresists.     

A high-resolution accurate mass approach to identification of graveoline metabolites using ultra-high-performance liquid chromatography combined with a photo diode array detector and quadrupole/time-of-flight tandem mass spectrometry

Graveoline is a biologically active ingredient extracted from Ruta graveolens. Current work aimed at investigating in vitro metabolism of graveoline using rat or human liver microsomes and hepatocytes. Graveoline (20 μM) was incubated with nicotinamide adenine dinucleotide phosphate–supplemented rat and human liver microsomes as well as hepatocytes. LC coupled to a photo diode array detector and quadrupole/time-of-flight tandem mass spectrometry was used to detect and identify the metabolites. The structures of the metabolites were identified by accurate mass, elemental composition, and indicative fragment ions. A total of 12 metabolites, comprising 6 phase I and 6 phase II metabolites, were obtained. The metabolic pathways included demethylenation, demethylation, hydroxylation, glucuronidation, and glutathion conjugation. The metabolite (M10) produced by opening the ring of the methylenedioxyphenyl moiety was detected as the most abundant in both liver microsomes and hepatocytes, mainly catalyzed by CYP1A2, 2C8, 2C9, 2C19, 2D6, 3A4, and 3A5. This study provides valuable information on the in vitro metabolism of graveoline, which is indispensable for further development and safety evaluation of this compound.     

A rapid simple approach to screening pharmaceutical products using ultra-performance LC coupled to time-of-flight mass spectrometry and pattern recognition

The comparison of batches of pharmaceutical product or raw active pharmaceutical ingredients (API) for product release can be time consuming and tedious process. It often requires long analysis times and potentially several liquid chromatography-tandem mass spectrometry (LC-MS-MS) analytical runs to determine the identity of the impurities and their relationship to the active pharmaceutical ingredient. The combination of a high resolution (sub 2 microm porous particle) LC coupled to exact mass MS, principal components analysis (PCA) allowed for the rapid classification of batches of Simvastatin tablets according to their impurity profile. Evaluating the ultra-performance LC-MS exact mass data with PCA allowed for the impurities of Simvastatin to be easily detected and identified. This approach to impurity batch analysis should be applicable to many other forms of batch analysis, fermentation broths, food production, and API manufacturing.     

Accelerated throughput metabolic route screening in early drug discovery using high-resolution liquid chromatography/quadrupole time-of-flight mass spectrometry and automated data analysis

The resource investment required to characterise the metabolic fate of a compound is relatively large, meaning that within a drug discovery environment relatively few compounds are characterised in depth. Rate-limiting steps include the setting up of a complex array of mass spectrometry experiments and the subsequent analysis of the large data sets produced. We describe here a strategy for the evaluation of metabolic routes using full-scan high-resolution liquid chromatography/quadrupole time-of-flight mass spectrometry (LC/QToFMS) with automated data analysis using Metabolynx, a commercially available software package. Data from several structurally diverse compounds taken from the literature illustrate that, with careful setting of key parameters, this approach is able to indicate the presence of a wide range of metabolites with only a limited requirement for manual intervention.     

A novel approach to identify plant parasitic nematodes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Plant parasitic nematodes are difficult to identify because different species are morphologically similar, and this makes their control more difficult. The aim of this work was to develop a rapid, simple method to identify plant parasitic nematodes, based on analysis of protein profiles of nematodes generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Two methods have been used: grinding and direct analysis of intact nematodes. Both methods were standardised using the nematode Anguina tritici (wheat seed-gall nematode) as a model. Development of the approach involved optimisation of experimental parameters to generate reproducible diagnostic protein profiles for plant parasitic nematodes. With alpha-cyano-4-hydroxycinnamic acid (CHCA) as the matrix, the most effective solvent extraction was with 90% acetone. With sinapinic acid (SA) as matrix, 90% ethanol was most effective. When intact nematodes were analysed directly by mixing with the matrix solution, 40 min extraction with CHCA matrix solution generated the best protein profiles. The standardised methods were applied to analyse the seed-gall nematodes A. tritici and A. funesta and to the root-knot nematode, Meloidogyne javanica, which infects many horticultural crops. Typical protein profiles and diagnostic peaks were identified for these nematode species and for mixtures of Anguina species. The results provide 'proof-of-concept' that these nematode species can be identified by protein profiling using MALDI-TOFMS. This new approach could be extended to identify other plant and non-plant parasitic nematodes.     

Multi-detection of corticosteroids in sports doping and veterinary control using high-resolution liquid chromatography/time-of-flight mass spectrometry

A liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS) method was developed using the latest high-resolution LC column technology, the ultra performance liquid chromatography (UPLC), and electrospray ionization (ESI) in the positive ion mode. Gradient UPLC separation conditions were optimized for a group of 22 analytes comprising 17 glucocorticosteroids, specific designer steroids such as tetrahydrogestrinone (THG) and specific beta2-agonists such as formoterol. The UPLC/TOFMS separation obtained required 5.5 min only for all the substances tested. Even the critical pair of dexamethasone and betamethasone isomers was almost completely resolved. Thanks to the over 10,000 full-width at half maximum (FWHM) mass resolution and high mass accuracy features of TOFMS 50 mDa window accurate mass chromatograms could be reconstructed for the individual analytes. Sensitive screening in human and calf urine samples fortified at the glucocorticosteroids minimum required performance limit (MRPL) of 30 microg L(-1) (human urine, sports doping) and 2 microg L(-1) (calf urine, veterinary control) could be obtained. The potential of UPLC/TOFMS for confirmatory analysis was shown by determining the accurate mass of all compounds and fragment ions upon in-source collision-induced dissociation (CID) at different energies. The exact mass measurement errors for all glucocorticosteroids were found to be within 6 ppm. Considering veterinary control, limits of detection (LOD) and limits of quantification (LOQ) were determined for most of the analytes in calf urine and found to range from 0.1 to 3.3 and from 0.4 to 4.4 microg L(-1), respectively. The method can be easily extended with other banned substances of interest, as demonstrated by the addition of 21 beta2-agonists to the original analyte mixture in urine, without causing any interferences.     

Multi-residue screening of veterinary drugs in egg,fish and meat using high-resolution liquid chromatography accurate mass time-of-flight mass spectrometry

The last 2 years multi-compound methods are gaining ground as screening methods. In this study a high-resolution liquid chromatography combined with time-of-flight mass spectrometry (HRLC–ToF-MS) is tested for the screening of about 100 veterinary drugs in three matrices, meat, fish and egg. While the results are satisfactory for 70–90% of the veterinary drugs, a more efficient sample preparation or extract purification is required for quantitative analysis of all analytes in more difficult matrices like egg. The average mass measurement error of the ToF-MS for the veterinary drugs spiked at concentrations ranging from 4 to 400 μg/kg, is 3.0 ppm (median 2.5 ppm) with little difference between the three matrices, but slightly decreases with increasing concentration. The SigmaFit value, a new feature for isotope pattern matching, also decreases with increasing concentration and, in addition, shows an increase with increasing matrix complexity. While the average SigmaFit value is 0.04, the median is 0.01 indicating some high individual deviations. As with the mass measurement error, the highest deviations are found in those regions of the chromatogram where most compounds elute from the column, be it analytes or matrix compounds. The median repeatability of the method ranges from 8% to 15%, decreasing with increasing concentration, while the median reproducibility ranges from 15% to 20% with little difference between matrices and concentrations. The median accuracy is in between 70% and 100% with a few compounds showing higher values due to matrix interference. The squared regression coefficient is >0.99 for 92% of the compounds showing a good overall linearity for most compounds. The detection capability, CCβ, is within 2 times the associated validation level for >90% of the compounds studied. By changing a few conditions in the analyses protocol and analysing a number of blank samples, it was determined that the method is robust as well as specific. Finally, an alternative validation strategy is proposed and tested for screening methods. While the results calculated for repeatability, within-lab reproducibility and CCβ show a good comparison for the matrices meat and fish, and a reasonable comparison for the matrix egg, only 27 analyses are required to obtain these results versus 63 analysis in the traditional, 2002/657/EC, approach. This alternative is suggested as a cost-effective validation procedure for screening methods.     

Top-down approach of completely sequencing a 4.9 kDa recombinant peptide using quadrupole time-of-flight mass spectrometry

A recombinant peptide (near the C-terminal region of head involution defective protein) of 4.9 kDa has been completely sequenced and characterized using medium-resolution mass spectrometry (QTOF). The observed difference in the experimental mass and the theoretical mass is due to beta-mercaptoethanol adduct formation on the cysteine residue. The fragmentation pattern is correlated with the primary structure of the protein. Top-down sequencing of the peptide was extended to small proteins like barstar of mass 10.3 kDa.     

Isotope pattern evaluation for the reduction of elemental compositions assigned to high-resolution mass spectral data from electrospray ionization fourier transform ion cyclotron resonance mass spectrometry

The number of possible chemical formulae assigned to an accurate determined mass was significantly reduced by comparing spectral and theoretical isotope patterns based on mass measurement obtained with an ultrahigh-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometer (ESI-FTICR-MS) at high field intensity (7 T). Reduction is performed by rating congruency between experimental and theoretical pattern intensity and mass, and filtering out compositions with insufficient user-definable results. The methods used for isotope pattern simulation, peak searching, and comparison will be briefly described and evaluated on molecule ion signals of 25 compounds (300-1000 Da) applying a mass accuracy of +/-5 ppm, a set of eight elements with constant constraints (C0-200H0-1000N0-15O0-15S0-2Cl0-2Br0-2Ru0-1), natural isotope abundances and experimental resolution (full width at half maximum).     

Parallel high-throughput accurate mass measurement using a nine-channel multiplexed electrospray liquid chromatography ultraviolet time-of-flight mass spectrometry system

A nine-channel multiplexed electrospray (MUX) liquid chromatography ultraviolet time-of-flight mass spectrometry (LC/UV/TOFMS) system has been used to simultaneously measure accurate masses of eluting components from eight parallel gradient LC columns. Accuracies better than 5 and 10 ppm were achieved for 50 and 80% of samples, respectively, from a single batch analysis of ten plates (960 samples) of a Fmoc-Asp(OtBu)-OH and reserpine mixture. Combinatorial library compounds were analyzed using this parallel high-throughput system in both positive and negative modes to rigorously verify expected products and identify side products. A mass accuracy of 10 ppm root mean square (RMS) is routinely obtained for combinatorial library samples from this high-throughput accurate mass LC/MS system followed by automated data processing. This mass accuracy is critical in revealing combinatorial synthesis problems that would be missed by unit mass measurement.     

A new pyrolysis—mass spectrometry approach to organic marine chemistry using chemical ionization

A new approach is being developed to obtain a great deal of information about the organic chemicals in the marine environment as rapidly as possible. The sample, after drying, is pyrolyzed at four different temperatures and the resulting pyrolyzates are swept into a mass spectrometer operating under chemical ionization conditions to obtain maximum sensitivity while at the same time maintaining to a large extent the integrity of the molecular structure of the pyrolyzates. This results in at least four different pyrogram peaks each composed of at least 100 different ion species. A sample size of only 200 μl is required and the analysis is completed in less than 10 min.Minimal sample manipulation decreases drastically the chance for contamination. Resulting data are computer processed. Possible uses for this approach are water mass differentiation, water mass tracing, determination of covariation between organics and a process of interest, and monitoring the interaction of organics with a process of interest. The chief advantage of this approach is that our interpretation of the role that organics play in the marine environment will be less limited by the availability of sample, personnel, and time. The chief limitation is our inadequate understanding of pyrolysis mechanisms and how pyrolyzates behave under chemical ionization-mass spectrometric conditions. This should rapidly improve with more research.The approach was tested successfully by looking at the similarities and differences between two coastal bodies of water, one more influenced by terrestrial run-off than the other.     

Global and selective detection of organohalogens in environmental samples by comprehensive two-dimensional gas chromatography-tandem mass spectrometry and high-resolution time-of-flight mass spectrometry

We successfully detected halogenated compounds from several kinds of environmental samples by using a comprehensive two-dimensional gas chromatograph coupled with a tandem mass spectrometer (GC×GC-MS/MS). For the global detection of organohalogens, fly ash sample extracts were directly measured without any cleanup process. The global and selective detection of halogenated compounds was achieved by neutral loss scans of chlorine, bromine and/or fluorine using an MS/MS. It was also possible to search for and identify compounds using two-dimensional mass chromatograms and mass profiles obtained from measurements of the same sample with a GC×GC-high resolution time-of-flight mass spectrometer (HRTofMS) under the same conditions as those used for the GC×GC-MS/MS. In this study, novel software tools were also developed to help find target (halogenated) compounds in the data provided by a GC×GC-HRTofMS. As a result, many dioxin and polychlorinated biphenyl congeners and many other halogenated compounds were found in fly ash extract and sediment samples. By extracting the desired information, which concerned organohalogens in this study, from huge quantities of data with the GC×GC-HRTofMS, we reveal the possibility of realizing the total global detection of compounds with one GC measurement of a sample without any pre-treatment.     

Aerosol time-of-flight mass spectrometry data analysis: a benchmark of clustering algorithms

Airborne particulate matter is an important component of atmospheric pollution, affecting human health, climate, and visibility. Modern instruments allow single particles to be analyzed one-by-one in real time, and offer the promise of determining the sources of individual particles based on their mass spectral signatures. The large number of particles to be apportioned makes clustering a necessary step. The goal of this study is to compare using mass spectral data the accuracy and speed of several clustering algorithms: ART-2a, several variants of hierarchical clustering, and K-means. Repeated simulations with various algorithms and different levels of data preprocessing suggest that hierarchical clustering methods using derivatives of Ward's algorithm discriminate sources with fewer errors than ART-2a, which itself discriminates much better than point-wise hierarchical clustering methods. In most cases, K-means algorithms do almost as well as the best hierarchical clustering. These efficient algorithms (clustering derived from Ward's algorithm, ART-2a and K-means) are most accurate when the relative peak areas have been pre-scaled by taking the square root. Analysis times vary within a factor of 30, and when accuracy above 95% is required, run times scale up as the square of the number of particles. Algorithms derived from Ward's remain the most accurate under a wide range of conditions and conversely, for an equal accuracy, can deliver a shorter list of clusters, allowing faster and maybe on-the-fly classification.     

Determination of osteocalcin in meat and bone meal of bovine and porcine origin using matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and high-resolution hybrid mass spectrometry

A method has been developed for determining the origin of meat and bone meal (MBM) by detecting species-specific osteocalcin (OC) using matrix-assisted laser desorption ionization/time-of-flight (MALDI/TOF) and high-resolution hybrid mass spectrometry (HR-Q/TOF MS). The analysis is based on the detection of typical species-specific OC and its tryptic peptide fragments which differ in mass due to differences in the amino-acid sequences between species. After dissolving the MBM samples in EDTA buffer, purification after ultrafiltration was performed using two methods: solid-phase extraction using Zip-Tip C(18) or size exclusion coupled with reverse-phase chromatography. Fractions containing partially purified intact OC were analyzed using LC-Q/TOF and MALDI/TOF mass spectrometry. Species-specific OC was detected at the typical protonated and doubly protonated molecular ions. Furthermore, typical porcine- and bovine-derived tryptic fragments from MBM were detected after enzymatic digestion. In order to determine the underlying amino-acid sequences and to confirm the assignment to OC-derived peptides, MS/MS analysis was carried out. In conclusion, we were able to detect OC in bovine and porcine MBM with high sensitivity and the MS-based method described here by which total OC mass and marker peptides of digested OC are recorded can be used as an alternative approach to detect genus-specific differences in MBM and can be applied as a confirmatory method to mainly immunological osteocalcin screening methods.     

Continuum background reduction in orthogonal-acceleration time-of-flight mass spectrometry with continuous ion sources

The continuum ion background in an inductively coupled plasma time-of-flight mass spectrometer (TOFMS) has been reduced by 2 orders of magnitude by using energy discrimination (ED). A potential barrier placed in front of the ion detector effectively discriminates between higher-energy signal ions and the lower-energy background ions. The signal-to-noise ratio was increased tenfold and detection limits of 0.4–4.2 ppt were achieved for 11 elements ranging from Li to U. The resolving power was observed to degrade from 1520 to 1230 with the addition of the potential barrier. The residual background count rate was found to be limited by neutrals formed after exiting the ion reflectron via charge exchange with the background gas. This ED method can be employed to effectively reduce the continuum ion background in any TOFMS that uses orthogonal acceleration with a continuous ion source.     

Non-target screening of organic contaminants in marine salts by gas chromatography coupled to high-resolution time-of-flight mass spectrometry

Gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF MS) has been applied to characterize the organic pollution pattern of marine salt samples collected in saltworks from the Spanish Mediterranean coast. After dissolving the samples in water, a solid-phase extraction was applied reaching with a 250-preconcentration factor. The screening methodology allowed the detection of sample components without any kind of pre-selection of target pollutants. The identity of components detected was established by accurate mass measurements and comparison of experimental full-acquisition spectra with theoretical MS libraries. Several organic pollutants were identified in the samples, like plasticizers - potentially toxic to humans - and fragrances -included within the group of pharmaceuticals and personal care products-, among others. Our results indicate that these contaminants can be found in the marine salt after the crystallization process. GC-TOF MS is a powerful technique for wide-scope screening of (semi)volatile, low-polar organic contaminants, able to investigate the presence of a large number of compounds. Searching of contaminants is not restricted to a target list of compounds. Therefore, unexpected contaminants can be discovered in an efficient way, with better sensitivity and selectivity than other conventional analytical techniques, and making use of the powerful qualitative information provided by full-spectrum acquisition at accurate mass.     

A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry

Glycans commonly exhibit variations in their branching structures and glycosidic bond linkages, in addition to their sequence variation. These glycan features are known to be highly correlated with their biological functions. It is relatively straightforward to deduce the composition and sequence of monosaccharides of a glycan from its tandem mass spectra. However, the characterization of the linkage types of each glycosidic bond is still analytically challenging. In this paper, we present a rank-based discriminative model to differentiate between two types of glycosidic linkages (namely, 1-4 and 1-6) based on the cross-ring fragmentation patterns of the corresponding glycans observed under high-energy collision-induced dissociation (CID). To train our models, we acquired tandem mass spectra for three groups of both native and permethylated linear oligoglucoses using a matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI/TOF/TOF) instrument. Based on a 5-fold cross-validation, the prediction accuracies of our model for native glycans are determined to be about 88.4% and 92.9% for 1-6 and 1-4 linkages, respectively. The accuracies determined for permethylated glycans are slightly lower, but comparable: 85.6% and 89.0% for 1-6 and 1-4 linkages, respectively. Our method is implemented as a web-hosted utility, thus making it readily accessible to the public which can be accessed through http://ggdb.informatics.indiana.edu:8080/glycanview.