Tandem mass spectrometry identification and LC-MS quantification of intact cytokinin nucleotides in K-562 human leukemia cells

We describe here a new reversed-phase high-performance liquid chromatography with mass spectrometry detection method for quantifying intact cytokinin nucleotides in human K-562 leukemia cells. Tandem mass spectrometry was used to identify the intracellular metabolites (cytokinin monophosphorylated, diphosphorylated, and triphosphorylated nucleotides) in riboside-treated cells. For the protein precipitation and sample preparation, a trichloroacetic acid extraction method is used. Samples are then back-extracted with diethyl ether, lyophilized, reconstituted, and injected into the LC system. Analytes were quantified in negative selected ion monitoring mode using a single quadrupole mass spectrometer. The method was validated in terms of retention time stabilities, limits of detection, linearity, recovery, and analytical accuracy. The developed method was linear in the range of 1-1,000 pmol for all studied compounds. The limits of detection for the analytes vary from 0.2 to 0.6 pmol.

Doubly charged ion mass spectra of alkyl-substituted furans and pyrroles

Doubly charged ion mass spectra of alkyl-substituted furans and pyrroles were obtained using a double-focusing magnetic mass spectrometer operated at 3.2 kV accelerating voltage. Molecular ions were the dominant species found in doubly charged spectra of lower molecular weight heterocydic compounds, whereas the spectra of the higher weight homologues were typified by abundant fragment ions from extensive decomposition. Measured doubly charged ionization and appearance energies ranged from 22.8 to 47.9 eV. Ionization energies were correlated with values calculated using self-consistent field–molecular orbital techniques. A multichannel diabatic curve-crossing model was developed to investigate the fundamental organic ion reactions responsible for development of doubly charged ion mass spectra. Probabilities for Landau–Zener type transitions between reactant and product curves were determined and used in the collision model to predict charge-transfer cross-sections, which compared favorably with experimental cross-sections obtained using time-of-flight techniques.

On-line SPE LC-MS/MS for the quantification of Δ9-tetrahydrocannabinol (THC) and its two major metabolites in human peripheral blood by liquid chromatography tandem mass spectrometry

A universal and robust analytical method for the determination of Δ9-tetrahydrocannabinol (THC) and two of its metabolites Δ9-(11-OH)-tetrahydrocannabinol (11-OH-THC) and 11-nor-Δ9-carboxy-tetrahydrocannabinol (THC-COOH) in human whole blood was developed and validated for use in forensic toxicology. Protein precipitation, integrated solid phase extraction and on-line enrichment followed by high-performance liquid chromatography separation and detection with a triple quadrupole mass spectrometer were combined. The linear ranges used for the three cannabinoids were from 0.5 to 20 ng/mL for THC and 11-OH-THC and from 2.5 to 100 ng/mL for THC-COOH, therefore covering the requirements for forensic use. Correlation coefficients of 0.9980 or better were achieved for all three analytes. No relevant hydrolysis was observed for THC-COOH glucuronide with this procedure--in contrast to our previous GC-MS procedure, which obviously lead to an artificial increase of the THC-COOH concentration due to the hydrolysis of the glucuronide-conjugate occurring at high pH during the phase-transfer catalyzed methylation step.

Collision-Induced Dissociation Of Dipeptides In Negative Ion Electrospray Ionization Tandem Mass Spectrometry

This purpose of this project was to investigate the collision-induced dissociation of dipeptides in negative ion electrospray ionization tandem mass spectrometry, with a focus on the mechanism of the production of imidazole-type fragments not previously reported from the fragmentation of the dipeptides being studied. The majority of the dipeptides studied were alanine N-terminal or serine C-terminal dipeptides. All dipeptides were dissolved in 50:50 methanol:water, 3 mM ammonium formate. Collision-induced dissociation in the collision cell of a triple quadrupole mass spectrometer was used to fragment [M-H]- precursor ions. Accurate mass measurements confirmed the molecular formula of the imidazole-type fragments. Further MS/MS studies were performed to provide information about the fragmentation mechanism for the formation of the imidazole-type fragments. The m/z values of intermediate ions in the formation of the imidazole-type fragments were confirmed through second-generation product ion scans and precursor ion scans. More sophisticated instrumentation will be required to further probe the structure of the intermediate ions.

A Computational Analysis of the Collision-Induced Dissociation Mechanisms of the Dipeptide Glycine-Serine Under Mass Spectrometry

Collision-induced dissociation (CID) of peptides using tandem mass spectrometry (MS) has been used to determine the identity of peptides and other large biological molecules. Mass spectrometry (MS) is a useful tool for determining the identity of molecules based on their interaction with electromagnetic fields. If coupled with another method like infrared (IR) vibrational spectroscopy, MS can provide structural information, but in its own right, MS can only provide the mass-to-charge (m/z) ratio of the fragments produced, which may not be enough information to determine the mechanism of the collision-induced dissociation (CID) of the molecule. In this case, theoretical calculations provide a useful companion for MS data and yield clues about the energetics of the dissociation. In this study, negative ion electrospray tandem MS was used to study the CID of the deprotonated dipeptide glycine-serine (Gly-Ser). Though negative ion MS is not as popular a choice as positive ion MS, studies by Bowie et al. show that it yields unique clues about molecular structure which complement positive ion spectroscopy, such as characteristic fragmentations like the loss of formaldehyde from the serine residue.2 The increase in the collision energy in the mass spectrometer alters the flexibility of the dipeptide backbone, enabling isomerizations (reactions not resulting in a fragment loss) and dissociations to take place. The mechanism of the CID of Gly-Ser was studied using two computational methods, B3LYP/6-311+G* and M06-2X/6-311++G**. The main pathway for molecular dissociation was analyzed in 5 conformers in an attempt to verify the initial mechanism proposed by Dr. James Swan after examination of the MS data. The results suggest that the loss of formaldehyde from serine, which Bowie et al. indicates is a characteristic of the presence of serine in a protein residue, is an endothermic reaction that is made possible by the conversion of the translational energy of the ion into internal energy as the ion collides with the inert collision gas. It has also been determined that the M06-2X functional¿s improved description of medium and long-range correlation makes it more effective than the B3LYP functional at finding elusive transition states. M06-2X also more accurately predicts the energy of those transition states than does B3LYP. A second CID mechanism, which passes through intermediates with the same m/z ratio as the main pathway for molecular dissociation, but different structures, including a diketopiperazine intermediate, was also studied. This pathway for molecular dissociation was analyzed with 3 conformers and the M06-2X functional, due to its previously determined effectiveness. The results suggest that the latter pathway, which meets the same intermediate masses as the first mechanism, is lower in overall energy and therefore a more likely pathway of dissociation than the first mechanism.

Probing the Allende meteorite with a miniature laser-ablation mass analyser for space application

We measured the elemental composition on a sample of Allende meteorite with a miniature laser ablation mass spectrometer. This Laser Mass Spectrometer (LMS) has been designed and built at the University of Bern in the Department of Space Research and Planetary Sciences with the objective of using such an instrument on a space mission. Utilising the meteorite Allende as the test sample in this study, it is demonstrated that the instrument allows the in situ determination of the elemental composition and thus mineralogy and petrology of untreated rocky samples, particularly on planetary surfaces. In total, 138 measurements of elemental compositions have been carried out on an Allende sample. The mass spectrometric data are evaluated and correlated with an optical image. It is demonstrated that by illustrating the measured elements in the form of mineralogical maps, LMS can serve as an element imaging instrument with a very high spatial resolution of µm scale. The detailed analysis also includes a mineralogical evaluation and an investigation of the volatile element content of Allende. All findings are in good agreement with published data and underline the high sensitivity, accuracy and capability of LMS as a mass analyser for space exploration.

On the interference of Kr during carbon isotope analysis of methane using continuous-flow combustion–isotope ratio mass spectrometry

Stable carbon isotope analysis of methane (delta C-13 of CH4) on atmospheric samples is one key method to constrain the current and past atmospheric CH4 budget. A frequently applied measurement technique is gas chromatography (GC) isotope ratio mass spectrometry (IRMS) coupled to a combustion-preconcentration unit. This report shows that the atmospheric trace gas krypton (Kr) can severely interfere during the mass spectrometric measurement, leading to significant biases in delta C-13 of CH4, if krypton is not sufficiently separated during the analysis. According to our experiments, the krypton interference is likely composed of two individual effects, with the lateral tailing of the doubly charged Kr-86 peak affecting the neighbouring m/z 44 and partially the m/z 45 Faraday cups. Additionally, a broad signal affecting m/z 45 and especially m/z 46 is assumed to result from scattered ions of singly charged krypton. The introduced bias in the measured isotope ratios is dependent on the chromatographic separation, the krypton-to-CH4 mixing ratio in the sample, the focusing of the mass spectrometer as well as the detector configuration and can amount to up to several per mil in delta C-13. Apart from technical solutions to avoid this interference, we present correction routines to a posteriori remove the bias.

Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides

The fragmentation of electrospray-generated multiply deprotonated RNA and mixed-sequence RNA/DNA pentanucleotides upon low-energy collision-induced dissociation (CID) in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The goal of unambiguous sequence identification of mixed-sequence RNA/DNA oligonucleotides requires detailed understanding of the gas-phase dissociation of this class of compounds. The two major dissociation events, base loss and backbone fragmentation, are discussed and the unique fragmentation behavior of oligoribonucleotides is demonstrated. Backbone fragmentation of the all-RNA pentanucleotides is characterized by abundant c-ions and their complementary y-ions as the major sequence-defining fragment ion series. In contrast to the dissociation of oligodeoxyribonucleotides, where backbone fragmentation is initiated by the loss of a nucleobase which subsequently leads to the formation of the w- and [a-base]-ions, backbone dissociation of oligoribonucleotides is essentially decoupled from base loss. The different behavior of RNA and DNA oligonucleotides is related to the presence of the 2'-hydroxyl substituent, which is the only structural alteration between the DNA and RNA pentanucleotides studied. CID of mixed-sequence RNA/DNA pentanucleotides results in a combination of the nucleotide-typical backbone fragmentation products, with abundant w-fragment ions generated by cleavage of the phosphodiester backbone adjacent to the deoxy building blocks, whereas backbone cleavage adjacent to ribonucleotides induces the formation of c- and y-ions. (C) 2002 American Society for Mass Spectrometry.

Enabling the Next Generation of Spaceborne Quadrupole Mass Spectrometers

The quadrupole mass spectrometer (QMS) has over 30 years of spaceflight heritage in making important neutral gas and low energy ion observations. Given their geometrical constraints, these instruments are currently operated at the extreme limit of their capabilities. However, a technique called higher order auxiliary excitation provides a set of novel, robust, electronics-based solutions for improving the performance of these sensors. By driving the quadrupole rods with an additional frequency nearly twice that of the normal RF operating frequency, substantially increased abundance sensitivity, maximum attainable mass resolution, and peak stability can be achieved through operation of voltage scan lines through the center of formed upper stability islands. Such improvements are modeled using numerical simulations of ion trajectories in a quadrupole field with and without applied higher order auxiliary excitation. When compared to a traditional QMS with a mass range up to 500Da, sensors can be designed with the same precision electronics to have expected mass ranges beyond 1500Da with a power increase of less than twice that of its heritage implementations.

Comparison of several wood smoke markers and source apportionment methods for wood burning particulate mass

Residential wood combustion has only recently been recognized as a major contributor to air pollution in Switzerland and in other European countries. A source apportionment method using the aethalometer light absorption parameters was applied to five winter campaigns at three sites in Switzerland: a village with high wood combustion activity in winter, an urban background site and a highway site. The particulate mass from traffic (PMtraffic) and wood burning (PMwb) emissions obtained with this model compared fairly well with results from the 14C source apportionment method. PMwb from the model was also compared to well known wood smoke markers such as anhydrosugars (levoglucosan and mannosan) and fine mode potassium, as well as to a marker recently suggested from the Aerodyne aerosol mass spectrometer (mass fragment m/z 60). Additionally the anhydrosugars were compared to the 14C results and were shown to be comparable to literature values from wood burning emission studies using different types of wood (hardwood, softwood). The levoglucosan to PMwb ratios varied much more strongly between the different campaigns (4–13%) compared to mannosan to PMwb with a range of 1–1.5%. Possible uncertainty aspects for the various methods and markers are discussed.

Characterization and source apportionment of organic aerosol using offline aerosol mass spectrometry

Field deployments of the Aerodyne Aerosol Mass Spectrometer (AMS) have significantly advanced real-time measurements and source apportionment of non-refractory particulate matter. However, the cost and complex maintenance requirements of the AMS make its deployment at sufficient sites to determine regional characteristics impractical. Furthermore, the negligible transmission efficiency of the AMS inlet for supermicron particles significantly limits the characterization of their chemical nature and contributing sources. In this study, we utilize the AMS to characterize the water-soluble organic fingerprint of ambient particles collected onto conventional quartz filters, which are routinely sampled at many air quality sites. The method was applied to 256 particulate matter (PM) filter samples (PM1, PM2:5, and PM10, i.e., PM with aerodynamic diameters smaller than 1, 2.5, and 10 μm, respectively), collected at 16 urban and rural sites during summer and winter. We show that the results obtained by the present technique compare well with those from co-located online measurements, e.g., AMS or Aerosol Chemical Speciation Monitor (ACSM). The bulk recoveries of organic aerosol (60–91 %) achieved using this technique, together with low detection limits (0.8 μg of organic aerosol on the analyzed filter fraction) allow its application to environmental samples. We will discuss the recovery variability of individual hydrocarbon ions, ions containing oxygen, and other ions. The performance of such data in source apportionment is assessed in comparison to ACSM data. Recoveries of organic components related to different sources as traffic, wood burning, and secondary organic aerosol are presented. This technique, while subjected to the limitations inherent to filter-based measurements (e.g., filter artifacts and limited time resolution) may be used to enhance the AMS capabilities in measuring size-fractionated, spatially resolved longterm data sets.

VERIFICATION OF DNA PREDICTED PROTEIN SEQUENCES BY ENZYME HYDROLYSIS AND MASS SPECTROMETRIC ANALYSIS

The focus of this thesis lies in the development of a sensitive method for the analysis of protein primary structure which can be easily used to confirm the DNA sequence of a protein's gene and determine the modifications which are made after translation. This technique involves the use of dipeptidyl aminopeptidase (DAP) and dipeptidyl carboxypeptidase (DCP) to hydrolyze the protein and the mass spectrometric analysis of the dipeptide products.^ Dipeptidyl carboxypeptidase was purified from human lung tissue and characterized with respect to its proteolytic activity. The results showed that the enzyme has a relatively unrestricted specificity, making it useful for the analysis of the C-terminal of proteins. Most of the dipeptide products were identified using gas chromatography/mass spectrometry (GC/MS). In order to analyze the peptides not hydrolyzed by DCP and DAP, as well as the dipeptides not identified by GC/MS, a FAB ion source was installed on a quadrupole mass spectrometer and its performance evaluated with a variety of compounds.^ Using these techniques, the sequences of the N-terminal and C-terminal regions and seven fragments of bacteriophage P22 tail protein have been verified. All of the dipeptides identified in these analysis were in the same DNA reading frame, thus ruling out the possibility of a single base being inserted or deleted from the DNA sequence. The verification of small sequences throughout the protein sequence also indicates that no large portions of the protein have been removed after translation. ^

MONITORING ENZYME REACTIONS BY FAST ATOM BOMBARDMENT MASS SPECTROMETRY

The potential for the direct analysis of enzyme reactions by fast atom bombardment (FAB) mass spectrometry has been investigated. Conditions are presented for the maintenance of enzymatic activity under FAB conditions along with FAB mass spectrometric data showing that these conditions can be applied to solutions of enzyme and substrate to follow enzymatic reactions inside the mass spectrometer in real-time. In addition, enzyme kinetic behavior under FAB mass spectrometric conditions is characterized using trypsin and its assay substrate, TAME, as an enzyme-substrate reaction model. These results show that two monitoring methods can be utilized to follow reactions by FAB mass spectrometry. The advantages of each method are discussed and illustrated by obtaining kinetic parameters from the direct analysis of enzyme reactions with assay or peptide substrates. ^

Mass spectrometry of ribosomes and ribosomal subunits

Nanoflow electrospray ionization has been used to introduce intact Escherichia coli ribosomes into the ion source of a mass spectrometer. Mass spectra of remarkable quality result from a partial, but selective, dissociation of the particles within the mass spectrometer. Peaks in the spectra have been assigned to individual ribosomal proteins and to noncovalent complexes of up to five component proteins. The pattern of dissociation correlates strongly with predicted features of ribosomal protein–protein and protein–RNA interactions. The spectra allow the dynamics and state of folding of specific proteins to be investigated in the context of the intact ribosome. This study demonstrates a potentially general strategy to probe interactions within complex biological assemblies.