Showing papers in "Rapid Communications in Mass Spectrometry in 2003"

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

Abstract: A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.

A method for reducing the time required to match protein sequences with tandem mass spectra

Abstract: An algorithm for reducing the time necessary to match a large set of peptide tandem mass spectra with a list of protein sequences is described. This algorithm breaks the process into multiple steps. A rapid survey step identifies all protein sequences that are reasonable candidates for a match with a set of tandem mass spectra. These candidates are then used as models, which are refined by detailed analysis of the set of tandem mass spectra for evidence of incomplete enzymatic hydrolysis, non-specific hydrolysis and chemical modifications of amino acid residues resulting from either post-translational modifications or sample handling. Compared with current one-step methods for matching proteins to mass spectra, this multiple-step method can decrease the time required for the calculation by several orders of magnitude.

Oxygen isotopes in nitrate: new reference materials for 18O:17O:16O measurements and observations on nitrate-water equilibration.

Abstract: Despite a rapidly growing literature on analytical methods and field applications of O isotope-ratio measurements of NO(3)(-) in environmental studies, there is evidence that the reported data may not be comparable because reference materials with widely varying delta(18)O values have not been readily available. To address this problem, we prepared large quantities of two nitrate salts with contrasting O isotopic compositions for distribution as reference materials for O isotope-ratio measurements: USGS34 (KNO(3)) with low delta(18)O and USGS35 (NaNO(3)) with high delta(18)O and 'mass-independent' delta(17)O. The procedure used to produce USGS34 involved equilibration of HNO(3) with (18)O-depleted meteoric water. Nitric acid equilibration is proposed as a simple method for producing laboratory NO(3)(-) reference materials with a range of delta(18)O values and normal (mass-dependent) (18)O:(17)O:(16)O variation. Preliminary data indicate that the equilibrium O isotope-fractionation factor (alpha) between [NO(3)(-)] and H(2)O decreases with increasing temperature from 1.0215 at 22 degrees C to 1.0131 at 100 degrees C. USGS35 was purified from the nitrate ore deposits of the Atacama Desert in Chile and has a high (17)O:(18)O ratio owing to its atmospheric origin. These new reference materials, combined with previously distributed NO(3) (-) isotopic reference materials IAEA-N3 (=IAEA-NO-3) and USGS32, can be used to calibrate local laboratory reference materials for determining offset values, scale factors, and mass-independent effects on N and O isotope-ratio measurements in a wide variety of environmental NO(3)(-) samples. Preliminary analyses yield the following results (normalized with respect to VSMOW and SLAP, with reproducibilities of +/-0.2-0.3 per thousand, 1sigma): IAEA-N3 has delta(18)O = +25.6 per thousand and delta(17)O = +13.2 per thousand; USGS32 has delta(18)O = +25.7 per thousand; USGS34 has delta(18)O = -27.9 per thousand and delta(17)O = -14.8 per thousand; and USGS35 has delta(18)O = +57.5 per thousand and delta(17)O = +51.5 per thousand.

Investigation of matrix effects in bioanalytical high-performance liquid chromatography/tandem mass spectrometric assays: application to drug discovery

Abstract: A series of studies was performed to investigate some of the causes for matrix effects ('ion suppression' or 'ion enhancement') in bioanalytical high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) assays. Previous studies have reported that matrix effects are mainly due to endogenous components in biological fluids and are a greater concern for electrospray ionization (ESI) than for atmospheric pressure chemical ionization (APCI). In this report we demonstrate that: (1) matrix effects can also be caused by exogenous materials, such as polymers contained in different brands of plastic tubes, or Li-heparin, a commonly used anticoagulant; (2) matrix effects are not only ionization mode (APCI or ESI) dependent, but also source design (Sciex, Finnigan, Micromass) dependent; and (3) for at least one vendor's design, we found the APCI mode to be more sensitive to matrix effects than the ESI mode. Based on these findings, we have proposed the following simple strategies to avoid matrix effects: (1) select the same brand of plastic tubes for processing and storing plasma samples and spiked plasma standards; (2) avoid using Li-heparin as the anticoagulant; and (3) try switching the ionization mode or switching to different mass spectrometers when matrix effects are encountered. These three strategies have allowed us to use protein precipitation and generic fast LC techniques to generate reliable LC/MS/MS data for the support of pharmacokinetic studies at the early drug discovery stage.

Ionization enhancement in atmospheric pressure chemical ionization and suppression in electrospray ionization between target drugs and stable-isotope-labeled internal standards in quantitative liquid chromatography/tandem mass spectrometry.

Abstract: The phenomena of ionization suppression in electrospray ionization (ESI) and enhancement in atmospheric pressure chemical ionization (APCI) were investigated in selected-ion monitoring and selected-reaction monitoring modes for nine drugs and their corresponding stable-isotope-labeled internal standards (IS). The results showed that all investigated target drugs and their co-eluting isotope-labeled IS suppress each other's ionization responses in ESI. The factors affecting the extent of suppression in ESI were investigated, including structures and concentrations of drugs, matrix effects, and flow rate. In contrast to the ESI results, APCI caused seven of the nine investigated target drugs and their co-eluting isotope-labeled IS to enhance each other's ionization responses. The mutual ionization suppression or enhancement between drugs and their isotope-labeled IS could possibly influence assay sensitivity, reproducibility, accuracy and linearity in quantitative liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). However, calibration curves were linear if an appropriate IS concentration was selected for a desired calibration range to keep the response factors constant.

ESI-MS/MS analysis of underivatised amino acids: a new tool for the diagnosis of inherited disorders of amino acid metabolism. Fragmentation study of 79 molecules of biological interest in positive and negative ionisation mode

Abstract: The diagnosis of inherited disorders of amino acids (AA) metabolism is usually performed on automated analysers by ion-exchange chromatography and quantification after ninhydrin derivatisation of about 50 different AA. A single run liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for these molecules can be an alternative to this time-consuming technique. The first step of this development is the infusion study of the fragmentation of 79 molecules of biological interest in electrospray ionisation tandem mass spectrometry (ESI-MS/MS), in positive and in negative ionisation mode. Among them, three molecules can be detected only in negative ionisation mode, 38 only in positive mode and 38 in the two modes. All the most abundant fragmentations are presented, with optimisation of the MS/MS parameters. The positive ionisation mode was retained for the simultaneous analysis of 76 molecules. One sensitive and/or specific transition is proposed for the monitoring of each molecule. Improvement in sensitivity of detection was obtained with the use of an acidic mobile phase. Flow injection analysis studies led us to highlight a number of interferences-due to isobaric molecules, to in-source collision-induced dissociation, or to natural isotopic distribution of the elements-which are listed. For a reliable quantification method, these molecules have to be separated by LC before analysis in the tandem mass spectrometer. Ion-pairing reversed-phase liquid chromatography (RPLC) using perfluorinated carboxylic acids as ion-pairing agents has already been found suitable for analysis of AA in MS/MS positive ionisation mode and is under development.

Automated quantitative and isotopic (13C) analysis of dissolved inorganic carbon and dissolved organic carbon in continuous-flow using a total organic carbon analyser.

Abstract: A method for the automated (13)C analysis of dissolved inorganic and organic carbon species has been developed to operate on a continuous-flow isotope ratio mass spectrometer (CF-IRMS). For natural and anthropogenic carbon species, the (13)C stable isotope has proven to be an excellent environmental tracer. Analytical performance tests were carried out on various organic compounds from easily oxidisable (sugar) to difficult (humic acid). A set of natural samples was also analysed to confirm the flexibility of the system. Analytical precision (2sigma) is typically <0.20 per thousand with sample reproducibility from 0.10-0.35 per thousand depending on reactivity of material. We believe this to be the first successful use of a total organic carbon (TOC) analyser for both dissolved inorganic and, specifically, dissolved organic species for (13)C stable isotope analysis in an automated CF-IRMS system. Routine analysis is achieved fairly quickly, is relatively simple with little or no sample manipulation, and will allow new and exciting studies for stable isotope research in both natural abundance and organic tracer studies not easily achieved before.

Nitrogen isotopomer site preference of N2O produced by Nitrosomonas europaea and Methylococcus capsulatus Bath.

Abstract: The original article to which this Erratum refers was published in Rapid Communications in Mass Spectrometry 17 (7) 2003, 738–745.

Liquid chromatography/tandem mass spectrometry methods for quantitation of mevalonic acid in human plasma and urine: method validation, demonstration of using a surrogate analyte, and demonstration of unacceptable matrix effect in spite of use of a stable isotope analog internal standard.

Abstract: Selective, accurate, and reproducible liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods were developed and validated for the determination of mevalonic acid, an intermediate in the biosynthesis of cholesterol and therefore a useful biomarker in the development of cholesterol lowering drugs, in human plasma and urine. A hepta-deuterated analog of mevalonic acid was used as the internal standard. For both methods, calibration standards were prepared in water, instead of human plasma and urine, due to unacceptably high levels of endogenous mevalonic acid. The lower quality control (QC) samples were prepared in water while the higher QC samples were prepared in the biological matrices. For the isolation/purification of mevalonic acid from the plasma and urine matrices, the samples were first acidified to convert the acid analyte into its lactone form. For the plasma samples, the lactone analyte was retained on and then eluted off a polymeric solid-phase extraction (SPE) sorbent. For the urine method, the sample containing the lactone analyte was passed through a C-18 SPE column, which did not retain the analyte, with the subsequent analyte retention on and then elution off a polymeric SPE sorbent. Chromatographic separation was achieved isocratically on a polar-endcapped C-18 analytical column with a water/methanol mobile phase containing 0.5 mM formic acid. Detection was by negative-ion electrospray tandem mass spectrometry. The standard curve range was 0.500-20.0 ng/mL for the plasma method and 25.0-1,000 ng/mL for the urine method. Excellent accuracy and precision were obtained for both methods at all concentration levels tested. It was interesting to note that for certain batches of urine, when a larger sample volume was used for analysis, a high degree of matrix effect was observed which resulted not only in the attenuation of the absolute response, but also in a change of analyte/internal standard response ratio. This demonstrated that, under certain conditions, the use of a stable isotope analog internal standard does not, contrary to conventional thinking, guarantee the constancy of the analyte/internal response ratio, which is a prerequisite for a rugged bioanalytical method. On the other hand, under conditions where the sample matrix does not have such a deleterious effect, we have found that a stable isotope analog could serve as a surrogate (substitute) analyte. Thus, we have shown that using calibration standards prepared by spiking plasma with tri-deuterated or tetra-deuterated mevalonic acid, instead of mevalonic acid itself (the analyte), plasma QC samples that contain mevalonic acid can be successfully analyzed for the accurate and precise quantitation of mevalonic acid. The use of a surrogate analyte provides the opportunity to gauge the daily performance of the method for the low concentration levels prepared in the biological matrix, which otherwise is not achievable because of the endogenous concentrations of the analyte in the biological matrices.

Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry.

Abstract: There is an increasing need to be able to conduct quantitative lipidomics analyses as a complement to proteomics studies. The highest specificity for proteomics analysis can be obtained using methodology based on electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) coupled with liquid chromatography/tandem mass spectrometry (LC/MS/MS). For lipidomics analysis it is often necessary to be able to separate enantiomers and regioisomers. This can be very challenging when using methodology based on conventional reversed-phase chromatography. Normal-phase chromatography using chiral columns can provide dramatic improvements in the resolution of enantiomers and regioisomers. However, conventional ESI- and APCI-MS/MS has limited sensitivity, which makes it difficult to conduct studies in cell culture systems where only trace amounts of non-esterified bioactive lipids are present. The use of electron capture APCI-MS/MS overcomes this problem. Enantiomers and regioisomers of diverse bioactive lipids can be quantified using stable isotope dilution methodology coupled with normal-phase chiral chromatography and electron capture APCI-MS/MS. This methodology has allowed a lipidomics profile from rat epithelial cells maintained in culture to be delineated and allowed the effect of a non-selective lipoxygenase inhibitor to be assessed.

Determination of patterns of biologically relevant aldehydes in exhaled breath condensate of healthy subjects by liquid chromatography/atmospheric chemical ionization tandem mass spectrometry

Abstract: A method for the simultaneous determination of several classes of aldehydes in exhaled breath condensate (EBC) was developed using liquid chromatography/atmospheric pressure chemical ionization tandem mass spectrometry (LC/APCI-MS/MS). EBC is a biological matrix obtained by a relatively new, simple and noninvasive technique and provides an indirect assessment of pulmonary status. The measurement of aldehydes in EBC represents a biomarker of the effect of oxidative stress caused by smoke, disease, or strong oxidants like ozone. Malondialdehyde (MDA), acrolein, alpha,beta-unsaturated hydroxylated aldehydes [namely 4-hydroxyhexenal (4-HHE) and 4-hydroxynonenal (4-HNE)], and saturated aldehydes (n-hexanal, n-heptanal and n-nonanal) were measured in EBC after derivatization with 2,4-dinitrophenylhydrazine (DNPH). Atmospheric pressure chemical ionization of the analytes was obtained in positive-ion mode for MDA, and in negative-ion mode for acrolein, 4-HHE, 4-HNE, and saturated aldehydes. DNPH derivatives were separated on a C18 column using variable proportions of 20 mM aqueous acetic acid and methanol. Linearity was established over 4-5 orders of magnitude and limits of detection were in the 0.3-1.0 nM range. Intra-day and inter-day precision were in the 1.3-9.9% range for all the compounds. MDA, acrolein and n-alkanals were detectable in all EBC samples, whereas the highly reactive 4-HHE and 4-HNE were found in only a few samples. Statistically significant higher concentrations of MDA, acrolein and n-hexanal were found in EBC from smokers.

Comparison between electrochemistry/mass spectrometry and cytochrome P450 catalyzed oxidation reactions.

Abstract: The extent to which electrochemistry on-line with electrospray mass spectrometry can be used to mimic cytochrome P450 catalyzed oxidations has been investigated. Comparisons on the mechanistic level have been made for most reactions in an effort to explain why certain reactions can, and some cannot, be mimicked by electrochemical oxidations. The EC/MS/MS system used successfully mimics in cases where the P450 catalyzed reactions are supposed to proceed via a mechanism initiated by a one-electron oxidation, such as N-dealkylation, S-oxidation, P-oxidation, alcohol oxidation and dehydrogenation. The P450 catalyzed reactions initiated via direct hydrogen atom abstraction, such as O-dealkylation and hydroxylation of unsubstituted aromatic rings, generally had a too high oxidation potential to be electrochemically oxidized below the oxidation potential limit of water, and were not mimicked by the EC/MS/MS system. Even though the EC/MS/MS system is not able to mimic all oxidations performed by cytochrome P450, valuable information can be obtained concerning the sensitivity of the substrate towards oxidation and in which position of the molecule oxidations are likely to take place. For small-scale electrochemical synthesis of metabolites, starting from the drug, the EC/MS/MS system should be very useful for quick optimization of the electrochemical conditions. The simplicity of the system, and the ease and speed with which it can be applied to a large number of compounds, make it a useful tool in drug metabolism research.

Two new organic reference materials for δ13C and δ15N measurements and a new value for the δ13C of NBS 22 oil

Abstract: Analytical grade L-glutamic acid is chemically stable and has a C/N mole ratio of 5, which is close to that of many of natural biological materials, such as blood and animal tissue. Two L-glutamic acid reference materials with substantially different 13C and 15N abundances have been prepared for use as organic reference materials for C and N isotopic measurements. USGS40 is analytical grade L-glutamic acid and has a delta13C value of -26.24 per thousand relative to VPDB and a delta15N value of -4.52 per thousand relative to N2 in air. USGS41 was prepared by dissolving analytical grade L-glutamic acid with L-glutamic acid enriched in 13C and 15N. USGS41 has a delta13C value of +37.76 per thousand and a delta15N value of +47.57 per thousand. The delta13C and delta15N values of both materials were measured against the international reference materials NBS 19 calcium carbonate (delta13C=+1.95 per thousand ), L-SVEC lithium carbonate (delta13C=-46.48 per thousand ), IAEA-N-1 ammonium sulfate (delta15N=0.43 per thousand ), and USGS32 potassium nitrate (delta15N=180 per thousand ) by on-line combustion continuous-flow and off-line dual-inlet isotope-ratio mass spectrometry. Both USGS40 and USGS41 are isotopically homogeneous; reproducibility of delta13C is better than 0.13 per thousand, and that of delta15N is better than 0.13 per thousand in 100-microg amounts. These two isotopic reference materials can be used for (i) calibrating local laboratory reference materials, and (ii) quantifying drift with time, mass-dependent fractionations, and isotope-ratio-scale contraction in the isotopic analysis of various biological materials. Isotopic results presented in this paper yield a delta13C value for NBS 22 oil of -29.91 per thousand, in contrast to the commonly accepted value of -29.78 per thousand for which off-line blank corrections probably have not been quantified satisfactorily.

Use of liquid chromatography/time‐of‐flight mass spectrometry and multivariate statistical analysis shows promise for the detection of drug metabolites in biological fluids

Abstract: The process of metabolite identification is essential to the drug discovery and development process; this is usually achieved by liquid chromatography/tandem mass spectrometry (LC/MS/MS) or a combination of liquid chromatography/mass spectrometry (LC/MS) and nuclear magnetic resonance (NMR) spectroscopy. Metabolite identification is, however, a time-consuming process requiring an experienced skilled scientist. Multivariate statistical analysis has been used in the field of metabonomics to elucidate differences in endogenous biological profiling due to a toxic effect or a disease state. In this paper we show how a combination of liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS) and multivariate statistical analysis can be used to detect drug metabolites in a biological fluid with no prior knowledge of the compound administered.

Effect of preparation and preservation procedures on carbon and nitrogen stable isotope determinations from zooplankton

Abstract: A literature survey of zooplankton stable isotope studies revealed inconsistencies between authors concerning (a) fixation and (b) allowance for gut clearance of zooplankton prior to δ13C and δ15N determinations. To address whether commonly used preservation techniques induce changes in stable isotope values, fresh lake zooplankton (control) were compared with preserved (ethanol, methanol, formaldehyde, gluteraldehyde, frozen and shock frozen) material. Differences of up to 1.1‰ for carbon and 1.5‰ for nitrogen isotopic signatures were found. Even freezing, the most frequently used method identified from the literature, caused significant changes compared with the control. We advocate the use of fresh material prepared immediately whenever possible, or complementary testing of the preservative method to be used. Larger organisms are routinely eviscerated, or specific tissues are dissected, and analysed for stable isotopes to reduce errors introduced via the gut contents. Yet zooplankton gut clearance is rarely performed: the gut content assumed to be negligible relative to organism mass. Experimental determinations of relative gut mass, from both original and compiled data, range from 1–26% for different zooplankton species. Using reported isotopic values of basal resources from natural systems, we calculated that, when analysing bulk zooplankton, inclusion of the gut mass may introduce substantial errors of >3‰. Thus it appears prudent to perform the simple procedure of gut clearance, especially for copepod species.

Analysis of Colubroidea snake venoms by liquid chromatography with mass spectrometry: evolutionary and toxinological implications

Abstract: The evolution of the venomous function of snakes and the diversification of the toxins has been of tremendous research interest and considerable debate. It has become recently evident that the evolution of the toxins in the advanced snakes (Colubroidea) predated the evolution of the advanced, front-fanged delivery mechanisms. Historically, the venoms of snakes lacking front-fanged venomdelivery systems (conventionally grouped into the paraphyletic family Colubridae) have been largely neglected. In this study we used liquid chromatography with mass spectrometry (LC/MS) to analyze a large number of venoms from a wide array of species representing the major advanced snake clades Atractaspididae, Colubrinae, Elapidae, Homalopsinae, Natricinae, Psammophiinae, Pseudoxyrhophiinae, Xenodontinae, and Viperidae. We also present the first sequences of toxins from Azemiops feae as well as additional toxin sequences from the Colubrinae. The large body of data on molecular masses and retention times thus assembled demonstrates a hitherto unsuspected diversity of toxins in all lineages, having implications ranging from clinical management of envenomings to venom evolution to the use of isolated toxins as leads for drug design and development. Although definitive assignment of a toxin to a protein family can only be done through demonstrated structural studies such as N-terminal sequencing, the molecular mass data complemented by LC retention information, presented here, do permit formulation of reasonable hypotheses concerning snake venom evolution and potential clinical effects to a degree not possible till now, and some hypotheses of this kind are proposed here. The data will also be useful in biodiscovery. Copyright # 2003 John Wiley & Sons, Ltd.

Matrix effects during analysis of plasma samples by electrospray and atmospheric pressure chemical ionization mass spectrometry: practical approaches to their elimination.

Abstract: Some cases of occurrence of matrix effects (mostly ion suppression) in protein-precipitated plasma samples, and their influence on the validity of plasma concentrations and pharmacokinetic parameters, are discussed. The comparison of matrix effects using either electrospray (TurboIonspray, TISP) or atmospheric pressure chemical ionization (APCI) indicated that APCI is less prone to matrix effects. Nevertheless, TISP is usually the first choice of ionization technique since unknown thermally labile metabolites might be present in the plasma samples causing erroneous results. A high impact of ion suppression on the plasma concentrations after intravenous (i.v.) administration was found, depending on the drug formulation (vehicle). Since ion suppression caused significantly lower plasma concentrations (by a factor of up to 5.5) after i.v. dosing, the area under the curve (AUC) was underestimated and the plasma clearance was consequently erroneously high, with an impact on drug candidate selection. By simple stepwise dilution (e.g. 10-fold and 50-fold) of the supernatant of protein-precipitated plasma samples, including all calibration and quality control samples, the matrix effects were recognized and eliminated.

Reconstruction of the isotopic history of animal diets by hair segmental analysis

Abstract: Carbon and nitrogen isotope signatures (δ13C and δ15N) of animal tissues provide information about the diet and, hence, the environment in which the animals are living. Hair is particularly useful as it provides a stable archive of temporal (e.g. seasonal) fluctuations in diet isotope composition. It can be sampled easily and with minimal disturbance from living subjects. However, derivation of the temporal record along the hair length may be subject to errors and uncertainties. This study investigates (and suggests means to minimize) several sources of error, including (a) incomplete sampling, (b) sampling during the quiescent (telogen) phase, (c) non-representative sub-sampling, (d) ignorance of hair growth rate, i.e. time–position relationship of isotope signatures, and (e) non-optimal compromise between analytical/procedural precision and effort/cost. Cattle tail switch hair was collected from animals of different breed, sex and age. Hair was washed, sectioned, and 5- or 10-mm-long sections were analyzed for C and N isotope composition. Signatures along paired hairs were similar (r2 ≈ 0.8) and distances between isotopic minima and maxima nearly identical, indicating that a single hair constituted a representative sample and (except for telogen hair) hair growth rate was the same for paired hairs. However, cutting hair, instead of plucking, caused a variable loss of recently grown hair and information. Telogen hair was identified and data loss due to cutting error reduced when more than one hair from the same animal and sampling region was compared to spot and delimit common and missing regions. Similarly, comparison of isotopic profiles from hair collected at different times identified the segment produced during the respective interval and allowed calculation of average hair growth rate, which varied between animals (0.69–1.06 mm d−1). Analysis of alternate 10-mm-long sections for two hairs per animal provided a good compromise between precision/resolution and effort. The method should be applicable to other mammalian species including man. Copyright © 2003 John Wiley & Sons, Ltd.

High-throughput screening of pKa values of pharmaceuticals by pressure-assisted capillary electrophoresis and mass spectrometry.

Abstract: A high-throughput pKa screening method based on pressure-assisted capillary electrophoresis (CE) and mass spectrometry (MS) is presented. Effects of buffer type and ionic strength on sensitivity and pKa values were investigated. Influence of dimethyl sulfoxide (DMSO) concentration present in the sample on effective mobility measurement was examined. A series of ten volatile buffers, covering a pH range from 2.5 to 10.5 with the same ionic strength, was employed. The application of volatile background electrolytes resulted in significant signal increase as compared with commonly used non-volatile phosphate buffers. In general, the CE/MS system provided a ten-fold higher sensitivity than conventional UV detection. The newly developed CE/MS method offers high-throughput capacity by pooling a number of compounds into a single sample. Simultaneous measurement of more than 50 compounds was readily achieved in less than 150 min. The measured pKa values are consistent with the published data obtained from the CE/UV method and are also in good agreement with data generated by other methods. Other advantages of using CE/MS for pKa screening are illustrated with typical examples, including poorly soluble compounds and non-UV-absorbing compounds.

Ionic matrices for matrix-assisted laser desorption/ionization time-of-flight detection of DNA oligomers.

Abstract: Salts with low melting points, also termed room-temperature ionic liquids, can be used as matrices in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). They have great vacuum stability, and can dissolve polar and apolar solutes including carbohydrates, biological oligomers and proteins. The ionic liquids give much more homogeneous sample solutions compared with solid matrices. We demonstrate the usefulness of using ionic matrices to determine the molecular weight of DNA oligomers by direct TOF mass spectrometric analysis. Three oligonucleotides were tested, (d(pT)10, d(pC)11, and d(pC)12), with several ionic matrices synthesized from different bases associated to two acids (3-hydroxypicolinic acid and 2,5-dihydroxybenzoic acid). The results obtained show that the best ionic matrices enhance the ion peak intensity of the oligonucleotides with respect to conventional molecular matrices under our experimental conditions. In one case, an ionic matrix provided a signal-to-noise ratio ten times higher than the corresponding molecular matrix. Several of the tested ionic matrices were liquids. However, all working ionic matrices were solids. Copyright © 2003 John Wiley & Sons, Ltd.

Product ion scanning using a Q‐q‐Qlinear ion trap (Q TRAPTM) mass spectrometer

Abstract: The use of a Q-q-Q(linear ion trap) instrument to obtain product ion spectra is described. The instrument is based on the ion path of a triple quadrupole mass spectrometer with Q3 operable as either a conventional RF/DC quadrupole mass filter or a linear ion trap mass spectrometer with axial ion ejection. This unique ion optical arrangement allows de-coupling of precursor ion isolation and fragmentation from the ion trap itself. The result is a high sensitivity tandem mass spectrometer with triple quadrupole fragmentation patterns and no inherent low mass cut-off. The use of the entrance RF-only section of the instrument as accumulation ion trap while the linear ion trap mass spectrometer is scanning enhances duty cycles and results in increased sensitivities by as much as a factor of 20. The instrument is also capable of all of the triple quadrupole scans including multiple-reaction monitoring (MRM) as well as precursor and constant neutral loss scanning. The high product ion scanning sensitivity allows the recording of useful product ion spectra near the MRM limit of quantitation.

Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteins

Abstract: The combination of hydrogen exchange and mass spectrometry has been widely used in structural biology, providing views on protein structure and protein dynamics. One of the constraints is to use proteases working at low pH and low temperature to limit back-exchange during proteolysis. Although pepsin works in these conditions and is currently used in such experiments, sequence coverage is not always complete especially for large proteins, and the spatial resolution of the exchange rate is limited by the size of the resulting peptides. In this study we tried two other proteases, protease type XIII from Aspergillus saitoi and protease type XVIII from Rhizhopus species. The penicillin-binding protein X (PBP-2X*), a 77-kDa protein, was selected as a model. Like pepsin, neither of these proteases is really specific, but we found very good reproducibility in the digestion pattern. Compared with using pepsin alone, combining the results of the three independent proteolyses increased the coverage for the peptide mapping, thus avoiding missing some potentially interesting regions of the protein. Furthermore, we obtained a better spatial resolution for deuterium incorporation data, specifying accurately the deuterated regions.

Quantification of acetaldehyde released by lung cancer cells in vitro using selected ion flow tube mass spectrometry

Abstract: The production of volatile compounds from cancer cell lines in vitro has been investigated using selected ion flow tube mass spectrometry (SIFT-MS). This technique enables on-line quantitative analyses of the headspace above cell/medium cultures. This paper reports the discovery that acetaldehyde is released by the lung cancer cell lines SK-MES and CALU-1. The concentration of acetaldehyde in the headspace of the medium/cell culture was measured after 16 h incubation at 37°C and found to be proportional to the number of cancer cells in the medium (typically 108). From these data, the acetaldehyde production rates of the SK-MES cells and the CALU-1 cells in vitro are determined to be 1 × 106 and 1.5–3 × 106 molecules/cell/min, respectively. The potential value of this new technique in cell biology and in industrial cell biotechnology is discussed. Copyright © 2003 John Wiley & Sons, Ltd.

A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry.

Abstract: Mass spectrometric analysis of wild-type proteins that have been covalently modified by bifunctional cross-linking reagents and then digested proteolytically can be used to obtain low-resolution distance constraints, which can be useful for protein structure determination. Limitations of this approach include time-consuming separation steps, such as the separation of internally cross-linked protein monomers from covalent dimers, and a susceptibility to artifacts due to low levels of natural and man-made peptide modifications that can be mistaken for cross-linked species. The results presented here show that when a crude cross-linked protein mixture is injected into an electrospray ionization Fourier transform mass spectrometry (ESI-FTMS) instrument, the cross-link positions can be localized by fragmentation and mass spectrometry on the ‘gas-phase purified’ singly internally cross-linked monomer. Our results show that reaction of ubiquitin with the homobifunctional lysine-lysine cross-linking reagent dissuccinimidyl suberate (DSS) resulted in two cross-links consistent with the known ubiquitin tertiary structure (K6-K11 and K48-K63). Because no protein or peptide chemistry steps are needed, other than the initial cross-linking, this new top down approach appears well suited for high-throughput experiments with multiple cross-linkers and reaction conditions. Published in 2002 by John Wiley & Sons, Ltd.

Combined infrared multiphoton dissociation and electron capture dissociation with a hollow electron beam in Fourier transform ion cyclotron resonance mass spectrometry

Abstract: Combined Infrared Multiphoton Dissociation and Electron Capture Dissociation with a Hollow Electron Beam in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

A new solution for an old problem: the regiochemical distribution of the acyl chains in galactolipids can be established by electrospray ionization tandem mass spectrometry

Abstract: Electrospray ionization-quadrupole ion trap mass spectrometry (ESI-QITMS), either in positive- or in negative-ion mode, has been used to establish the chemical structures (chain length, degree of unsaturation, positional distribution) of the fatty acids attached to the primary (sn-1) and secondary (sn-2) hydroxyl groups of the glycerol moiety of natural monogalactosyl- (MGDG) and digalactosyldiacylglycerols (DGDG), isolated from the freshwater dinoflagellate Glenodinium sanguineum and from a marine diatom belonging to the genus Chaetoceros Fragmentation by collision-induced dissociation of a single component in MGDG and DGDG mixtures, separated by high-performance liquid chromatography (HPLC) and detected on-line by tandem positive-ion ESI-MS, leads to a clear-cut determination of the positional distribution of the sn-glycerol-bound fatty acyl chains Reversed-phase liquid chromatography allowed a partial resolution of the component mixture before ESI-MS/MS analysis These results were validated by comparison with ESI-MS data obtained for the sn-2 lysoglyceroglycolipids synthesized via regiospecific enzymatic hydrolysis of the corresponding diacylglycerols by Rhizopus arrhizus lipase

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of lipids: ionization and prompt fragmentation patterns

Abstract: Ionization and prompt fragmentation patterns of triacylglycerols, phospholipids (PLs) and galactolipids were investigated using matrix-assisted laser desorption/ionization (MALDI). Positive ions of non-nitrogen-containing lipids appeared only in the sodiated form, while nitrogen-containing lipids were detected as both sodiated and protonated adducts. Lipids containing acidic hydroxyls were detected as multiple sodium adducts or deprotonated ions in the positive and negative modes, respectively, with the exception of phosphatidylcholines. The positive MALDI spectra of triacylglycerols contained prompt fragments equivalent to the loss of RCOO(-) from the neutral molecules. Prompt fragment ions [PL-polar head](+) were observed in the positive MALDI spectra of all phospholipids except phosphatidylcholines. The phosphatidylcholines produced only a minor positive fragment corresponding to the head group itself (m/z 184). Galactolipids did not undergo prompt fragmentation. Post-source decay (PSD) was used to examine the source of prompt fragments. PSD fragment patterns indicated that the lipid prompt fragment ions did not originate from the observed molecular ions (sodiated or protonated), and suggested that the prompt fragmentation followed the formation of highly unstable, probably protonated, precursor ions. Pathways leading to the formation of prompt fragment ions are proposed.

Analysis of aromatic amines in cigarette smoke

Abstract: A method for the analysis of o-toluidine, o-anisidine, 2-naphthylamine, and 4-aminobiphenyl in cigarette mainstream smoke has been developed, which combines the sensitivity of their pentafluoropropionyl (PFP) derivatives in negative ion chemical ionization (NICI) mode with the selectivity of the gas chromatography/tandem mass spectrometry (GC/MS/MS) technique. The use of four deuterated analogues as internal standards along with the application of the standard addition method results in accurate and precise results; the interday precision for the aromatic amines was 3-10% and the accuracy ranged from 97-100%. This method was applied to two American-blend University of Kentucky reference cigarettes, eight American-blend market cigarettes, a bright (flue-cured) tobacco cigarette, and an electrically heated cigarette smoking system (EHCSS). For the American-blend cigarettes there was a linear correlation between aromatic amine yields and mainstream smoke 'tar' ('tar' = total particulate matter - (nicotine + water)), whereas the bright tobacco cigarette and the EHCSS demonstrated significantly lower aromatic amine yields on an equal 'tar' basis. The results support the hypothesis that the nitrogen content of the tobacco, and above all the cigarette combustion temperature, are determining factors for the yields of aromatic amines in smoke.

High-temperature elemental analysis and pyrolysis techniques for stable isotope analysis.

Abstract: A universal method for pyrolysis and elemental analysis, suitable for the online determination of deuterium, carbon, nitrogen and oxygen isotopes for organic and inorganic substances, is presented. The samples are pyrolytically decomposed in a high-temperature pyrolysis (HTP) system, at a temperature exceeding 1400 degrees C, in the presence of reactive carbon. The method is suitable for the analysis of stable isotope ratios from hydrogen, carbon, nitrogen and oxygen. The instrumentation and experimental procedure are simple and cost-effective. The reproducibility of the delta values for D/H is better than 3 per thousand, and for (18)O, (13)C (organic) and (15)N (inorganic) it is approximately 0.2 per thousand. The HTP system is suitable for solid and liquid samples and can use an autosampler for the samples. Results are presented for the isotopic composition of international reference materials and selected laboratory reference materials, which demonstrate the precision and accuracy of the method. Possible problems in the measurement of nitrates and their solutions are particularly discussed. The analyses of oxygen isotopes in selected geological samples (carbonates, silicate, biotite) are demonstrated.