Abstract: Mass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos™ ETD (Thermo Fisher Scientific) mass spectrometer. In our dataset, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides.

Abstract: Biofuels from photosynthetic microalgae are quickly gaining interest as a viable carbon-neutral energy source. Typically, characterization of algal feedstock involves breaking down triacylglycerols (TAG) and other intact lipids, followed by derivatization of the fatty acids to fatty acid methyl esters prior to analysis by gas chromatography (GC). However, knowledge of the intact lipid profile could offer significant advantages for discovery stage biofuel research such as the selection of an algal strain or the optimization of growth and extraction conditions. Herein, lipid extracts from microalgae were directly analyzed by ultra-high pressure liquid chromatography–mass spectrometry (UHPLC-MS) using a benchtop Orbitrap mass spectrometer. Phospholipids, glycolipids, and TAGs were analyzed in the same chromatographic run, using a combination of accurate mass and diagnostic fragment ions for identification. Using this approach, greater than 100 unique TAGs were identified over the six algal strains studied and TAG profiles were obtained to assess their potential for biofuel applications. Under the growth conditions employed, Botryococcus braunii and Scenedesmus obliquus yielded the most comprehensive TAG profile with a high abundance of TAGs containing oleic acid.

Abstract: Currently there is limited information available on the accuracy and precision of relative isotopic abundance (RIA) measurements using high-resolution direct-infusion mass spectrometry (HR DIMS), and it is unclear if this information can benefit automated peak annotation in metabolomics. Here we characterize the accuracy of RIA measurements on the Thermo LTQ FT Ultra (resolution of 100 000–750 000) and LTQ Orbitrap (R = 100 000) mass spectrometers. This first involved reoptimizing the SIM-stitching method (Southam, A. D.Anal. Chem. 2007, 79, 4595−4602) for the LTQ FT Ultra, which achieved a ca. 3-fold sensitivity increase compared to the original method while maintaining a root-mean-squared mass error of 0.16 ppm. Using this method, we show the quality of RIA measurements is highly dependent on signal-to-noise ratio (SNR), with RIA accuracy increasing with higher SNR. Furthermore, a negative offset between the theoretical and empirically calculated numbers of carbon atoms was observed for both mass spectr...

Abstract: Higher energy collision dissociation (HCD) is a complementary fragmentation tool that has recently become available on mass spectrometers of the LTQ Orbitrap family. We report on a shotgun bottom-up lipidomics approach that relies on HCD of the isolated lipid precursors. HCD, together with the high mass resolution and mass accuracy of the Orbitrap analyzer, improved the confidence of molecular species assignment and accuracy of their quantification in total lipid extracts. These capabilities were particularly important for accounting for biologically interesting lipid species comprising polyunsaturated and odd numbered fatty acid moieties. We argue that now both bottom-up and top-down shotgun lipidomics could be performed on the same instrumentation platform.

Abstract: We report a new method for fast and sensitive analyses of biologically relevant fatty acids (FAs) in red blood cells (RBC) by liquid chromatography mass spectrometry (LC−MS). A new chemical derivatization approach was developed forming picolylamides from FAs in a quantitative reaction. Fourteen derivatized FA standards, including saturated and unsaturated FAs from C14 to C22, were efficiently separated within 15 min. In addition, the use of a recently introduced benchtop orbitrap mass spectrometer under positive electrospray ionization (ESI) full scan mode showed a 2−10-fold improvement in sensitivity compared with a conventional tandem MS method, with a limit of detection in the low femtomole range for saturated and unsaturated FAs. The developed method was applied to determine FA concentrations in RBC with intra- and interday coefficients of variation below 10%.

Abstract: The quantitative and confirmative performance of two different mass spectrometry (MS) techniques (high-resolution MS and tandem MS) was critically compared. Evaluated was a new extraction and clean-up protocol which was developed to cover more than 100 different veterinary drugs at trace levels in a number of animal tissues and honey matrices. Both detection techniques, high-resolution mass spectrometry (HRMS) (single-stage Orbitrap instrument operated at 50 000 full width at half maximum) and tandem mass spectrometry (MS/MS) (quadrupole technology) were used to validate the method according to the EU Commission Decision 2002/657/EEC. Equal or even a slightly better quantitative performance was observed for the HRMS-based approach. Sensitivity is higher for unit mass resolution MS/MS if only a subset of the 100 compounds has to be monitored. Confirmation of suspected positive findings can be done by evaluating the intensity ratio between different MS/MS transitions, or by accurate mass based product ion traces (no precursor selection applied). MS/MS relies on compound-specific optimized transitions; hence the second, confirmatory transition generally shows relatively high ion abundance (fragmentation efficacy). This is often not the case in single-stage HRMS, since a generic (not compound-optimized) collision energy is applied. Hence, confirmation of analytes present at low levels is superior when performed by MS/MS. Slightly better precision, but poorer accuracy (fortified matrix extracts versus pure standard solution) of ion ratios were observed when comparing data obtained by HRMS versus MS/MS.

Abstract: High-mass resolution multi-stage mass spectrometry (MSn) fragmentation was tested for differentiation and identification of metabolites, using a series of 121 polyphenolic molecules. The MSn fragmentation approach is based on the systematic breakdown of compounds, forming a so-called spectral tree. A chip-based nanoelectrospray ionization source was used combined with an ion-trap, providing reproducible fragmentation, and accurate mass read-out in an Orbitrap Fourier transform (FT) MS enabling rapid assignment of elemental formulas to the molecular ions and all fragment ions derived thereof. The used protocol resulted in reproducible MSn fragmentation trees up to MS5. Obtained results were stable over a 5 month time period, a concentration change of 100-fold, and small changes in normalized collision energy, which is key to metabolite annotation and helpful in structure and substructure elucidation. Differences in the hydroxylation and methoxylation patterns of polyphenolic core structures were found to b...

Abstract: Sweetness contributes notably to the taste-balance of dry wines and increases during oak-barrel aging owing to the release of natural sweeteners from wood. The search for such taste-active molecules, which are sometimes present at very low concentrations in wine or other complex matrixes, requires both reliable purification tools and powerful identification techniques. Here, we report the development of an original inductive method using centrifugal partition chromatography (CPC) and sensorial analysis. This method, called CPC–gustatometry, was implemented to isolate a sweet fraction with only four compounds from a complex oak wood extract. The recently developed Fourier transform mass spectrometry (FT-MS, Orbitrap analyzer) was used jointly with two-dimensional nuclear magnetic resonance (2D 1H and 13C NMR) to obtain the structural elucidation of the purified compounds. The tandem mass spectrometry (MS/MS) spectra obtained with resonant and nonresonant fragmentation modes were compared, thus providing co...

Abstract: A generic method based on LC with full-scan high-resolution (Orbitrap) mass spectrometry (MS) was systematically investigated for the simultaneous detection of a wide range of plant toxins in a variety of food and feed matrices. For a selection of 150 substances, representing various chemical classes, the limit of detection was established using fixed LC-MS conditions. Ion suppression effects and selectivity were evaluated using generic extracts from representative and relevant matrices (food supplement, honey, silage, compound feed). The majority of the substances could be measured as positive ions after electrospray ionisation (ESI+). Using a mass resolving power of 100,000 a reliable high mass accuracy was obtained despite the high abundance of co-extractants in the sample extracts. This enabled the use of ±5 ppm mass extraction windows, which in turn resulted in a high degree of selectivity. On the other hand, except for honey, strong ion suppression effects were frequently observed which adversely af...

Abstract: A method for the extraction of agmatine, cadaverine, histamine, phenyethylamine, putrescine, tryptamine, tyramine, and urocanic acid from canned tuna and frozen tuna loin matrices by matrix solid-phase dispersion, followed by separation and quantification of these compounds by ultrahigh-performance hydrophilic interaction chromatography (UHPLC-HILIC) with orbitrap mass spectrometric detection, is described. Tuna samples are dispersed in a CN-silica sorbent and eluted with a mixture of aqueous ammonium formate buffer and acetonitrile. Separation and detection are carried out on an Agilent 1200 high-performance liquid chromatograph coupled to a Thermo Exactive orbitrap mass spectrometer, and metformin is used as the internal standard. Spike recoveries are determined across a range of 20-100 ppm for each compound, and the method is validated with respect to linearity, reproducibility, accuracy, and limits of quantitation and detection. The method is demonstrated to be suitable for use in quantifying these target compounds in the studied matrices.

Abstract: Currently, mass spectrometry-based protein bioanalysis is primarily achieved through monitoring the representative peptide(s) resulting from analyte protein digestion. However, this approach is often incapable of differentiating the measurement of protein analyte from its post-translational modifications (PTMs) and/or potential biotransformation (BTX) products. This disadvantage can be overcome by direct measurement of the intact protein analytes. Selected reaction monitoring (SRM) on triple quadrupole mass spectrometers has been used for the direct measurement of intact protein. However, the fragmentation efficiency though the SRM process could be limited in many cases, especially for high molecular weight proteins. In this study, we present a new strategy of intact protein bioanalysis by high-resolution (HR) full scan mass spectrometry using human lysozyme as a model protein. An HR linear ion-trap/Orbitrap mass spectrometer was used for detection. A composite of isotopic peaks from one or multiple charg...

Abstract: As recently reported, the synthetic cannabinoid JWH-018 is the subject of extensive phase I and II metabolic reactions in vivo. Since these studies were based on LC-MS/MS and/or GC-MS identification and characterisation of analytes, the explicit structural assignment of the metabolites was only of preliminary nature, if possible at all. Here, we report the chemical synthesis of five potential in vivo metabolites of JWH-018 derivatives featuring an alkylcarboxy (M1), a terminal alkylhydroxy (M2), a 5-indolehydroxy (M3), an N-dealkylated 5-indolehydroxy (M4) and a 2′-naphthylhydroxy (5) analogue, respectively, and their characterisation by nuclear magnetic resonance spectroscopy. The collision-induced dissociation (CID) patterns of the protonated compounds were studied by high-resolution/high-accuracy tandem mass spectrometry (MS n ) applying an LTQ Orbitrap with direct infusion and electrospray ionisation of target analytes. An unusual dissociation behaviour including a reversible ion–molecule reaction between a naphthalene cation (m/z 127) and water in the gas phase of the MS was shown to be responsible for nominal neutral losses of 10 u in the course of the CID pathway. LC-MS/MS-supported comparison of synthesised reference standards with an authentic urine sample using an API 4000 QTrap mass spectrometer identified the synthetic JWH-018 analogues M1–M4 as true in vivo metabolites, presuming a chromatographic separation of potentially present regioisomeric analogues. Existing doping control methods were expanded and validated according to international guidelines in order to allow for the detection of the carboxy and the alkylhydroxy metabolites, respectively, as urinary markers for the illegal intake of the synthetic cannabinoid JWH-018. Both metabolites were quantified in authentic doping control urine samples that had been suspicious of JWH-018 abuse after routine screening procedures, and a stable isotope-labelled 13C8-15N-carboxy metabolite was synthesised for future analytical applications.

Abstract: A liquid chromatography–high resolution mass spectrometry (LC-HRMS) method for the simultaneous identification and quantification of 28 benzodiazepines, including 6 metabolites, in 50 mg of hair has been validated. Positive ion electrospray ionization and HRMS determination in full-scan mode were realized on an Orbitrap mass spectrometer at a nominal resolving power of 60,000. In-source collisional experiments were conducted to obtain additional information for a more reliable identification of the investigated drugs. HRMS in full-scan mode allowed the exact determination of molecular masses of all analytes eluting in the HPLC run, so that both the immediate and retrospective screening of results for drugs and their metabolites were available. Sample preparation consisted of an overnight incubation in phosphate buffer pH 8.4 and a subsequent liquid/liquid extraction with methylene chloride/diethyl ether (90:10). Gradient elution was performed on a Luna C18 analytical column and four deuterated analogues were used as internal standards (IS). Validation was performed using both spiked hair samples and hair samples from subjects treated with benzodiazepines. Selectivity was evaluated by analysis of 20 certified blank hair samples. Extraction efficiency and matrix effects were evaluated by analysis of true positive samples. The lowest limits of quantification (LLOQs) ranged from 1 to 10 pg/mg. Linearity was investigated in the range from LLOQ to 1,000 pg/mg, for each compound (R2 0.998–0.999). Mean relative errors, calculated at three concentration levels, ranged from 1 to 20% (absolute value). Precision, at concentrations higher than the LLOQs, was always less than 15% expressed as percentage relative standard deviation. After validation, the procedure was applied to real samples collected for clinical and forensic toxicology purposes from subjects who were assumed to have taken benzodiazepines.

Abstract: The gas-phase dissociation reactions of chlorantraniliprole (Rynaxypyr) and cyantraniliprole (Cyazypyr) have been studied in triple-quadrupole, ion trap, and orbitrap mass spectrometers equipped with electrospray and desorption electrospray ion sources, revealing the formation of odd-electron fragment ions, the structures of which were elucidated. The odd-electron fragments were unusually abundant, and their formation is proposed to occur via a tricyclic intermediate. The applicability of the QuEChERS multiresidue method for the quantitation of chlorantraniliprole and cyantraniliprole was also assessed in this study. Four matrices representative of oily, watery, acidic, and dry crop groups were tested, with a targeted limit of quantitation (LOQ) of 0.01 mg/kg. Average recoveries ranged between 87 and 107%, with relative standard deviations (RSD) of ≤ 8%. Linear calibration functions with correlation coefficients r > 0.99 were obtained. The study provides an expansion of the QuEChERS method to include anthranilic diamides and a mass spectrometric assessment for these two novel agrochemical active ingredients.

Abstract: High-resolution mass spectrometry can provide a detailed fingerprint of the composition of the nonvolatile fraction of petroleum. That analysis is typically performed using Fourier transform ion cy...

Abstract: Naphthenic acids are surfactants with the general chemical formula of CnH2n-zO2 in which n is the number of carbon atoms and Z is zero or a negative even number and represents the number of hydrogen atoms lost as the structures become more cyclic. Naphthenic acids and other polar acid compounds are released from bitumen during the mining of oil sands and the processing of bitumen for oil production. Thus, up to 110mg/L of these components are found in the large volumes of oil sands processedwater (OSPW) produced at oil sands operations in Fort McMurray, Alberta, Canada. The large volumes of OSPW must eventually be remediated and natural biodegradation has been reported to be slow. Furthermore, the fate and transport of naphthenic acids and other related components in the acid fraction on OSPW are of toxicological concern in the environment because these compounds have acute aquatic toxicity to a variety of aquatic organisms including fish. Earlier investigations into the bioremediation of naphthenic acids used low-, mediumand ultra-high-resolution electrospray ionization mass spectrometry (ESI-MS) to determine if wetland plants selectively dissipate individual naphthenic acid compounds from Athabasca oil sands naphthenic acid mixtures. For hydroponic systems investigated by Armstrong et al., the characterization of oil sands components was limited to water samples with no determination of components directly in the plant tissue itself. Ultrahigh resolution using Fourier transform ion cyclotron resonance (FTICR)-MS analysis was likewise based on the detailed characterization of water systems. The determination of naphthenic acids in plant tissue presents a significant analytical challenge. Analytical methodologies are required that allow for the resolving and quantification of diagnostic components from structurally and chemically similar natural plant components. Here we report the use of high-resolution mass spectrometry to determine if OSPW acid fraction components can be distinguished from co-extracted plant components. We demonstrate that characteristic polar oil sands components (naphthenic acids and other related acid fraction components, herein indicated by ’NA’) spiked into plant tissue prior to extraction can be differentiated from co-extracted endogenous plant components using an Orbitrap mass spectrometer. We also show that the use of the orbitrap technology allows for the establishment of a linear calibration curve using extracts of plant tissue spiked prior to extraction. An NA standard was prepared as previously described by Rogers et al. and Janfada et al. from OSPW produced as a by-product of an oil sands extraction operation (Fort McMurray, AB, Canada). This standard which is comprised of the acid-extractable components (which includes naphthenic acids) of OSPW, which have been previously characterized by FTICR, was spiked into the tissue of alder saplings (Alnus spp.) obtained from the Athabasca oil sands region of Alberta, Canada, which are under investigation for use in the bioremediation of oil sands tailings. These alder samples were then extracted as outlined in Fig. 1. For ultra-high-resolution mass spectral analysis, 10 mL of ammonium hydroxide (29%) was added to each 1mL of sample extract solution to ensure efficient deprotonation for negative ion ESI analysis. All solvents were HPLC grade (Fisher Scientific, Pittsburgh, PA, USA). Sample solutions (5 mL) were loop injected by use of a Surveyor MS pump (Thermo Fisher Scientific, San Jose, CA, USA) with 50:50 acetonitrile/water containing 0.1% ammonium hydroxide as the eluent at 200 mL/min. The effluent from the liquid chromatograph was coupled directly to a dual pressure linear ion trap-orbitrap mass spectrometer (LTQ Orbitrap Velos, Thermo Fisher Scientific). The mass spectrometer was equipped with an ESI interface that was operated in the negative ion mode. Data were acquired in the full scan mode fromm/z 80 to 600. All observed ions were singly charged and the average mass resolving power (m/Dm50%) was 100 000. To date, there are no published methods for the direct analysis of oil sands NAs in plant tissue. This communication is thus considered to describe a first step toward the full quantification of oil sands acids by demonstrating the identification of NA congeners in alder tissue. Quantitative analyses of complex oil sands mixtures in biota are best based on congener-specific analysis. For a full quantitative method reproducible recoveries should be demonstrated for specific congeners of oil sands components extracted from the plant matrix. The first step towards this goal is the detection of diagnostic oil sands components in plant tissue at Rapid Commun. Mass Spectrom. 2011, 25, 459–462 (wileyonlinelibrary.com) DOI: 10.1002/rcm.4877 Letter to the Editor

Abstract: A selective and sensitive approach, called extraction of product ion (XoPI) method, was developed for the detection of l-glutathione (GSH)-trapped reactive metabolites employing an Orbitrap high resolution mass spectrometer. Fragmentation of GSH conjugates in the negative ion mode leads to a product ion, deprotonated γ-glutamyl-dehydroalanyl-glycine (m/z 272.0888). As a means of utilizing this property, negative ion high resolution MS data were collected from in vitro incubations by monitoring ions from m/z 269.5 to 274.5 under in-source collision-induced dissociation. Extraction of product ions at m/z 272.0888 ± 5 ppm from this data resulted in a chromatogram exhibiting deprotonated γ-glutamyl-dehydroalanyl-glycine as the major peaks with no or very few interferences. Therefore, peaks in this extracted product ion chromatogram potentially came from GSH-trapped reactive metabolites. The GSH conjugate parent ions were then confirmed in the corresponding full scan MS data, and their structures were identifi...

Abstract: Some twenty cultured fish samples were analyzed for possible residues of veterinary drugs with high resolution mass spectrometry (single stage Orbitrap) coupled to ultra performance liquid chromatography. Quantitative analysis based on external standards covered 110 analytes. Some 116 additional compounds were monitored without having access to reference materials. Detection was based on calculated exact masses and narrow mass windows. Furthermore, a number of semi-targeted techniques were evaluated and compared to corresponding triple quadrupole precursor scan experiments. Single stage high resolution mass spectrometry was used to monitor compound specific product ions (without relying on a previous precursor selection). The capabilities of neutral loss searches based on exact masses were shown by detecting small concentrations of incurred oxytetracycline residues. High resolution mass spectrometry provided more sensitivity and selectivity than corresponding tandem quadrupole precursor and neutral loss scans. The currently limiting factor is the not adequate performance of the available software used for data mining. The high number of false positives that were produced, when searching for chlorine isotopic patterns, was clearly linked to the fact that the utilized software does not perform a peak deconvolution, but simply investigates one individual spectrum after another.

Abstract: The plasma proteome holds enormous clinical potential, yet an in-depth analysis of the plasma proteome remains a daunting challenge due to its high complexity and the extremely wide dynamic range in protein concentrations. Furthermore, existing antibody-based approaches for depleting high-abundance proteins are not adaptable to the analysis of the animal plasma proteome, which is often essential for experimental pathology/pharmacology. Here we describe a highly comprehensive method for the investigation of the animal plasma proteome which employs an optimized combinatorial peptide ligand library (CPLL) treatment to reduce the protein concentration dynamic range and a dual-enzyme, dual-activation strategy to achieve high proteomic coverage. The CPLL treatment enriched the lower abundance proteins by >100-fold when the samples were loaded in moderately denaturing conditions with multiple loading-washing cycles. The native and the CPLL-treated plasma were digested in parallel by two enzymes (trypsin and GluC) carrying orthogonal specificities. By performing this differential proteolysis, the proteome coverage is improved where peptides produced by only one enzyme are poorly detectable. Digests were fractionated with high-resolution strong cation exchange chromatography and then resolved on a long, heated nano liquid chromatography column. MS analysis was performed on a linear triple quadrupole/orbitrap with two complementary activation methods (collisionally induced dissociation (CID) and electron transfer dissociation). We applied this optimized strategy to investigate the plasma proteome from swine, a prominent animal model for cardiovascular diseases (CVDs). This large-scale analysis results in identification of a total of 3421 unique proteins, spanning a concentration range of 9-10 orders of magnitude. The proteins were identified under a set of commonly accepted criteria, including a precursor mass error of <15 ppm, Xcorr cutoffs, and ≥2 unique peptides at a peptide probability of ≥95% and a protein probability of ≥99%, and the peptide false-positive rate of the data set was 1.8% as estimated by searching the reversed database. CPLL treatment resulted in 55% more identified proteins over those from native plasma; moreover, compared with using only trypsin and CID, the dual-enzyme/activation approach enabled the identification of 2.6-fold more proteins and substantially higher sequence coverage for most individual proteins. Further analysis revealed 657 proteins as significantly associated with CVDs (p < 0.05), which constitute five CVD-related pathways. This study represents the first in-depth investigation of a nonhuman plasma proteome, and the strategy developed here is adaptable to the comprehensive analysis of other highly complex proteomes.

Abstract: A method based on LC-ESI-high-resolution (HR)-MS analysis, using a single-stage Orbitrap mass spectrometer, was developed for the quantification of casein allergens potentially present in white wines as a result of fining by caseinate. The method consists of (1) extraction from the matrix by ultrafiltration, (2) digestion with trypsin and (3) detection/quantification of residual caseins, obtained by monitoring the LC-MS response of representative tryptic peptides (peak areas in extracted-ion chromatograms). Method linearity was assessed first on caseinate solutions prepared either in water or in wine matrix (the ultrafiltration residue of a protein-free white wine). Limits of detection (LOD) ranged from 0.1 to 0.3 µg ml−1 (S/N = 3) in water, and between 0.15 and 0.7 µg ml−1 in wine matrix, depending on the selected peptide. Method repeatability and reproducibility, measured as response variability (standard deviation) due to LC-MS analysis alone and to both enzymatic digestion and LC-MS analysis, were ass...