MS-MS Spectra Research Articles

Detection and Identification of Leachables in Vaccine from Plastic Packaging Materials Using UPLC-QTOF MS with Self-Built Polymer Additives Library.

The direct contact of plastic parts with the medical products raises the possibility that plastic-related contaminants (leachables) may be present in the finished medical product. The leachable components from plastic materials may impact the safety and efficacy of the final medical product, so identification and determination of the leachables are essential for the safety assessment of medical products. A method to identify main leachables-polymer additives in medical products was developed by ultraperformance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UPLC-QTOF MS) and a self-built library. The library contains 174 additives and the information on their names, formulas, structures, retention times, fragments, classifications, origin, and corresponding MS(E) and MSMS spectra. The reliability of the construction process of the library was guaranteed by the system stability and suitability test. Identification parameters of library application, such as mass error, retention times, fragments, and isotope pattern, were evaluated. Leachables in real vaccine and the intermediates were identified using automatic library searching. In vaccine, the peak m/z 239.0887 that could not be assigned by the library was identified as dimethyl 2-hydroxy-1,3-cyclohexanedicarboxylate using a series of elucidation tools. As a result, the concentrations of leachables in vaccine and the intermediates ranged from 0.85 to 21.91 μg/L.

Atractylosides, chlorogenic acids and antioxidant capacity of raw Arabica green coffee beans (AGCB) used by regular and spontaneous dieters to supports body weight loss and slimming

Using DPPH, ABTS and Folin-Ciocalteu procedures [1] the antioxidant capacity was characterized of fresh infusions of the raw AGCB distributed in Poland and originating from Central and South America. Next, UHPLC-TOF-MS/MS analyses of all infusions and MeOH extracts of raw AGCB were made using a Waters ACQUITY UPLC TabMode system interfaced with a Bruker microOTOF-Q mass spectrometer with an ESI source operating in negative mode at 150 °C and 4.5 kV with N2 nebulisation at 1.2 bar and a dry gas flow at 6 mL/min. An Agilent Poroshell 120EC-C18 column (2.1 × 150, 2.7 µm) was used operating at 0.6 mL/min flow rate with a mobile phase consisted of a linear gradient of 0.1% formic acid in water (A) and 0.1% formic acid in AcN (B), mixed by increasing eluate B in the range 5 – 90% from 0 – 20 min and followed by a split of column effluent flow 3:2 before the ESI ion source was used. MSMS spectra were analyzed with a Bruker Compass Data Analyzer v.4. The atractyligenin derivatives, i.e. 2-O-beta-D-glucopyranosyl-carboxyatractyligenin (m/z 525) (1), 2-O-(2'-O-isovaleryl-beta-D-glucopyranosyl)-carboxyatractyligenin (m/z 608) (2) and 3'-O-beta-D-glucopyranosyl-2'-O-isovaleryl-2-beta-(2-desoxy-carboxyatractyligenin)-beta-D-glucopyranoside (m/z 771) (3), were identified in the MeOH extracts of the raw but not milled AGCB from Colombia. Only compound 1 with a high inhibitory activity of adenine nucleotide translocase (ANT) [2] was confirmed by MSMS in the infusions of this AGCB sample. This indicates that some atractylosides in raw AGCB were hydrolyzed by hydrothermal treatment [3]. Compounds 1 and 3 with, respectively, significant and non-significant ANT inhibition were recently detected in the AGCB [2], but glucoside 2 was identified here for the first time.

Speciation of the Potential Antitumor Agent Vanadocene Dichloride in the Blood Plasma and Model Systems.

The speciation of the potential antitumor agent vanadocene dichloride ([Cp2VCl2], abbreviated with VDC) in the blood plasma was studied by instrumental (EPR, ESI-MS, MS-MS, and electronic absorption spectroscopy) and computational (DFT) methods. The behavior of VDC at pH 7.4 in aqueous solution, the interaction with the most important bioligands of the plasma (oxalate, carbonate, phosphate, lactate, citrate, histidine, and glycine among those with low molecular mass and transferrin and albumin between the proteins) was evaluated. The results suggest that [Cp2VCl2] transforms at physiological pH to [Cp2V(OH)2] and that only oxalate, carbonate, phosphate, and lactate are able to displace the two OH(-) ions to yield [Cp2V(ox)], [Cp2V(CO3)], [Cp2V(lactH(-1))], and [Cp2V(HPO4)]. The formation of the adducts with oxalate, carbonate, lactate, and hydrogen phosphate was confirmed also by ESI-MS and MS-MS spectra. The stability order is [Cp2V(ox)] ≫ [Cp2V(CO3)] > [Cp2V(lactH(-1))] > [Cp2V(HPO4)]. No interaction between VDC and plasma proteins was detected under our experimental conditions. Several model systems containing the bioligands (bL) in the same relative ratio as in the blood samples were also examined. Finally, the speciation of VDC in the plasma was studied. The results obtained show that the model systems behave as the blood plasma and indicate that when V concentration is low (10 μM) VDC is transported in the bloodstream as [Cp2V(ox)]; when V concentration is high (100 μM) oxalate binds only 9.2 μM of [Cp2V](2+), whereas the remaining part distributes between [Cp2V(CO3)] (main species) and [Cp2V(lactH(-1))] (minor species); and when V concentration is in the range 10-100 μM [Cp2V](2+) distributes between [Cp2V(ox)] and [Cp2V(CO3)].

Flavonoids and Hydroxycinnamic Acids from Leonurus quinquelobatus

Little information is available in the literature on the composition and contents of phenolic compounds in Leonurus quinquilobatus Gilib. A coumaroylapigenin glycoside was isolated and called quinqueloside [1]. Plants of other species of the genus Leonurus L. contained 8-hydroxyflavone 7-allosylglucoside, p-coumaroylglucoside, quercetin, rutin, hyperoside, epicatechin, procyanidin B2, quercetin-3-O-[3,4-hydroxy-3,5-dimethoxybenzyl-L-rhamnopyranosyl]-D-galactopyranoside, quercetin-3-O-arabinoside, isoquercitrin, hyperoside, apigenin, genkwanin, quercetin-O-hexosylhexoside, quercetin-Odeoxyhexosylhexoside [2–10], leonuriside A and B, lavandulifolioside and verbascoside, leucosceptoside A, eugenylrutinoside, and kaempferol-3-O-glucoside [10, 11] and ferulic, caffeic, and chlorogenic acids [10, 12–15]. The goal of the present work was to define the composition of phenolic compounds in L. quinquelobatus grown in western Siberia. HPLC-MS analysis used an Agilent 1200 SL liquid chromatograph (with a diode-matrix detector) and a Bruker micrOTOFQ hybrid quadrupole–time-of-flight mass spectrometer. The herb (medicinal raw material) of L. quinquilobatus growing in the three western Siberian regions: Novosibirsk, Kemerovo, and Kamlak village (Gornyi Altai) was studied. Raw material was collected in early July (flowering of lower verticils) according to requirements of the State Pharmacopoeia (1990) and extracted with aqueous EtOH (70%) [16, 17]. An aliquot was passed through a Diapak C16 cartridge and eluted with MeOH. The sample was analyzed by reversed-phase HPLC-MS with elution by HCOOH (2%)–MeOH with a stepped gradient using a Zorbax SB-C18 column (2.1 150 mm, 3.5 m) at 25°C and flow rate 0.2 mL/min. Chromatograms were recorded at 340 50 nm. Electrospray ionization (ESI) used 2 bar, 8 L/min, 240°C; 4 kV, m/z 100–1200; and mass accuracy 0.01 Da. MS-MS spectra were obtained at 20 and 40 eV. The qualitative compositions of extracts of raw material from the various regions did not differ. Nine principal constituents were detected. Comparison with a mixture of standards identified in the extracts chlorogenic acid and rutin. The other compounds were identified using UV and mass spectra. Chlorogenic (caffeoylquinic) acid (1), tR 16.9 min, C7H11O6 –. The UV spectrum was identical to that of the standard. Ester of caffeic and malic acids (2), tR 20.8 min, C13H12O8, MW 296.053 Da (MeOH, max = 330 nm, 304sh nm). The UV spectrum was similar to that of chlorogenic acid but shifted by 4 nm. The MS-MS spectrum had three fragment ions at 179 (caffeic acid anion, C9H7O4 –), 135 (loss of CO2 from caffeic acid anion, [C9H7O4 – CO2] –), and 133 (malic acid anion, C4H5O5 –). Tetrosodipentoside of caffeoylquinic acid (3), tR 22.5 min. UV spectrum (MeOH, max = 332 nm, 304sh nm). C30H44O22. MW 756.228 Da [M – H] – 755. MS-MS spectrum m/z: 461, 315, 297; 191 (quinic acid anion); 179 (caffeic acid anion); 161 (fragment ion C9H5O3 –, [X – ROH – H+]–, formed by decomposition of caffeic acid derivative [X – H+]–, where X = [C9H7O3 – O – R]); and 135 (fragment ion after loss of CO2 from caffeic acid anion); 133 (fragment ion after loss of CO from the anion with m/z 161). The difference of m/z values for anions of this derivative (755) and caffeoylquinic acid (353) was 402, which corresponded to the trisaccharide C14(H2O)13, a dipentosotetrose.

Interpretation of Tandem Mass Spectrometry (MSMS) Spectra for Peptide Analysis.

The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines we demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus is on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides.

Ultra-performance liquid chromatography quadrupole time-of-flight MS for identification of electron beam from accelerator degradation products of aflatoxin B1.

Electron beam irradiation was proven to be a successful method in aflatoxin degradation in earlier researches. However, the exact nature of the result radiation products generated by the aflatoxins remains unknown. Based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF MS) analysis, the solution of aflatoxin B1 (AFB1) in acetonitrile irradiated by electron beam degraded to two kinds of major products. The doses employed were in the range of 0 (control) to 8.60 kGy. The absorbed doses were monitored with FWT-60-00 radio-chromic dosimeters. By using UPLC-Q-TOF MS, accurate masses and proposed molecular formula for the degradation products, 261.1233 m/z (C14H13O5) and 299.1104 m/z (C17H15O5), were obtained from low mass error and high matching properties. Structural formula for the radio-degradation products and the degradation pathways leading to the compounds were proposed, based on the molecular formula and MS-MS spectra. The results showed that electron beam (EB) irradiation is an effective method for degrading AFB1.

Transformation of methadone and its main human metabolite, 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP), during water chlorination

The reaction kinetics and reaction pathway of methadone and its main human metabolite, 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP) in chlorine containing waters were investigated by direct injection of individual reaction time aliquots in a liquid chromatography-quadrupole-time-of-flight-mass spectrometry (LC-QTOF-MS) system. Factors potentially affecting the rate of the reaction were evaluated in detail by means of a Box-Behnken experimental design in which methadone and EDDP were considered separately. Sample pH and chlorine concentration turned out to be the two significant variables, enhancing the kinetics with an increase in their values. Transformation products (TPs) were first searched over sample chromatograms by comparing control, blank and time zero samples to aliquots stopped at different reaction times. Their tentative identity was further inferred by generating their empirical formulae from their accurate single MS spectra and, subsequently, by interpreting their fragmentation pattern from their tandem MS (MS/MS) spectra. In total, 8 TPs, arising from intra-molecular cyclation, dehydrogenation, oxidation and chlorination, could be detected in the case of methadone, one of them being the EDDP and another 3 coming from EDDP, so being common to both the precursor drug and its metabolite. A tentative transformation pathway was proposed, and the reaction was evaluated under potential real circumstances by chlorinating two different river samples. In this way, it was possible to demonstrate that its extension is highly affected by the content of dissolved organic matter, so both compounds were highly or completely transformed in samples with a low anthropogenic impact, whereas they were considerably more stable in waters with a high concentration of organic matter. Finally, the ecotoxicity of precursors and transformation species was predicted by software tools, revealing that, in some cases, the toxicological responses displayed by the TPs were up to 100 times higher than those of methadone.

Improved high sensitivity analysis of polyphenols and their metabolites by nano-liquid chromatography–mass spectrometry

This study was conducted to assess the value of a high resolution, high mass accuracy time-of-flight analyzer in combination with nanoliquid chromatography for the analysis of polyphenols and their metabolites. The goal was to create a method that utilizes small volumes of biological fluids and provides a significant improvement in sensitivity compared with existing methods. Accordingly, nanoLC–MS and nanoLC-pseudo-multiple reaction monitoring (MRM) methods were developed that had a lower limit of quantification of 0.5nM for several polyphenols and were linear over 2–3 orders of magnitude (R2>0.999). Using urine samples, the ability to observe and quantify polyphenols in such a complex biological fluid depended on much narrower mass windows (0.050amu or less) on a TOF analyzer than those used on a quadrupole analyzer (0.7amu). Although a greater selectivity was possible with the low mass resolution of a triple quadrupole instrument using the MRM approach, for the daidzein metabolite O-DMA, a chromatographically resolvable second peak could only be substantially reduced by using a 0.01amu mass window. The advantage of a TOF analyzer for product ion data is that the whole MSMS spectrum is collected at high mass accuracy and MRM experiments are conducted in silico after the analysis.

Detection of cresyl phosphate-modified butyrylcholinesterase in human plasma for chemical exposure associated with aerotoxic syndrome

Flight crews complain of illness following a fume event in aircraft. A chemical in jet engine oil, the neurotoxicant tri-o-cresyl phosphate, after metabolic activation to cresyl saligenin phosphate makes a covalent adduct on butyrylcholinesterase (BChE). We developed a mass spectrometry method for detection of the cresyl phosphate adduct on human BChE as an indicator of exposure. Monoclonal mAb2, whose amino acid sequence is provided, was crosslinked to cyanogen bromide-activated Sepharose 4B and used to immunopurify plasma BChE treated with cresyl saligenin phosphate. BChE was released with acetic acid, digested with pepsin, and analyzed by liquid chromatography–tandem mass spectrometry (LC–MSMS) on the Triple TOF 5600 mass spectrometer. Peptide FGES198AGAAS with an added mass of 170Da from cresyl phosphate on serine 198 (Ser198) was detected as parent ion 966.4Da. When characteristic daughter ions were monitored in the MSMS spectrum, the limit of detection was 0.1% cresyl saligenin phosphate inhibited plasma BChE. This corresponds to 2×10–9g in 0.5ml or 23×10–15moles of inhibited BChE in 0.5ml of plasma. In conclusion, a sensitive assay for exposure to tri-o-cresyl phosphate was developed. Laboratories that plan to use this method are cautioned that a positive result gives no proof that tri-o-cresyl phosphate is toxic at low levels.

Proteomic Analysis of Purified Dog Cardiac Sacroplasmic Reticulum Membrane Subcompartments

Ca2+ homeostasis primarily involves two major morphological subdivisions of the sarcoplasmic reticulum (SR): junctional (jSR) cisterna that appose sarcolemma, and free (fSR) tubules surrounding myofilaments. Biochemical isolation of jSR and fSR membranes involves selective increases in density of SR membrane vesicles using the SR Ca2+ pump (SERCA2a) (Jones and Cala, J. Biol. Chem. 1981). The purpose of the current study was to comprehensively characterize cardiac SR subproteomes. Purified SR membranes were solubilized, trypsinized and analyzed by LC-MS/MS on a LTQ-XL mass spectrometer. Abundant species were fragmented with collision-induced dissociation (CID). Data analysis was performed using Proteome Discoverer 1.1 (Thermo) which incorporated the Mascot algorithm (Matrix Science). In replicate experiments, a total of 199 junctional SR and 191 free SR proteins were identified from 16,344 MSMS spectra with protein false discovery rate (FDR) at 0.8% and peptide FDR at 0.0%. SERCA2a was the most abundant protein in both fractions, as expected, and virtually all of the known cardiac SR proteins were also identified. In jSR, the major 4 components of the Ca2+-release complex were found exclusively, including calsequestrin-2, ryanodine receptor 2 and 3, triadin, and junctin. Another 57 proteins were also identified as specific to this subcompartment. In fSR, 53 proteins were exclusively identified. Relative enrichments in one of the SR subcompartments were found for an additional 86 proteins, and 52 additional proteins were identified in the cardiac SR, without obvious subcompartment origin. SR proteins that showed less specificity were mitochondrial proteins (more enriched in the lower-density jSR), ER chaperones (roughly evenly distributed), lipid-metabolizing enzymes, and filamentous proteins. Proteomic analyses of classical cardiac SR subfractions extends our understanding of the cardiac secretory compartments, and serves as foundation for future exploration and understanding of cardiac cell biology.

Understanding collision-induced dissociation of dofetilide: a case study in the application of density functional theory as an aid to mass spectral interpretation

Fragmentation of molecules under collision-induced dissociation (CID) conditions is not well-understood. This may make interpretation of MSMS spectra difficult and limit the effectiveness of software tools intended to aid mass spectral interpretation. Density Functional Theory (DFT) has been successfully applied to explain the thermodynamics of fragmentation in the gas phase by the modelling the effect that protonation has on the bond lengths (and hence bond strengths). In this study, dofetilide and four methylated analogues were used to investigate further the potential for using DFT to understand and predict the CID fragmentation routes. The products ions present in the CID spectra of all five compounds were consistent with charge-directed fragmentation, with protonation adjacent to the cleavage site being required to initiate fragmentation. Protonation at the dissociative site may have occurred either directly or via proton migration. A correlation was observed between protonation-induced bond lengthening and the bonds which were observed to break in the CID spectra. This correlation was quantitative in that the bonds calculated to elongate to the greatest extent gave rise to the most abundant of the major product ions. Thus such quantum calculations may offer the potential for contributing to a predictive tool for aiding the accuracy and speed mass spectral interpretation by generating numerical data in the form of bond length increases to act as descriptors flagging potential bond cleavages.

Evaluating the challenges associated with time-of-fight secondary ion mass spectrometry for metabolomics using pure and mixed metabolites

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is potentially well placed to contribute to metabolomic analysis while bringing the added benefit of high resolution, label free imaging. The focused ion beams used to desorb species from the sample can be focused below 1 μm allowing chemical imaging on a sub-cellular scale. In this study we test the capability of ToF-SIMS to generate mass spectrometry and MSMS spectra from a set of standard metabolites that can be compared with open access metabolite databases containing ESI-CID MSMS spectra. The influence of the chemical environment, the matrix effect, on the observed mass spectra is assessed using a mixed metabolite sample and the data discussed in terms of compound identification and quantification. Radical ions and small fragment ions seem to be less sensitive to ion suppression or enhancement and may provide a route to quantification. Understanding such parameters will be key for the successful application of the technique for in situ metabolomics with ToF-SIMS.

Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide

BackgroundCurrently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations.MethodsMSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds.ResultsWe were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation.ConclusionsThese results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification.

Fragmentation of toxicologically relevant drugs in negative‐ion liquid chromatography–tandem mass spectrometry

Negative-ion LC-MS analysis of drugs is applied far less frequently than positive-ion LC-MS. Data on the interpretation of negative-ion MS-MS spectra are even more scarce. Therefore, following the recent review on the class-specific fragmentation of toxicologically relevant compounds in positive-ion MS-MS, it was decided to perform a similar study in negative-ion MS-MS. To this end, a set of over 500 negative-ion MS-MS spectra was collected from three libraries applied in toxicological general unknown screening and systematic toxicological analysis. The compounds involved were classified by chemical and therapeutic class. The MS-MS spectra were manually interpreted and relevant interpretation data were searched for in the scientific literature. The emphasis in the discussion is on class-specific fragmentation, because discussing fragmentation of all individual compounds would take far too much space. Negative-ion MS-MS fragmentation is discussed for a wide variety of toxicologically relevant compounds, including dihydropyridine calcium channel blockers, diuretics, barbiturates, anti-inflammatory drugs, anti-diabetics, sulfonamide and betalactam antibiotics, and a number of classes of pesticides.

Doped silica nanoparticles for the detection of pharmaceutical terbinafine in latent fingerprints by mass spectrometry

A detailed study on terbinafine excretion in latent fingerprints of a patient prescribed with the medication was carried out for a period of 14 days. Latent fingerprints collected from the patient were dusted with a fingerprint developing agent consisting of magnetized carbon black doped silica nanoparticles and directly analyzed by surface assisted laser desorption ionization-time of flight-mass spectrometry (SALDI-TOF-MS). MS and MSMS spectra of the latent fingerprints confirmed the presence of terbinafine, with the parent ion at m/z 292 and the fragment ion at m/z 141. Coupled with imaging, a gradual increment in the amount of terbinafine detected on the latent fingerprints from day 0 to day 14 was observed. When compared against commonly used 2,5-dihydroxybenzoic acid (DHB), these nanoparticles were more effective as a matrix for MS analysis of terbinafine, recording improved signal-to-noise values. The results demonstrate the efficacy of this technique for the detection of exogenous pharmaceutical drugs in latent fingerprints, providing information pertaining to the donor which may prove useful in cases of smudged prints.

Molecular mass spectrometric identification of superoxide dismutase in the liver of mice Mus musculus and Mus spretus using a metallomics analytical approach

This paper reports the identification and quantification of superoxide dismutase in the liver of Mus musculus and Mus spretus mice using a metallomics analytical approach. The approach consisted of using orthogonal chromatographic systems coupled to ICP-MS and UV detectors. Size-exclusion fractionation of the cytosolic extracts was followed by anion-exchange chromatographic separation of Cu- and Zn-containing species. After purification then tryptic digestion, Cu- and Zn-containing superoxide dismutase was identified by nESI-QqTOF. The MS-MS spectra of doubly charged peptides, with the Mascot searching engine, were used to obtain the sequence of the protein.

The Acylation State of Surface Lipoproteins of Mollicute Acholeplasma laidlawii

Acylation of the N-terminal Cys residue is an essential, ubiquitous, and uniquely bacterial posttranslational modification that allows anchoring of proteins to the lipid membrane. In gram-negative bacteria, acylation proceeds through three sequential steps requiring lipoprotein diacylglyceryltransferase, lipoprotein signal peptidase, and finally lipoprotein N-acyltransferase. The apparent lack of genes coding for recognizable homologs of lipoprotein N-acyltransferase in gram-positive bacteria and Mollicutes suggests that the final step of the protein acylation process may be absent in these organisms. In this work, we monitored the acylation state of eight major lipoproteins of the mollicute Acholeplasma laidlawii using a combination of standard two-dimensional gel electrophoresis protein separation, blotting to nitrocellulose membranes, and MALDI-MS identification of modified N-terminal tryptic peptides. We show that for each A. laidlawii lipoprotein studied a third fatty acid in an amide linkage on the N-terminal Cys residue is present, whereas diacylated species were not detected. The result thus proves that A. laidlawii encodes a lipoprotein N-acyltransferase activity. We hypothesize that N-acyltransferases encoded by genes non-homologous to N-acyltransferases of gram-negative bacteria are also present in other mollicutes and gram-positive bacteria.

Fragmentation of toxicologically relevant drugs in positive‐ion liquid chromatography–tandem mass spectrometry

The identification of drugs and related compounds by LC-MS-MS is an important analytical challenge in several application areas, including clinical and forensic toxicology, doping control analysis, and environmental analysis. Although target-compound based analytical strategies are most frequently applied, at some point the information content of the MS-MS spectra becomes relevant. In this article, the positive-ion MS-MS spectra of a wide variety of drugs and related substances are discussed. Starting point was an MS-MS mass spectral library of toxicologically relevant compounds, available on the internet. The positive-ion MS-MS spectra of ∼570 compounds were interpreted by chemical and therapeutic class, thus involving a wide variety of drug compound classes, such benzodiazepines, beta-blockers, angiotensin-converting enzyme inhibitors, phenothiazines, dihydropyridine calcium channel blockers, diuretics, local anesthetics, vasodilators, as well as various subclasses of anti-diabetic, antidepressant, analgesic, and antihistaminic drugs. In addition, the scientific literature was searched for available MS-MS data of these compound classes and the interpretation thereof. The results of this elaborate study are presented in this article. For each individual compound class, the emphasis is on class-specific fragmentation, as discussing fragmentation of all individual compounds would take far too much space. The recognition of class-specific fragmentation may be quite informative in determining the compound class of a specific unknown, which may further help in the identification. In addition, knowledge on (class-specific) fragmentation may further help in the optimization of the selectivity in targeted analytical approaches of compounds of one particular class.

MzServer: Web-based Programmatic Access for Mass Spectrometry Data Analysis

Continued progress toward systematic generation of large-scale and comprehensive proteomics data in the context of biomedical research will create project-level data sets of unprecedented size and ultimately overwhelm current practices for results validation that are based on distribution of native or surrogate mass spectrometry files. Moreover, the majority of proteomics studies leverage discovery-mode MS/MS analyses, rendering associated data-reduction efforts incomplete at best, and essentially ensuring future demand for re-analysis of data as new biological and technical information become available. Based on these observations, we propose to move beyond the sharing of interpreted spectra, or even the distribution of data at the individual file or project level, to a system much like that used in high-energy physics and astronomy, whereby raw data are made programmatically accessible at the site of acquisition. Toward this end we have developed a web-based server (mzServer), which exposes our common API (mzAPI) through very intuitive (RESTful) uniform resource locators (URL) and provides remote data access and analysis capabilities to the research community. Our prototype mzServer provides a model for lab-based and community-wide data access and analysis.

Interpretation of ESI(+)-MS-MS spectra—Towards the identification of “unknowns”

We report a systematic empirical investigation of ESI(+)-MS-MS dissociation pathways of over 1000 spectra of small organic compounds, containing more than 30 chemical functional groups. The dissociation processes of the protonated molecular ions were explored and interpretated. We derived typical basic fragmentation channels for individual functional groups and established a unified set of fragmentation rules. Multiple bond cleavages of molecules containing single and multiple functional groups were explored as well and the corresponding fragmentation rules were derived. Applying these rules enabled to match between proposed chemical structures and an ESI(+)-MS-MS spectrum of an “unknown”. Comparison to EI fragmentation routes was also carried out. Despite the general dissimilarity between ESI(+)-MS-MS and EI-MS spectra, we exploit the minor similarities between the spectra, and utilizing NIST-EI database and search option, can be successfully reduced the number of proposed structures. The two step methodology developed here is demonstrated and evaluated in the identification of various “unknowns”.