Analysis Of Mass Spectral Data Research Articles

Automated Analysis of Mass Spectral Data Using Fuzzy Logic Classification

Automation of the instrument has also been described in the literature. It includes a Fuzzy-logic inference engine that color codes ‘pixels’ according to classification. A user friendly graphical interface (Figure 2) allows the user to check the cursor from one spot to the next; the user can see the line spectrum the inference engine used to generate that pixel. Data can then be displayed directly in the program or exported in formats compatible with commercial graphics programs.

Automated Analysis of Mass Spectral Data Using Fuzzy Logic Classification

Automated Analysis of Mass Spectral Data Using Fuzzy Logic Classification

Isolation and antifungal and antioomycete activities of aerugine produced by Pseudomonas fluorescens strain MM-B16.

The bacterial strain MM-B16, which showed strong antifungal and antioomycete activity against some plant pathogens, was isolated from a mountain forest soil in Korea. Based on the physiological and biochemical characteristics and 16S ribosomal DNA sequence analysis, the bacterial strain MM-B16 was identical to Pseudomonas fluorescens. An antibiotic active against Colletotrichum orbiculare and Phytophthora capsici in vitro and in vivo was isolated from the culture filtrates of P. fluorescens strain MM-B16 using various chromatographic procedures. The molecular formula of the antibiotic was deduced to be C(10)H(11)NO(2)S (M(+), m/z 209.0513) by analysis of electron impact mass spectral data. Based on the nuclear magnetic resonance and infrared spectral data, the antibiotic was confirmed to have the structure of a thiazoline derivative, aerugine [4-hydroxymethyl-2-(2-hydroxyphenyl)-2-thiazoline]. C. orbiculare, P. capsici, and Pythium ultimum were most sensitive to aerugine (MICs for these organisms were approximately 10 micro g ml(-1)). However, no antimicrobial activity was found against yeasts and bacteria even at concentrations of more than 100 micro g ml(-1). Treatment with aerugine exhibited a significantly high protective activity against development of phytophthora disease on pepper and anthracnose on cucumber. However, the control efficacy of aerugine against the diseases was in general somewhat less than that of the commercial fungicides metalaxyl and chlorothalonil. This is the first study to isolate aerugine from P. fluorescens and demonstrate its in vitro and in vivo antifungal and antioomycete activities against C. orbiculare and P. capsici.

Facile syntheses and antimicrobial studies of 6-(aryloxy/arylthio/chloroethoxy)-2,10-dichloro-4,8-dinitro-12-trichloromemyl-12H-dibenzo[d,g][13,2]dioxaphosphocin 6-oxides

Synthesis of several novel 6-aryloxy/arylmio/chloroethoxy-2,10-dichloro-4,8-dinitro-12-trichloro-memyl-12H-dibenzo[d,g][1,3,2]dioxaphosphocin 6-oxides (4a-k) was accomplished by reacting 2,2-bis (2-hydroxy-5-chloro-3-nitrophenyl)-1,1,1-trichloroethane 2 with different aryl phosphorodichloridates (3a-g) and O-2-chloroethyl phosphoryldichloride (3h) in the presence of triethylamine in dry toluene at 60–65 °C. Actually some of these compounds were prepared by reacting monochloride 5 resulting from the condensation of phosphorus oxychloride with 2 in situ, with different phenols and thiophenols. The chemical structures were confirmed by elemental, ir and 1H, 13C, 31P nmr and mass spectral data analyses. These compounds were screened for antifungal activity against Aspergillus flavus, Alternaria alternata, Fusarium solani, Curvularia lunata and Pyricularia oryzae and antibacterial activity on Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Pseudomonas syringae and Klebsiella pneumoniae. Some of them possessed significant activity.

Detection of five new hydroxyl analogues of azaspiracids in shellfish using multiple tandem mass spectrometry

The polyether dinoflagellate toxins, azaspiracids, are responsible for azaspiracid poisoning (AZP), a new human toxic syndrome arising from the consumption of shellfish. To date, five azaspiracids have been isolated and fully structurally elucidated, including, AZA1, its 8-methyl and 22-demethyl analogues, AZA2 and AZA3, respectively, and two hydroxyl derivatives of AZA3, named AZA4 and AZA5. Using a recently developed method involving liquid chromatography with multiple tandem mass spectrometry (LC–MS n ), five new azaspiracids, AZA7–AZA11, have been found in mussels ( Mytilus edulis). AZA6 is a positional isomer of AZA1 and four of the new compounds are isomers with a mass of 857.5 amu. AZA7 and AZA8 are hydroxyl analogues of AZA1 while AZA9 and AZA10 are hydroxyl analogues of AZA6. AZA11 is a hydroxyl analogue of AZA2. The separation of all 11 azaspiracids was achieved using isocratic reversed phase liquid chromatography using a combination of eluent additives, trifluoroacetic acid and ammonium acetate. The ion-trap MS experiments, with electrospray ionisation, involved the fragmentation of the protonated molecule [M+H] +, trapping and fragmenting the product ions due to the loss of a water molecule [M+H–H 2O] +, together with mass spectral data analysis that included the characteristic A-ring fragmentation for each compound.

Characterization of amino acid side chain losses in electron capture dissociation

We have used electrospray ionization (ESI) Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry to characterize amino acid side chain losses observed during electron capture dissociation (ECD) of ten 7- to 14-mer peptides. Side-chain cleavages were observed for arginine, histidine, asparagine or glutamine, methionine, and lysine residues. All peptides containing an arginine, histidine, asparagine or glutamine showed the losses associated with that residue. Methionine side-chain loss was observed for doubly-protonated bombesin. Lysine side-chain loss was observed for triply-protonated dynorphin A fragment 1–13 but not for the doubly-protonated ion. The proximity of arginine to a methoxy C-terminal group significantly enhances the extent of side-chain fragmentation. Fragment ions associated with side-chain losses were comparable in abundance to those resulting from backbone cleavage in all cases. In the ECD spectrum of one peptide, the major product was due to fragmentation within an arginine side chain. Our results suggest that cleavages within side chains should be taken into account in analysis of ECD mass spectral data. Losses from arginine, histidine, and asparigine/glutamine can be used to ascertain their presence, as in the analysis of unknown peptides, particularly those with non-linear structures.

Mechanistic insight into the inactivation of carboxypeptidase A by alpha-benzyl-2-oxo-1,3-oxazolidine-4-acetic acid, a novel type of irreversible inhibitor for carboxypeptidase A with no stereospecificity.

On the basis of the active site topology and enzymic catalytic mechanism of carboxypeptidase A (CPA), a prototypical zinc-containing proteolytic enzyme, alpha-benzyl-2-oxo-1,3-oxazolidine-4-acetic acid (1), was designed as a novel type of mechanism-based inactivator of the enzyme. All four possible stereoisomers of the inhibitor were synthesized in an enantiomerically pure form starting with optically active aspartic acid, and their CPA inhibitory activities were evaluated to find that surprisingly all of the four stereoisomers inhibit CPA in a time dependent manner. The inhibited enzyme did not regain its enzymic activity upon dialysis. The inactivations were prevented by 2-benzylsuccinic acid, a competitive inhibitor that is known to bind the active site of the enzyme. These kinetic results strongly support that the inactivators attach covalently to the enzyme at the active site. The analysis of ESI mass spectral data of the inactivated CPA ascertained the conclusion from the kinetic results. The values of second-order inhibitory rate constants (k(obs)/[I](o)) fall in the range of 1.7-3.6 M(-1) min(-1). The lack of stereospecificity shown in the inactivation led us to propose that the ring cleavage occurs by the nucleophilic attack at the 2-position rather than at the 5-position and the ring opening takes place in an addition-elimination mechanism. The tetrahedral transition state that would be generated in this pathway is thought to be stabilized by the active site zinc ion, which was supported by the PM3 semiemprical calculations. In addition, alpha-benzyl-2-oxo-1,3-oxazolidine-5-acetic acid (18), a structural isomer of 1 was also found to inactivate CPA in an irreversible manner, reinforcing the nucleophilic addition-elimination mechanism. The present study demonstrates that the transition state for the inactivation pathway plays a critical role in determining stereochemistry of the inactivation.

Using an ion-trap MS sensor to differentiate and identify individual components in grapefruit juice headspace volatiles.

An ion-trap mass spectrometer chemical sensor has been utilized to differentiate between grapefruit juices that differ only in the concentration of a single component, and the sensor was able to identify that component. Grapefruit juice was fortified with 40 to 2000 ppm vanillin, a low-level naturally occurring compound in citrus juices. Principal components analysis and discriminant analysis of mass spectral data (m/z 50-200) provided clear separation of the grapefruit juice samples. Vanillin was observed in the juice headspace at the 40 ppm level, with identification possible at the 100 ppm level using either MS or MS/MS.

Two antifeedant lignans from the freshwater macrophyte Saururus cernuus

Two diarylbutane derivatives of dihydroguaiaretic acid have been isolated from emergent portions of the southeastern United States freshwater angiosperm Saururus cernuus L. (Saururaceae). Bioassay-guided fractionation of organic extracts of S. cernuus led to the compounds, sauriols A and B, in addition to five previously known lignoids. These metabolites deter feeding by the omnivorous crayfish Procambarus clarkii. The two lignans were identified by analysis of nuclear magnetic resonance and mass spectral data, and by comparison with spectral data of dihydroguaiaretic acid.

Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and e-mailing of high-resolution exact-mass electrospray ionization mass spectral data

A system has been designed to automatically acquire high-resolution (>50,000 FWHM), exact-mass (mass measurement error ≤3 mmu) electrospray ionization mass spectra with a commercial Fourier transform ion cyclotron resonance mass spectrometer equipped with a high-field (9.4 tesla) superconducting magnet and a commercial autosampler. Upon the injection of each individual sample, the autosampler transmits a contact closure signal to the previously tuned and calibrated mass spectrometer to initiate data acquisition. A software package was designed to run off-line and to accept a sample list with input information for each of the samples. Then for each of the samples, the software automatically processes the acquired data, interprets the exact-mass data by correlating the observed masses with predicted masses computed from proposed elemental formulas, and then finally prints the spectra, peak lists, and exact-mass reports, and e-mails the exact-mass reports to the submitting chemists. With this automation package, large numbers of samples can be run unattended while obtaining exact masses for all the abundant ions in the spectra. Sample turnaround times are reduced with a corresponding increase in sample throughput. The performance of the system was evaluated with nearly 700 samples with a precalibrated instrument, without the presence of an internal standard. The system was found to be reliable and robust with a fitted standard deviation of 0.32 mmu and a small average systematic mass error of −0.28 mmu. Typical data acquired with the system have resolving powers >50,000 (FWHM) and mass errors <1.0 mmu.

Fast gas chromatography/mass spectrometry analysis in support of risk‐based decisions

A new data analysis software system (Ion Fingerprint DetectionTM) has been developed to provide fast mass spectral data analysis. Methods have been developed that can provide screening to quantitative gas chromatography/mass spectrometry (GC/MS) data in 30 s to minutes. Compound selectivity is provided through a unique set of algorithms rather than GC separation. The data quality produced for volatile and semivolatile organic contaminants under fast GC/MS conditions during dynamic site investigations carried out at Hanscom Air Force Base (Bedford, MA) and Joliet Army Ammunition Plant (Joliet, IL) are discussed. More than 800 samples were analyzed in each project, with state and federal regulators accepting the data to complete remedial investigation/feasibility (RI/FS) studies. ©1999 John Wiley & Sons, Inc. Field Analyt Chem Technol 3:55–66, 1999

Fast gas chromatography/mass spectrometry analysis in support of risk-based decisions

A new data analysis software system (Ion Fingerprint DetectionTM) has been developed to provide fast mass spectral data analysis. Methods have been developed that can provide screening to quantitative gas chromatography/mass spectrometry (GC/MS) data in 30 s to minutes. Compound selectivity is provided through a unique set of algorithms rather than GC separation. The data quality produced for volatile and semivolatile organic contaminants under fast GC/MS conditions during dynamic site investigations carried out at Hanscom Air Force Base (Bedford, MA) and Joliet Army Ammunition Plant (Joliet, IL) are discussed. More than 800 samples were analyzed in each project, with state and federal regulators accepting the data to complete remedial investigation/feasibility (RI/FS) studies. ©1999 John Wiley & Sons, Inc. Field Analyt Chem Technol 3:55–66, 1999

Knowledge-based data generation

Data analysts may not always have the data they need to effectively carry out the analysis task and, in certain circumstances, these data can only be derived or generated using existing information. In this paper, we describe a problem solving framework which involves data generation as an important component and present a complex real-world application involving mass spectral data analysis where a substantial amount of domain knowledge is required to infer an essential set of data crucial for achieving the application task. We show how the framework is applied to achieve the analysis task and how relevant domain knowledge was acquired, represented and applied to generate the data set. Finally the work is evaluated and its implications are discussed.

Characterization of the anionic intracluster polymerization reaction product of 2-chloroacrylonitrile trimers by photoelectron spectroscopy

Photoelectron spectra are presented for the [(CAN) 3-3HCl] − product formed by electron attachment onto clusters of 2-chloroacrylonitrile (CAN; CH 2CClCN), and for the molecular anion of 1,3,5-tricyanobenzene (TCB; C 6H 3(CN) 3). The spectra show that the vertical detachment energy (VDE) of [(CAN) 3-3HCl] − (1.83 ± 0.015 eV) is in good agreement with the VDE of TCB − (1.84±0.015 eV). This result suggests that electron attachment onto CAN clusters intiates an anionic polymerization reaction to form the cyclic trimer reaction product, TCB −, as inferred previously by Kondow and co-workers from an analysis of mass-spectral data.

Statistical analysis of mass spectral data obtained from singly protonated peptides under high-energy collision-induced dissociation conditions.

A statistical study of the fragmentation behaviour of 138 model peptides, containing 3-9 amino acid residues (n = 3-9) under high-energy collision conditions is presented. The aim was to identify characteristic patterns of ions in the spectra of peptides which can be translated into general rules to be used in the spectral interpretation and provide a better insight into their fragmentation behaviour. It was found that both number and nature of the amino acids are important factors directing the fragmentation behaviour. The spectra of tri- and tetrapeptides exhibit a comparable probability for the formation of B2- and Y"n-2 ions, whereas larger peptides show a preference for the formation of Bn-1 ions. This generally observed fragmentation pattern of peptides is changed significantly when basic amino acid residues (Arg, Lys and His) and/or Pro are present Arginine appears to have the most pronounced influence on the fragmentation behaviour and overrules that of the other amino acid residues.

Software Development for Mass Spectrometric Analysis

Software programs have been developed for online and offline analysis of mass spectral data. The programs for online analysis take advantage of instrument control languages provided with commercial instrumentation. On-line analysis is important when data-dependent instrument control decisions are required or to make maximum use of sampling time. Software for a prototype explosives detector and online analysis routines for direct sampling ion-trap mass spectrometry (DSITMS) data are presented as examples. A program that is used for quantitative offline analysis of DSITMS data from different ion-trap instruments has also been developed. This program allows rapid manipulation and quantitative analysis of mass spectra generated with the direct sampling interfaces developed at Oak Ridge National Laboratory.

New Destruxins from the Entomopathogenic Fungus Aschersonia sp.

Two new insecticidal cyclic depsipeptides, destruxins A4 (1) and A5 (2), were isolated by bioassay-guided fractionation of organic extracts from an undescribed species of entomopathogenic fungus from the genus Aschersonia. Another previously identified but related compound, homodestruxin B (3), was also isolated as a product of this fungus. The chemical structures of 1−3 were determined based on analysis of NMR and mass spectral data. In common with homodestruxin B (3), the novel compounds destruxins A4 (1) and A5 (2) have a MeIle moiety in place of the MeVal residue more typically found in destruxins. In addition, destruxin A5 has a β-MePro unit in place of the Pro residue found in most destruxins. LC50 values for 1 and 2 in an insecticidal assay against Drosophila melanogaster were estimated at 41 and 52 ppm, respectively. Homodestruxin B (3) showed no activity at 400 ppm in the same assay. Destruxins A4 (1) and A5 (2) are the first biologically active secondary metabolites reported from the fungal genu...

The resolution of mixtures using data from automated probe mass spectrometry

This paper describes the application of self-modeling mixture analysis to automated mass spectral data analysis. The particular method chosen here is SIMPLISMA (Simple to use Interactive Self-Modelling Mixture Analysis). This method requires extensive user-interaction and as such is not applicable to automated procedures. We describe here a modified SIMPLISMA approach (TSIMPLISMA) and demonstrate its successful application. The number of components in a set of mixtures has been successfully determined, and the “pure” mass spectra for each component successfully resolved. TSIMPLISMA requires less user-interaction than the original method and lends itself to incorporation in automated routines.

Inhibitors of sterol synthesis. Chemical syntheses and spectral properties of 26-oxygenated derivatives of 3β-hydroxy-5α-cholest-8(14)-en-15-one and their effects on 3-hydroxy-3-methylglutaryl coenzyme A reductase activity in CHO-K1 cells

26-Oxygenated derivatives of Δ 8(14)-15-ketosterols have been synthesized from (25R)-3β,26-diacetoxy-5α-cholest-8(14)-en-15-one ( IX) as part of a program to prepare potential metabolites and analogs of 3β-hydroxy-5α-cholest-8(14)-en-15-one ( I), a potent regulator of cholesterol metabolism. Partial hydrolysis of IX gave a mixture, from which the 3β,26-diol II and the 26-acetate ( XI) and 3β-acetate ( X) monoesters were isolated. Mitsunobu reaction of XI followed by hydrolysis gave (25R)-3α,26-dihydroxy-5α-cholest-8(14)-en-15-one ( VI). Oxidation of XI with pyridinium chlorochromate followed by hydrolysis of the acetate gave (25R)-26-hydroxy-5α-cholest-8(14)-ene-3,15-dione ( VII). Oxidation of X with Jones reagent followed by hydrolysis of the acetate gave (25R)-3β-hydroxy-15-keto-5α-cholest-8(14)-en-26-oic acid ( IVa). Jones oxidation of II gave (25R)-3,15-diketo-5α-cholest-8(14)-en-26-oic acid ( VII). 1H and 13C nuclear magnetic resonance assignments and analyses of mass spectral fragmentation data are presented for each of the new compounds and their derivatives. The 3,15-diketone VII was found to be highly active in lowering the levels of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity in CHO-K1 cells, with a potency comparable to that of I. In contrast, 3α,26-diol VI was less potent than I or VII. The two carboxylic acid analogs IVa and VIII were considerably less potent than VI in lowering the levels of HMG-CoA reductase activity.

What's hot and what's not in Washington

Next week's American Chemical Society meeting to be held in Washington, DC, USA will feature a collection of US patents on CD-ROM, a protein sequencer and software for the analysis of mass spectral data of proteins and peptides.