Analysis Of Mass Spectral Data Research Articles

Group IIB-VIA semiconductor oxide cluster ions

Metal oxide cluster ions, MnOm± (M = Zn, Cd) and HgnOm− of various stoichiometry have been generated from solid IIB-VIA semiconductor oxides targets, (ZnO(s), CdO(s), and HgO(s)) by using pulse laser desorption ionization time of flight mass spectrometry with a laser of λ = 355 nm. Analysis of mass spectral data indicates the formation of stoichiometric cluster ions viz., (ZnO)n=1-30+ and (CdO)n=1-40+ along with –O bound anions, (ZnO)n=1-30O−, (CdO)n=1-40O− and (HgO)n=1-36O− from their respective solids. Further, metal oxoanions such as ZnOn=2,3−, CdOn=2,3,6−, and HgOn=2,3,6,7− have also been noted signifying the higher coordination ability of both Cd and Hg with O/O2/O3 species.

Structural Elucidation of Alkaloids from Aerial Parts of Rivea hypocrateriformis and Their Antihemolytic and Cytotoxic Activity

Two new alkaloids, designated as hypocretine 1 and 2, have been extracted from the aerial parts of Rivea hypocrateriformis, and their structures were established as 1-(4-(((1R,5S,6R)-(4-acetyl-2,6-dibutylphenoxy)- 8-methyl-8-azabicyclo[3.2.1]octan-6-yl)oxy)-2,6-dibutylphenyl)ethan-1-one and 1-(4-((3-(4-acetyl-2-butyl- 6-(4-hydroxybutyl)phenoxy)-8-methyl-8 azabicyclo[3.2.1]octan-6-yl)oxy)-2-butyl-6-(4- hydroxybutyl)phenyl)ethan-1-one. These alkaloids were further characterized by mass and NMR spectral data analysis. Further studies were conducted to evaluate their antihemolytic and cytotoxic activity. The extracted compounds exhibited potent antihemolytic activity against cow erythrocytes. The results of the MTT assay for cytotoxicity revealed the antiproliferative activity of compounds 1and 2 against MCF-7 breast cancer cell line.

Nematotoxic coumarins from Angelica pubescens Maxim. f. biserrata Shan et Yuan roots and their physiological effects on Bursaphelenchus xylophilus.

Abstract The ethanol extracts from the roots of Angelica pubescens Maxim. f. biserrata Shan et Yuan was toxic against the pine wood nematode Bursaphelenchus xylophilus. The ethyl acetate-soluble fraction derived from this extract increased its potency with a mortality of 95.25% in 72 hr at 1.0 mg/mL. Four nematotoxic coumarins were obtained from the ethyl acetate extract by bioassay-guided isolation. These were identified as osthole 1 , columbianadin 2 , bergapten 3 and xanthotoxin 4 by mass and nuclear magnetic resonance spectral data analysis. The LC50 values against B. xylophilus in 72 hr were 489.17, 406.74, 430.08, and 435.66 μM, respectively. These compounds also altered the smooth morphology of the B. xylophilus exoskeleton to a rough and pitted appearance as visualized by electron microscopy. The coumarins 1-4 possessed significant acetylcholinesterase inhibitory activities but had negligible effects on amylase and cellulase. This research provides additional clues to the nematotoxic mechanism of coumarins against the pine wood nematode B. xylophilus. This work will assist in the development of coumarin nematicides with enhanced activity using molecular modifications of the core coumarin structure.

Gelatin speciation using real-time PCR and analysis of mass spectrometry-based proteomics datasets

Authentication of gelatin, an ingredient in food and drug products, is of interest with respect to some regulations and religion rules. Determination of the gelatin origin is particularly challenging because of the similarity in amino acid sequences of collagen types in different species. In this study, Polymerase Chain Reaction (PCR) technique using species-specific primers and also chemometrics analysis of mass spectral data were investigated to differentiate bovine, porcine and fish source of gelatin in commercial pure gelatin and gelatin-containing food and drug products. The specific PCR primer set was optimized using real-time PCR approach to routinely determine the gelatin source. Real-time PCR is sensitive to identify gelatin origin from traces of species-specific DNA. However, source determination is impossible when DNA is denatured or removed during production process. Alongside, chemometrics methods (PLS/DA and PCA) were used for mining LC/MS data sets to obtain patterns for discrimination of gelatin origins. LC/MS data sets involve MS spectrum of tryptic gelatin peptides generated from gelatin samples. Using PLS/DA method, a discrimination model is developed for identifying origin of the extracted gelatin. The method is practical to determine the halal authenticity of gelatin in the pure and processed products.

Temporal Characteristics of Brown Carbon over the Central Indo-Gangetic Plain.

Recent global models estimate that light absorption by brown carbon (BrC) in several regions of the world is ∼30-70% of that due to black carbon (BC). It is, therefore, important to understand its sources and characteristics on temporal and spatial scales. In this study, we conducted semicontinuous measurements of water-soluble organic carbon (WSOC) and BrC using particle-into-liquid sampler coupled with a liquid waveguide capillary cell and total organic carbon analyzer (PILS-LWCC-TOC) over Kanpur (26.5°N, 80.3°E, 142 m amsl) during a winter season (December 2015 to February 2016). In addition, mass concentrations of organic and inorganic aerosol and BC were also measured. Diurnal variability in the absorption coefficient of BrC at 365 nm (babs_365) showed higher values (35 ± 21 Mm-1) during late evening to early morning hours and was attributed to primary emissions from biomass burning (BB) and fossil fuel burning (FFB). The babs_365 reduced by more than 80% as the day progressed, which was ascribed to photo bleaching/volatilization of BrC and/or due to rising boundary layer height. Further, diurnal variability in the ratios of babs_405/babs_365 and babs_420/babs_365 suggests that the BrC composition was not uniform throughout a day. WSOC exhibited a strong correlation with babs_365 (slope = 1.22 ± 0.007, r2 = 0.70, n = 13 265, intercept = -0.69 ± 0.17), suggesting the presence of a significant but variable fraction of chromophores. Mass absorption efficiency (MAE) values of WSOC ranged from 0.003 to 5.26 m2 g-1 (1.16 ± 0.60) during the study period. Moderate correlation (r2 = 0.50, slope = 1.58 ± 0.019, n = 6471) of babs_365 was observed with the semivolatile oxygenated organic aerosols (SV-OOA) fraction of BB resolved from positive matrix factorization (PMF) analysis of organic mass spectral data obtained from a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). The low-volatility OOA (LV-OOA) fraction of BB had a similar correlation to babs_365 (r2 = 0.54, slope = 0.38 ± 0.004, n = 6471) but appears to have a smaller contribution to the absorption.

Efficient synthesis, fluorescence and DFT studies of different substituted 2-chloroquinoline-4-amines and benzo[g][1,8]naphthyridine derivatives

Abstract An efficient and single step strategy for synthesizing new functionalized benzo[b][1,8]naphthyridine derivatives is presented. Benzo[g][1,8]naphthyridines have been synthesized by the condensation of substituted 2-chloroquinoline-3-carbaldehydes with various 2-chloroquinoline-4-amines, 1H-Indazole-6-amine in basic medium. The electro luminescence and photophysical properties of a series of benzo[g][1,8]naphthyridines 5(a–d), 6(a–d) and 2-chloroquinoline-4-amines 3(a–f) are reported and investigated with the aim of arriving at good fluorescent materials. Moreover, the effect of electron donor-acceptor substituent on fluorescence properties of all molecules has been investigated along with their fluorescent quantum yields. Furthermore we analyzed for band gap energy associated with HOMO-LUMO, through density functional (DFT M06-HF) studies. The experimental observations are in close agreement with the theoretical calculation. All the synthesized compounds were identified on the basis of their NMR, Mass spectral data analyses.

A nematicidal tannin from Punica granatum L. rind and its physiological effect on pine wood nematode (Bursaphelenchus xylophilus)

The ethanol extract of Punica granatum L. rind was tested to show significant nematicidal activity against pine wood nematode. Three nematicidal compounds were obtained from the ethanol extract by bioassay-guided fractionation and identified as punicalagin 1, punicalin 2, and corilagin 3 by mass and nuclear magnetic resonance spectral data analysis. Punicalagin 1 was most active against PWN among the purified compounds with the LC50 value of 307.08μM in 72h. According to the enzyme assays in vitro, punicalagin 1 could inhibit the activity of acetylcholinesterase, amylase and cellulase from PWN with IC50 value of 0.60mM, 0.96mM and 1.24mM, respectively. The morphological structures of PWNs treated by punicalagin 1 were greatly changed. These physiological effects of punicalagin 1 on PWN may helpful to elucidate its nematicidal mechanism.

Hit to lead optimization of a series of N-[4-(1,3-benzothiazol-2-yl)phenyl]acetamides as monoacylglycerol lipase inhibitors with potential anticancer activity

A total of thirty five new N-[4-(1,3-benzothiazol-2-yl)phenyl]acetamide derivatives were synthesized and structures of all the compounds were confirmed on the basis of elemental analysis and collective use of IR, 1H NMR, 13C NMR and mass spectral data. Compounds were tested for their ability to inhibit human monoacylglycerol lipase (hMAGL) enzyme. Eight compounds 4, 19–21, 24–26, and 34 reduced the hMAGL activity less than 50% at 100 nM concentrations. The halogen substituted aniline derivatives 20, 21 and 24–26 were found to be most active among all the synthesized compounds having IC50 value in the range of 6.5–9 nM. Twenty five compounds were selected by NCI, USA for one dose anticancer screening. Compound 21 (NSC: 780167) and 24 (NSC: 780168) fulfilled prearranged doorstep growth inhibition criteria and further selected for NCI full panel five dose assay at 10-fold dilutions of five different concentrations (0.01, 0.1, 1, 10 and 100 μM). Both the compounds 21 and 24 were found to be most active against MCF7 and MDA-MB-468 breast cancer cell lines. The GI50 value of 32.5 nM (MCF7) and 23.8 nM (MDA-MB-468) was observed for compound 21. Compound 24 showed GI50 values of 37.1 nM against MCF7 breast cancer cell line and 25.1 nM against MDA-MB-468 breast cancer cell line.

PTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification.

There has been tremendous progress in top-down proteomics (TDP) in the past 5 years, particularly in intact protein separation and high-resolution mass spectrometry. However, bioinformatics to deal with large-scale mass spectra has lagged behind, in both algorithmic research and software development. In this study, we developed pTop 1.0, a novel software tool to significantly improve the accuracy and efficiency of mass spectral data analysis in TDP. The precursor mass offers crucial clues to infer the potential post-translational modifications co-occurring on the protein, the reliability of which relies heavily on its mass accuracy. Concentrating on detecting the precursors more accurately, a machine-learning model incorporating a variety of spectral features was trained online in pTop via a support vector machine (SVM). pTop employs the sequence tags extracted from the MS/MS spectra and a dynamic programming algorithm to accelerate the search speed, especially for those spectra with multiple post-translational modifications. We tested pTop on three publicly available data sets and compared it with ProSight and MS-Align+ in terms of its recall, precision, running time, and so on. The results showed that pTop can, in general, outperform ProSight and MS-Align+. pTop recalled 22% more correct precursors, although it exported 30% fewer precursors than Xtract (in ProSight) from a human histone data set. The running speed of pTop was about 1 to 2 orders of magnitude faster than that of MS-Align+. This algorithmic advancement in pTop, including both accuracy and speed, will inspire the development of other similar software to analyze the mass spectra from the entire proteins.

Two nematicidal furocoumarins from Ficus carica L. leaves and their physiological effects on pine wood nematode (Bursaphelenchus xylophilus)

The ethanol extract of the Ficus carica L. leaves was tested to show strong nematicidal activity against pine wood nematode (PWN), Bursaphelenchus xylophilus, causing 90.93% corrected mortality within 72 h at 1.0 mg/mL. From the ethyl acetate soluble fraction of the F. carica L. leaves extract, the main nematicidal constituents were obtained by bioassay-guided isolation and identified as linear furocoumarins bergapten (1) and psoralen (2) by mass and NMR spectral data analysis. Bergapten and psoralen had significant nematicidal activity against PWN with the LC50 values of 97.08 aKSnd 115.03 μg/mL within 72 h, respectively. The two furocoumarins could inhibit the activities of amylase, cellulase and acetylcholinesterase (AchE) from PWN. The morphologies of PWNs changed much after they were treated by bergapten and psoralen. The physiological effects of bergapten and psoralen on PWN might provide helpful clues to elucidate their nematicidal mechanisms.

Mining Novel Allergens from Coconut Pollen Employing Manual De Novo Sequencing and Homology-Driven Proteomics.

Coconut pollen, one of the major palm pollen grains is an important constituent among vectors of inhalant allergens in India and a major sensitizer for respiratory allergy in susceptible patients. To gain insight into its allergenic components, pollen proteins were analyzed by two-dimensional electrophoresis, immunoblotted with coconut pollen sensitive patient sera, followed by mass spectrometry of IgE reactive proteins. Coconut being largely unsequenced, a proteomic workflow has been devised that combines the conventional database-dependent analysis of tandem mass spectral data and manual de novo sequencing followed by a homology-based search for identifying the allergenic proteins. N-terminal acetylation helped to distinguish "b" ions from others, facilitating reliable sequencing. This led to the identification of 12 allergenic proteins. Cluster analysis with individual patient sera recognized vicilin-like protein as a major allergen, which was purified to assess its in vitro allergenicity and then partially sequenced. Other IgE-sensitive spots showed significant homology with well-known allergenic proteins such as 11S globulin, enolase, and isoflavone reductase along with a few which are reported as novel allergens. The allergens identified can be used as potential candidates to develop hypoallergenic vaccines, to design specific immunotherapy trials, and to enrich the repertoire of existing IgE reactive proteins.

Asperginine, an Unprecedented Alkaloid from the Marine-derived Fungus Aspergillus sp

Asperginine (1), an alkaloid possessing a rare skeleton, was isolated from the cultural broth of the marine fungus Aspergillus sp. (Z-4) isolated from the gut of the marine isopod Ligia oceanica. The planar structure and relative configuration of 1 was determined by analysis of NMR and mass spectral data. Its absolute configuration was elucidated by Marfey's method, together with NOESY correlations of key hydrogen atoms. The cytotoxicity against prostate cancer PC3 and human HCT116 was assayed by the MTT method. Unfortunately, asperginine did not show any activity.

Synthesis and Quantitative Structure-Antioxidant Activity Relationship Analysis of Thiazolidine-2,4-dione Analogues

Three series of thiazolidine-2,4-dione analogues (1–17, 14a-h, 15a-h, 16a-h, 17a-h) were synthesized by Knoevenagel condensation/N-alkylation/combination of both the reactions. The structure of the compounds was established based on IR, 1H NMR and Mass spectral data analysis. In the in vitro antioxidant potential evaluation, the compound 14g bearing 4-hydroxyl,3-methoxyl substitution on 5-aryl functionality shown significant reducing power (IC50 22.7±0.43 μM). Descriptor-based QSAR analysis was utilized to study the structural contribution to the radical scavenging potential. Among various QSAR models, model 12 was found to be best and the R2 value 0.858 is indicative of good correlation between in vitro and in silico activity. The QSAR studies revealed the potential contribution of the descriptors HOMO, HBD, DM and SASA towards the antioxidant activity.

An efficient algorithm for the blocked pattern matching problem

Tandem mass spectrometry (MS) has become the method of choice for protein identification and quantification. In the era of big data biology, tandem mass spectra are often searched against huge protein databases generated from genomes or RNA-Seq data for peptide identification. However, most existing tools for MS-based peptide identification compare a tandem mass spectrum against all peptides in a database whose molecular masses are similar to the precursor mass of the spectrum, making mass spectral data analysis slow for huge databases. Tag-based methods extract peptide sequence tags from a tandem mass spectrum and use them as a filter to reduce the number of candidate peptides, thus speeding up the database search. Recently, gapped tags have been introduced into mass spectral data analysis because they improve the sensitivity of peptide identification compared with sequence tags. However, the blocked pattern matching (BPM) problem, which is an essential step in gapped tag-based peptide identification, has not been fully solved. In this article, we propose a fast and memory-efficient algorithm for the BPM problem. Experiments on both simulated and real datasets showed that the proposed algorithm achieved high speed and high sensitivity for peptide filtration in peptide identification by database search. cswangl@cityu.edu.hk or xwliu@iupui.edu Supplementary data are available at Bioinformatics online.

Antibacterial flavanones and dihydrochalcones from Macaranga trichocarpa.

Previously we had isolated two prenylated flavanones and two prenylated dihydrochalcones, macatrichocarpins A-D (1-4), from the acetone extract of the leaves of Macaranga trichocarpa. Re-examination of the fractions containing minor components resulted in the isolation of four more flavonoid derivatives, including two new prenylated dihydrochalcones, oxymacatrichocarpin C (5) and isomacatrichocarpin C (6). The structures of these compounds were determined by the analysis of UV, NMR, and mass spectral data. The eight isolated flavonoids were tested on eight pathogenic bacteria and found to be mostly moderate antibacterial agents, with the lowest MIC value of 26.5 μM achieved by the flavanone macatrichocarpin A (1) against Bacillus subtilis.

Methylthio-aspochalasins from a marine-derived fungus Aspergillus sp.

Two novel aspochalasins, 20-β-methylthio-aspochalsin Q (named as aspochalasin V), (1) and aspochalasin W (2), were isolated from culture broth of Aspergillus sp., which was found in the gut of a marine isopod Ligia oceanica. The structures were determined on the basis of NMR and mass spectral data analysis. This is the first report about methylthio-substituted aspochalasin derivatives. Cytotoxicity against the prostate cancer PC3 cell line and HCT116 cell line was assayed using the MTT method. Apochalasin V showed moderate activity at IC50 values of 30.4 and 39.2 μM, respectively.

Isolation and Structure Elucidation of Rebaudioside D2 from Bioconversion Reaction of Rebaudioside A to Rebaudioside D

We report the isolation and complete structure of an isomer of rebaudioside D, known as rebaudioside D2. This novel steviol glycoside was isolated from a bioconversion reaction of rebaudioside A to rebaudioside D. Rebaudioside D2 possesses a relatively rare 1 --> 6 sugar linkage, which was discovered by extensive analysis of NMR (1H, 13C, COSY, HSQC-DEPT, HMBC, 1D TOCSY and NOESY) and mass spectral data.

Synthesis and Screening of Some Novel 2-[5-(Substituted phenyl)-[1,3,4]oxadiazol-2-yl]-benzoxazoles as Potential Antimicrobial Agents

A series of some novel 2-[5-(substituted phenyl)-[1,3,4]oxadiazol-2-yl]-benzoxazoles were synthesized by using benzoxazole-2-carboxylic acid on reaction with thionyl chloride in presence of ethanol solvent at room temperature gave benzoxazole-2-carbonyl chloride, which is turned into benzoxazole-2-carboxylic acid hydrazide on reaction with hydrazine hydrate in ethanol solvent under reflux. The subsequent treatment of benzoxazole-2-carboxylic acid hydrazide with an appropriate aromatic carboxylic acid in presence of polyphosparic acid under reflux afforded the title compounds. The chemical structures of the newly synthesized compounds were elucidated by their IR, <TEX>$^1H$</TEX> NMR and Mass spectral data analysis. Further the compounds are used to find out their ability towards anti microbial and nematicidal activity.

New Inhibitors of ROS Generation and T-Cell Proliferation from Myrtus communis

Phytochemical investigation on Myrtus communis Linn. afforded myrtucommuacetalone (1) with an unprecedented carbon skeleton and a new phloroglucinol-type compound, myrtucommulone M (2), along with four known constituents 3-6. Their structures were established by extensive analyses of NMR and mass spectral data as well as by single-crystal X-ray diffraction studies. These constituents were evaluated for their ability to modulate the immune response, based on their effects on various components of immune system. Compounds 1 and 5 exhibited significant inhibitory effect against nitric oxide (NO(•)) production. Compound 1 also exhibited significant antiproliferative activity (IC50 < 0.5 μg/mL) against T-cell proliferation. Myricetin (3) exerted a significant inhibition (IC50 = 1.6 μg/mL) on zymosan-stimulated whole blood phagocytes ROS production. Compounds 1 and 3 were active against PMA-stimulated ROS generation.

BRAIN: A Universal Tool for High-Throughput Calculations of the Isotopic Distribution for Mass Spectrometry

This Letter presents the R-package implementation of the recently introduced polynomial method for calculating the aggregated isotopic distribution called BRAIN (Baffling Recursive Algorithm for Isotopic distributioN calculations). The algorithm is simple, easy to understand, highly accurate, fast, and memory-efficient. The method is based on the application of the Newton-Girard theorem and Viète's formulae to the polynomial coding of different aggregated isotopic variants. As a result, an elegant recursive equation is obtained for computing the occurrence probabilities of consecutive aggregated isotopic peaks. Additionally, the algorithm also allows calculating the center-masses of the aggregated isotopic variants. We propose an implementation which is suitable for high-throughput processing and easily customizable for application in different areas of mass spectral data analyses. A case study demonstrates how the R-package can be applied in the context of protein research, but the software can be also used for calculating the isotopic distribution in the context of lipidomics, metabolomics, glycoscience, or even space exploration. More materials, i.e., reference manual, vignette, and the package itself are available at Bioconductor online (http://www.bioconductor.org/packages/release/bioc/html/BRAIN.html).