• Mass Spectrometry Letters
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• v.10 no.3
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• pp.93-101
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• 2019

Algorithms and software for predicting tandem mass spectra have been developed in recent years. In this work, we explore how distinct in silico $MS^2$ spectra are predicted for isomers, i.e. compounds having the same formula and similar molecular structures, to differentiate between them. We used the CFM-ID 2.0/3.0 predictor with regard to (a) test compounds, whose experimental mass spectra had been randomly sampled from the MassBank of North America (MoNA) collection, and to (b) the most widespread isomers of test compounds searched in the PubChem database. In the first validation test, in silico mass spectra constitute a reference library, and library searches are performed for test experimental spectra of "unknowns". The searches led to the true positive rate (TPR) of ($46-48{\pm}10$)%. In the second test, in silico and experimental spectra were interchanged and this resulted in a TPR of ($58{\pm}10$)%. There were no significant differences between results obtained with different metrics of spectral similarity and predictor versions. In a comparison of test compounds vs. their isomers, a statistically significant correlation between mass spectral data and structural features was observed. The TPR values obtained should be regarded as reasonable results for predicting tandem mass spectra of related chemical structures.

• Journal of Microbiology and Biotechnology
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• v.29 no.6
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• pp.887-896
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• 2019

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based pathogen identification relies on the ribosomal protein spectra provided in the proprietary database. Although these mass spectra can discern various pathogens at species level, the spectra-based method still has limitations in identifying closely-related microbial species. In this study, to overcome the limits of the current MALDI-TOF MS identification method using ribosomal protein spectra, we applied MALDI-TOF MS of low-mass profiling to the identification of two genetically related Bacillus species, the food-borne pathogen Bacillus cereus, and the insect pathogen Bacillus thuringiensis. The mass spectra of small molecules from 17 type strains of two bacilli were compared to the morphological, biochemical, and genetic identification methods of pathogens. The specific mass peaks in the low-mass range (m/z 500-3,000) successfully identified various closely-related strains belonging to these two reference species. The intensity profiles of the MALDI-TOF mass spectra clearly revealed the differences between the two genetically-related species at strain level. We suggest that small molecules with low molecular weight, 714.2 and 906.5 m/z can be potential mass biomarkers used for reliable identification of B. cereus and B. thuringiensis.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.749-752
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• 2014

New software was developed for the assignment of elemental formulae based on high-resolution mass spectra and subsequent hydrogen/deuterium exchange data. Entire peaks in high-resolution mass spectra were grouped by their Kendrick mass defect values, and the weighted RMS deviations between theoretical and experimental values were used to determine elemental formulae. After this initial assignment, formulae containing deuterium atoms were sorted in order to interpret hydrogen/deuterium exchange spectra. The software was successfully applied to hydrogen/deuterium exchange spectra of resins and aromatic fractions from heavy crude oil.

• The Bulletin of The Korean Astronomical Society
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• v.37 no.2
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• pp.80.1-80.1
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• 2012

The $2.5-5.0{\mu}m$ spectrum of AGN was poorly understood due to the atmosphere effect beyond $2{\mu}m$. Nevertheless, the $2.5-5.0{\mu}m$ range includes several important lines, such as $Br{\beta}$ ($2.63{\mu}m$), $Br{\alpha}$ ($4.05{\mu}m$), PAH (3.3${\mu}m$) and many molecular or atomic lines. We compile $2.5-5.0{\mu}m$ spectra of 79 AGNs and QSOs from infrared camera (IRC) on AKARI infrared astronomy satellite. Our $2.5-5.0{\mu}m$ spectra will provide an access to full wavelength spectra of AGNs for the first time. Moreover, we present the Brackett line properties, FWHMs and luminosities, of AGNs. Using these Brackett line properties, we derive new black hole (BH) mass estimators. The new BH mass estimators using NIR hydrogen lines will be very useful to estimate BH mass of dusty red AGNs in the future.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.477-482
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• 2011

The structural analysis of polytrimethylene terephthalate (PTT) and characterization of the hydrolytic degradation products after acid hydrolysis were performed using MALDI-TOF mass spectrometry. Mass spectra of the PTT samples were analyzed using a self-calibration method as well as an internal calibration method with standard materials of known masses. PTT structures constituting the samples were determined from the analyses of the spectra, and their relative compositions were estimated. The MALDI-TOF mass spectra of the acid-hydrolyzed PTT sample showed three main series of oligomer products with different end groups in accordance with the hydrolysis schemes. From the spectra of both $Na^+$ and $K^+$ adducts, it was concluded that the PTT samples have higher affinity for $Na^+$ compared with $K^+$ and therefore show higher ionization efficiency with sodium ions when dithranol is used as a matrix. Two different wavelength laser beams ($\lambda$ = 337 nm and 355 nm) were tested and it was observed that the 355 nm beam was more efficient in obtaining the MALDI spectra of PTT using dithranol as a matrix under our experimental conditions.

• Mass Spectrometry Letters
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• v.6 no.4
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• pp.99-104
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• 2015

A liquid chromatography mass spectrometry (LC-MS) system was used to identify and distinguish oligostilbene diastereoisomers. A polyphenolic extract from Neobalanocarpus heimii known to be rich in oligostilbenes of various degrees of condensation was used as test material. Fourteen oligostilbenes were isolated from this extract on a fully automated semi-preparative HPLC system. Out of these, two pairs of dimers, one pair of trimers, two pairs of tetramers and a group of four tetramers with similar skeleton were identified as diastereoisomers. Their structures and configurations were established by spectroscopic methods. All isolated compounds were subjected to an LC-MS/MS to study their fragmentation patterns. The experiments were performed on a liquid chromatography-mass spectrometry (LC-MS) with electrospray-ionization (ESI) interface in positive mode. MS/MS spectra of each pure compound were recorded by direct infusion in identical conditions and their product ion spectra were analysed. Some subtle yet significant differences were observed between the spectra of oligostilbenes from the various diastereoisomeric series.

• Mass Spectrometry Letters
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• v.10 no.2
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• pp.50-55
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• 2019

The fragmentation statistics of ion trap CID (Collision-Induced Dissociation) spectra using 87,661 tandem mass spectra of doubly charged tryptic peptides are analyzed here. In contrast to the usual method of using intensity information, the frequency of occurrence of fragment ions, with respect to the position of the cleavage site and the residues at these sites is studied in this paper. The analysis shows that the frequency of occurrence of fragment ion peaks is more towards the middle of the peptide than its ends. It was noted that amino acid with an aromatic and basic side chain at N- & C- terminal end of the peptide stimulates more peaks at the lower end of the spectrum. The residue pair effect was shown when the amide bond occurs between acidic and basic residues. The fragmentation at these sites (D/E-H/R/K) stimulates the generation of the y-ion peak. Also, the cleavage site H-H/R/K stimulates the generation of b-ions. K-P environment in the peptide sequence has more tendency to generate y-ions than b-ions. Statistical analysis helps in the visualization of the CID fragmentation pattern. Cleavage pattern along the length of the peptide and the residue pair effects, enhance the knowledge of fragmentation behavior, which is useful for the better interpretation of tandem mass spectra.

• Journal of the Korean Chemical Society
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• v.17 no.6
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• pp.444-449
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• 1973

From the methanol extract of the fruits of Forsythia Koreana NAKAI a sapogenin and its derivatives were isolated. Through the mass spectra, ultraviolet spectra, nuclear magnetic resonance spectra, elemental analysis and chemical tests it was identified as ursolic acid.

• BMB Reports
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• v.30 no.4
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• pp.253-257
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• 1997

Negative ion fast atom bombardment (FAB) mass spectra were found to allow the determination of the linkage positions in a series of underivatized linkage-isomeric oligosaccharides. A previous work (Laine et al., 1988) reported that ion patterns of linkage-isomeric trisaccharides could be distinguished by a positive ion. Negative ion FAB collison-activated dissociation (CAD) mass spectrometry (MS) spectra of trisaccharides exhibited better sensitivity than the positive ion mode and provided specific fragmentation patterns according to the linkage positions. Especially, the fragmentations, m/z 205 in F6 and m/z 221 in G6, not occuring in 1-3 or 1-4 linkage. were an indication of 1-6 linkage, by changing collision energies from + 10 eV to +60 eV. The survival ratios of molecular ions in each collision energy set gave support to previous results in which the order of bond stability was 1-6>1-4>1-3 linkage.

• The Bulletin of The Korean Astronomical Society
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• v.36 no.2
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• pp.63.1-63.1
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• 2011

In understanding AGN physics, it is fundamental to determine black hole masses. Based on the gas kinematics of the broad-line region, black hole masses can be derived from the product of the width of the broad emission lines and the continuum/line luminosities. For a sample of 37 intermediate-luminosity AGN at z~0.4, we obtained high quality spectra (S/N~100) using the Low Resolution Imaging Spectrometer(LRIS) at the KECK telescope, in order to calibrate various black hole mass estimators based on the Mg II (2798A), the $H{\beta}$ (4861A), and the $H{\alpha}$ (6563$\bar{A}$) emission lines. Based on our multicomponent fitting analysis, we subtract continuum, FeII emission, and host galaxy starlight, reducing systematic errors in measuring emission line widths. Combining low S/N SDSS spectra with our high S/N keck spectra, we determine a set of ~30 black hole masses of the sample for each emission line. Then by comparing various sets of black hole masses, we internally calibrate each mass estimators and investigate uncertainties and limitations of each mass estimator.