• Mass Spectrometry Letters
• /
• v.12 no.2
• /
• pp.41-46
• /
• 2021

Collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD) are the widely used fragmentation technique in mass spectrometry-based proteomics studies. Understanding the fragmentation pattern from the tandem mass spectra using statistical methods helps to implement efficient spectrum analysis algorithms. The study characterizes the frequency of occurrence of multi-charged fragment ions and their neutral loss events of doubly and triply charged peptides in the CID and HCD spectrum. The dependency of the length of the fragment ion on the occurrence of multi-charged fragment ion is characterized here. Study shows that the singly charged fragment ions are generally dominated in the doubly charged peptide spectrum. However, as the length of the product ion increases, the frequency of occurrence of charge 2 fragment ions increases. The y- ions have more tendencies to generate charge 2 fragment ions than b- ions, both in CID and HCD spectrum. The frequency of occurrence of charge 2 fragment ion peaks is prominent upon the dissociation of the triply charged peptides. For triply charged peptides, product ion of higher length occurred in multiple charge states in CID spectrum. The neutral loss peaks mostly exist in charge 2 states in the triply charged peptide spectrum. The b-ions peaks are observed in much less frequency than y-ions in HCD spectrum as the length of the fragment increases. Isotopic peaks are occurred in charge 2 state both in doubly and triply charged peptide's HCD spectrum.

• Korean Journal of Pharmacognosy
• /
• v.10 no.2
• /
• pp.55-59
• /
• 1979

Mass spectra of the dammarane triterpenes having open side chain and $C_{20}-C_{25}-epoxy$ side chain were measured. Principal fragment ions were assigned and plausible mechanisms for the formation of the fragment ions were proposed. In general, the triter-penoids of $C_{20}-C_{25}-epoxy$ side chain. produce $h_{1}-species$ fragment ions by the deletion of side chain at $C_{20}-C_{22}$ bond and open side chain triterpenoids produce $h_{2}$ species fragmentions whose mass numbers are higher by two mass unit than those of $h_{1}$ species. The mass number of h species fragment ions will serve as the diagnostic tool for the elucidation of side chain structure of tetracyclic triterpenoids.

• Bulletin of the Korean Chemical Society
• /
• v.21 no.8
• /
• pp.785-792
• /
• 2000

Mass spectral fragmentations of six chlorinated organophosphorus pesticides were investigated using electron impact mass spectrometry. Understanding the fragmentation pathways, based on the fragment ions of mass spectra, should be useful in the structural elucidation and chemical identification of these compounds. The pro-posed fragmentation pathways were verified by collision-induced dissociation B/E-linked scan spectra. ln most cases,the structures of characteristic fragment ions could be expected by the observation of the peak clusters due to 35Cl and 37Cl isotopes. According to substituted groups on phosphorus atom, phosphate and phospho-rothioate exhibited significantIy differentfragmentation patterns. Especially, phosphate and phosphorothioate with diethyl ester produced more diverse fragment ions than that with dimethyl ester.

• Analytical Science and Technology
• /
• v.30 no.6
• /
• pp.379-389
• /
• 2017

In this study, we set up an analytical method that can be used for rapid and accurate determination of representative isoquinoline alkaloids in medicinal plants using UPLC-ESI-Q-TOF MS (ultra pressure liquid chromatography-electrospray ionization-quadrupole-time-of-flight mass spectrometry). The compounds were eluted on a C18 column with 0.1 % formic acid and acetonitrile, and separated with good resolution within 13 min. Each of the separated components was characterized by precursor ions (generated by ESI-Q-TOF) and fragment ions (produced by collision-induced dissociation, CID), which were used as a reliable database. We also performed method validation: analytes showed excellent linearity ($R^2$, 0.9971-0.9996), LOD (5-25 ng/mL), LOQ (17-82 ng/mL), accuracy (91.6-97.4 %) as well as intra- and inter-day precisions (RSD, 1.8-3.2 %). In the analysis of Chelidonium majus L., magnoflorine, coptisine, sanguinarine, berberine and palmatine were detected by matching retention times and characteristic fragment ion patterns of reference standards. We also confirmed that, among the quantified components, coptisine was present in the highest quantity. Furthermore, alkaloid profiling was carried out by analyzing the fragment ion patterns corresponding to peaks of unknown components. In this manner, protopine, chelidonine, stylopine, dihydroberberine, canadine, and nitidine were tentatively identified. We also proposed the molecular structure of the fragment ions that appear in the mass spectrum. Therefore, we concluded that our suggested method for the determination of major isoquinoline alkaloids by UPLC-Q-TOF can be useful not only for quality control, but also for rapid and accurate investigation of phytochemical constituents of medicinal plants.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.10
• /
• pp.1538-1544
• /
• 2004

Fragmentations and proton transfer reactions of mono-, di-, and triethanolamines were studied using FTMS. It was found that the most abundant fragment ion was $[M-CH_2OH]^+$. The $[M-CH_2OH-H_2O]^+$ was observed in the mass spectra of diethanolamine and triethanolamine. By increasing the ion trapping time in the ICR cell, the $[M+H]^+$ and $[M+H-H_2O]^+$ ions were notably increased for all the samples while the $[M+H-2H_2O]^+$ was observed in the mass spectra of diethanolamine and triethanolamine. The proton transfer reactions between the fragment ions and neutral molecules occurred predominantly by increasing the ion trapping time. The rate constants for the proton transfer reactions were calculated from experimental results. The proton transfer reaction of $CHO^+$ was the fastest one, which is consistent with the heats of reaction. The rate constants for proton transfer reactions of triethanolamine were much slower than those of ethanolamine and diethanolamine because of the steric hindered structure of triethanolamine. The plausible structures of observed ions and heats of reaction for proton transfer were calculated with AM1 semiempirical method.

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

• Analytical Science and Technology
• /
• v.9 no.1
• /
• pp.1-12
• /
• 1996

The thermally labile compounds with hydroxyl group generate the [${MNH_4}^+$] ion, [$MH^+$] and [$MH^+-OH$] ion by ion-molecule reaction in LC/TSP/MS. But these ions create the trouble in the estimation of molecular weight of an unknown compound because the margin of [${MNH_4}^+$] ion and [$MH^+$] ion is same to that of [$MH^+$] ion and [$MH^+-OH$] ion. If it is compensated for the results by using of the $CF_3COOD+NH_4OH$ LC eluent, the molecular weight of analyte will be able to be confirmed. And this study was tried to recognize whether the fragment ions of thermally labile compound are generated by electron impact or by thermal degradation in ion source.

• Bioinformatics and Biosystems
• /
• v.1 no.2
• /
• pp.109-114
• /
• 2006

In proteomics research, proteins are digested into peptides by an enzyme and in mass spectrometer, these peptides break into fragment ions to generate tandem mass spectra. The tandem mass spectral data obtained from the mass spectrometer consists of the molecular weights of the precursor ion and fragment ions. The precursor ion mass of tandem mass spectrum is the first value that is fetched to sort the candidate peptides in the database search. We look far the peptide sequences whose molecular weight matches with precursor ion mass of the mass spectrum. Then, we choose one peptide sequence that shows the best match with fragment ions information. The precursor ion mass of the tandem mass spectrum is compared with that of the digested peptides of protein database within the mass tolerance that is assigned by users according to the mass spectrometer accuracy. In this study, we used reversed sequence database method to analyze the molecular weight distribution of precursor ions of the tandem mass spectra obtained by the FT LTQ mass spectrometer for human plasma sample. By reinterpreting the precursor ion mass distribution, we could compute the experimental accuracy and we suggested a method to improve the protein identification performance.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.8
• /
• pp.874-880
• /
• 1997

Various classes of phospholipids were investigated for the structural determination of fatty acyl groups by fast atom bombardment tandem mass spectrometry (FAB-MS/MS). Phospholipids were desorbed by FAB as molecules chelated with sodium ion (or ions). Collision-induced dissociation (CID) of intact sodium adduct molecular ions ([M+Na]+, [M-H+2Na]+ or [M+Na-2H]-) produced a series of homologous fragment ions via the charge-remote fragmentation along the fatty acid chains. These ions were found useful to locate the double bond positions even for the polyunsaturated fatty acid chains. The regiospecificity of the acyl chain linkages in phosphatidylcholine (PC) could also be determined based on the ratio of relative abundance of the product ions (i.e., [M+Na-85-R2COOH]+ vs [M+Na-85-R1COOH]+) in CID-MS/MS of [M+Na]+. These are generated by the loss of fatty acyl groups at sn-1 and sn-2, respectively, together with the choline group. In all the phospholipid compounds investigated, loss of the fatty acid at the sn-2 position was dominant. The present method was applied to the structural determination of molecular species of phosphatidylglycerols (PG) isolated from cyanobacterium Synechocystis sp. PCC 6803.

• Journal of Conservation Science
• /
• v.34 no.2
• /
• pp.129-135
• /
• 2018

Scientific investigation of cultural heritage can provide important information to understand the context of the object. To know the characteristics of the material is also an essential part of objects management and conservation. However, the identification and characterization of organic dyes used in archaeological and historical textiles are often limited by the restrictions in sampling. To cope with the difficulties, applications of high-performance techniques of surface analysis, such as Time of Flight-Secondary Ion Mass Spectra (TOF-SIMS) could be considered as a non or micro-destructive option. This study aims to examine the applicability of TOF-SIMS analysis to the detection of organic dyes from historical textiles. A group of silk fabrics dyed with vegetable dyes were artificially photo-aged to different degrees and analyzed with TOF-SIMS. Molecular and fragment ions from indigo were successfully detected from the aged samples; however, only some fragment ions were observed from gardenia and safflower dyed fabrics. Further studies with actual historical samples with extended examination scope would be necessary to assess the validity of this technique.