Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry

Screening and identifying cucurbitacins and cucurbitacin glycosides in Cucumis sativus using high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry combined with in-source fragmentation and alkali adduct ions

RATIONALE

Cucumber, as a popular fruit and vegetable, has tremendously contributed to providing a sufficient and high-quality food supply. However, the cucumber plant metabolites, which may possess potential benefits for human health, were rarely reported. In addition, rapid detection of these metabolites from the complex biological matrix of cucumber samples is a tremendous challenge.

METHODS

A rapid detection method was established to systematically screen cucurbitacins and cucurbitacin glycosides in cucumber plants by combining high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (HPLC-Q-TOF-MS) with in-source fragmentation (ISF). Moreover, the alkali cations, including acetic acid, 0.1% LiCl, 0.1% NH₄ Cl, 0.1% NaCl, and 0.1% KCl, were added to the mobile phase for improving the ion response.

RESULTS

The fragmentation pathways of seven cucurbitacins and cucurbitacin glycosides were primarily investigated. The characteristic ISF ions at m/z 501.3211 and 503.3367 were identified and employed to screen 40 cucurbitacins and cucurbitacin glycosides from the complex biological matrix. Their structures were identified by their tandem mass spectrometry (MS/MS) spectra and fragmentation pathways of references. Finally, the metabolic distribution and network of cucurbitacins and cucurbitacin glycosides in cucumber plants were also proposed.

CONCLUSIONS

This work marks the first systematic and comprehensive study of the metabolites in cucumber plants using HPLC-Q-TOF-MS technology, providing a template for screening and identifying the triterpenoids from other plant-derived medicines or food.

Specific Interactions of Antitumor Metallocenes with Deoxydinucleoside Monophosphates

Bent metallocenes Cp₂MCl₂ (M = Ti, V, Nb, Mo) are known to exhibit cytotoxic activity against a variety of cancer types. Though the mechanism of action is not fully understood yet, the accumulation of the metal ions in the nucleus points towards DNA as one of the primary targets. A set of eight deoxydinucleoside monophosphates was used to study the adduct yields with metallocenes and cisplatin. The binding affinities are reflected by the relative intensities of the adducts and were found to follow the order of Pt > V > Ti > Mo (no adducts were detected with Nb). High-resolution tandem mass spectrometry was applied to locate the binding patterns in the deoxydinucleoside monophosphates. Whereas cisplatin binds to the soft nitrogen atoms in the purine nucleobases, the metallocenes additionally interact with the hard phosphate oxygen, which is in good agreement with the hard and soft (Lewis) acids and bases (HSAB) concept. However, the binding specificities were found to be unique for each metallocene. The hard Lewis acids titanium and vanadium predominantly bind to the deprotonated phosphate oxygen, whereas molybdenum, an intermediate Lewis acid, preferentially interacts with the nucleobases. Nucleobases comprise alternative binding sites for titanium and vanadium, presumably oxygen atoms for the first and nitrogen atoms for the latter. In summary, the intrinsic binding behavior of the different metallodrugs is reflected by the gas-phase dissociation of the adducts. Consequently, MS/MS can provide insights into therapeutically relevant interactions between metallodrugs and their cellular targets. Graphical Abstract ᅟ.

Characterization of nucleic acids by tandem mass spectrometry - The second decade (2004-2013): From DNA to RNA and modified sequences

Nucleic acids play key roles in the storage and processing of genetic information, as well as in the regulation of cellular processes. Consequently, they represent attractive targets for drugs against gene-related diseases. On the other hand, synthetic oligonucleotide analogues have found application as chemotherapeutic agents targeting cellular DNA and RNA. The development of effective nucleic acid-based chemotherapeutic strategies requires adequate analytical techniques capable of providing detailed information about the nucleotide sequences, the presence of structural modifications, the formation of higher-order structures, as well as the interaction of nucleic acids with other cellular components and chemotherapeutic agents. Due to the impressive technical and methodological developments of the past years, tandem mass spectrometry has evolved to one of the most powerful tools supporting research related to nucleic acids. This review covers the literature of the past decade devoted to the tandem mass spectrometric investigation of nucleic acids, with the main focus on the fundamental mechanistic aspects governing the gas-phase dissociation of DNA, RNA, modified oligonucleotide analogues, and their adducts with metal ions. Additionally, recent findings on the elucidation of nucleic acid higher-order structures by tandem mass spectrometry are reviewed. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:483-523, 2016.

Structure of the Pb²⁺-deprotonated dGMP complex in the gas phase: a combined MS-MS/IRMPD spectroscopy/ion mobility study

The structure of the Pb(2+)-deprotonated 2'-deoxyguanosine-5'-monophosphate (dGMP) complex, generated in the gas phase by electrospray ionization, was examined by combining tandem mass spectrometry, mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and ion mobility. In the gas phase, the main binding site of Pb(2+) onto deprotonated dGMP is the deprotonated phosphate group, but the question is whether an additional stabilization of the metallic complex can occur via participation of the carbonyl group of guanine. Such macrochelates indeed correspond to the most stable structures according to theoretical calculations. A multiplexed experimental approach was used to characterize the gas-phase conformation of the metallic complex and hence determine the binding mode of Pb(2+) with [dGMP](-). MS/MS analysis, observation of characteristic bands by IRMPD spectroscopy, and measurement of the ion mobility collision cross section suggest that gaseous [Pb(dGMP)-H](+) complexes adopt a macrochelate folded structure, which consequently differs strongly from the zwitterionic forms postulated in solution from potentiometric studies.

Direct evidence for tautomerization of the uracil moiety within the Pb2+/uridine-5'-monophosphate complex: a combined tandem mass spectrometry and IRMPD study

The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.

Study of fragmentation pathways of lithiated alpha,beta-unsaturated thioesters by electrospray ionization mass spectrometry

The fragmentation pathways of lithiated alpha,beta-unsaturated thioesters with different substituents were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in positive ion mode. In mass spectrometry of the alpha,beta-unsaturated thioesters, Ar-CH=CH-CO-S-Ph, loss of PhSLi and elimination of a thiophenol were the two major fragmentation reactions of the lithiated molecules. The elemental compositions of all the ions were confirmed by high-resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS). The thioesters studied here were para-monosubstituted on the phenyl ring of cinnamoyl and the electron-withdrawing groups favored loss of a thiophenol, whereas the electron-releasing groups strongly favored the competing reaction leading to the loss of PhSLi to form a cinnamoyl cation, Ar-CH=CHCO(+). The intensity ratios of the two competitive product ions were well correlated with the sigma(p) (+) substituent constants. The mechanisms of these two competing routes were further investigated by density functional theory (DFT) calculations.

Investigation of metal-oligonucleotide complexes by nanoelectrospray tandem mass spectrometry in the positive mode

The formation and fragmentation of multiply metal-coordinated oligonucleotides was studied by nanoelectrospray tandem mass spectrometry in the positive ion mode. Fundamental aspects of the gas-phase behavior of metal-oligonucleotide complexes are revealed. The addition of transition metal ions, such as iron(II), iron(III), and zinc(II), leads to very stable metal-oligonucleotide complexes which show heavily altered fragmentation patterns in contrast to uncomplexed oligonucleotides. The site of metal ion complexation was located by collision-induced dissociation (CID) experiments. It was found that all three metal ions investigated predominantly coordinate to the central phosphate groups of the oligonucleotides. Furthermore, it is demonstrated that the fragmentation of such complexes depends highly upon the metal ion complexed as well as on the sequence of the nucleobases in the oligonucleotide.

Electrospray ionization mass spectrometry of pyrimidine base-rubidium complexes

Nucleobases and alkali metal cations, under electrospray ionisation conditions, tend to form the so-called magic number clusters (unusually stable clusters in comparison with the neighbouring ones). The effect of the ion source parameters, namely cone voltage and desolvation temperature and relative concentrations of thymine and RbCl on the [T5+Rb]+ ion abundance has been studied.