Extending a Tandem Mass Spectral Library to Include MS<Superscript>2</Superscript> Spectra of Fragment Ions Produced In-Source and MS<Superscript>n</Superscript> Spectra

Tandem mass spectral library searching is finding increased use as an effective means of determining chemical identity in mass spectrometry-based omics studies. We previously reported on constructing a tandem mass spectral library that includes spectra for multiple precursor ions for each analyte. Here we report our method for expanding this library to include MS² spectra of fragment ions generated during the ionization process (in-source fragment ions) as well as MS³ and MS⁴ spectra. These can assist the chemical identification process. A simple density-based clustering algorithm was used to cluster all significant precursor ions from MS¹ scans for an analyte acquired during an infusion experiment. The MS² spectra associated with these precursor ions were grouped into the same precursor clusters. Subsequently, a new top-down hierarchical divisive clustering algorithm was developed for clustering the spectra from fragmentation of ions in each precursor cluster, including the MS² spectra of the original precursors and of the in-source fragments as well as the MSⁿ spectra. This algorithm starts with all the spectra of one precursor in one cluster and then separates them into sub-clusters of similar spectra based on the fragment patterns. Herein, we describe the algorithms and spectral evaluation methods for extending the library. The new library features were demonstrated by searching the high resolution spectra of E. coli extracts against the extended library, allowing identification of compounds and their in-source fragment ions in a manner that was not possible before.

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Data-dependent neutral gain MS<Superscript>3</Superscript>: Toward automated identification of the N-Oxide functional group in drug metabolites

We report here an automated method for the identification of N-oxide functional groups in drug metabolites by using the combination of liquid chromatography/tandem mass spectrometry (LC/MS ⁿ ) based on ion-molecule reactions and collision-activated dissociation (CAD). Data-dependent acquisition, which has been readily utilized for metabolite characterization using CAD-based methods, is adapted for use with ion-molecule reaction-based tandem mass spectrometry by careful choice of select experimental parameters. Two different experiments utilizing ion-molecule reactions are demonstrated, data-dependent neutral gain MS³ and data-dependent neutral gain pseudo-MS³, both of which generate functional group selective mass spectral data in a single experiment and facilitate increased throughput in structural elucidation of unknown mixture components. Initial results have been generated by using an LC/MS ⁿ method based on ion-molecule reactions developed earlier for the identification of the N-oxide functional group in pharmaceutical samples, a notoriously difficult functional group to identify via CAD alone. Since commercial software and straightforward, external instrument modification are used, these experiments are readily adaptable to the industrial pharmaceutical laboratory.     

Thermodynamics of Complex Formation of Ce<Superscript>3+</Superscript> and La<Superscript>3+</Superscript> Ions with Glycylglycine in Aqueous Solution

Enthalpy of the complex formation between diglycine (HL^±) and Ce³⁺ or La³⁺ at 308.15 K and ionic strength of 0.5 mol/L (KNO₃) has been determined by means of calorimetry. Thermodynamic parameters of the diglycine complexes formation with Ce³⁺ and La³⁺ at different metal to ligand molar ratios have been determined.     

Effect of Ca<Superscript>2+</Superscript>, Mg<Superscript>2+</Superscript>, Fe<Superscript>3+</Superscript>, and Al<Superscript>3+</Superscript> Ions on the Deposition of Electrolytic Manganese Dioxide from Chloride Solutions

The effect of Ca²⁺, Mg²⁺, Fe³⁺, and Al³⁺ ions on the deposition of electrolytic manganese dioxide from chloride solutions was studied.__________Translated from Zhurnal Prikladnoi Khimii, Vol. 78, No. 5, 2005, pp. 751–754.Original Russian Text Copyright © 2005 by Kolosnitsyn, Minnikhanova, Karaseva, Dmitriev, Muratov.     

Determination of <Superscript>3</Superscript>H, <Superscript>226</Superscript>Ra, <Superscript>222</Superscript>Rn and <Superscript>238</Superscript>U in Austrian ground- and drinking water

Screening measurements for ³H, ²²⁶Ra, ²²²Rn and ²³⁸U in ground water were performed within a ground- and drinking water project in Austria. The aim of this project is to get an overview of the distribution of natural radionuclide activity concentration levels in ground water bodies. In some cases this water is used for drinking water abstraction. In this paper methods and results of the screening measurements are presented. Regions with high activity concentrations were identified and in these regions further investigation for ²²⁸Ra, ²¹⁰Pb and ²¹⁰Po will be conducted.     

New and automated MS<Superscript>n</Superscript> approaches for top-down identification of modified proteins

An automated top-down approach including data-dependent MS(3) experiment for protein identification/characterization is described. A mixture of wild-type yeast proteins has been separated on-line using reverse-phase liquid chromatography and introduced into a hybrid linear ion trap (LTQ) Fourier transform ion cylclotron resonance (FTICR) mass spectrometer, where the most abundant molecular ions were automatically isolated and fragmented. The MS(2) spectra were interpreted by an automated algorithm and the resulting fragment mass values were uploaded to the ProSight PTM search engine to identify three yeast proteins, two of which were found to be modified. Subsequent MS(3) analyses pinpointed the location of these modifications. In addition, data-dependent MS(3) experiments were performed on standard proteins and wild-type yeast proteins using the stand alone linear trap mass spectrometer. Initially, the most abundant molecular ions underwent collisionally activated dissociation, followed by data-dependent dissociation of only those MS(2) fragment ions for which a charge state could be automatically determined. The resulting spectra were processed to identify amino acid sequence tags in a robust fashion. New hybrid search modes utilized the MS(3) sequence tag and the absolute mass values of the MS(2) fragment ions to collectively provide unambiguous identification of the standard and wild-type yeast proteins from custom databases harboring a large number of post-translational modifications populated in a combinatorial fashion.     

Scalar-relativistic 5f-in-core pseudopotentials and core-polarization potentials for trivalent actinides: calibration calculations for Ac<Superscript>3+</Superscript>, Cm<Superscript>3+</Superscript> and Lr<Superscript>3+</Superscript> complexes

The performance of recently proposed 5f-in-core pseudopotentials for the trivalent actinides was investigated in calculations for model complexes An³⁺L ⁿ⁻ for three selected actinides (An³⁺ = Ac³⁺, Cm³⁺, Lr³⁺) and eight simple ligands with atoms from the first three periods of the table of elements (L ⁿ⁻ = F⁻, Cl⁻, OH⁻, SH⁻, CO, NH₂⁻, H₂O, H₂S, NH₃). Results of Hartree-Fock and Coupled Cluster with singles, doubles and perturbative triples calculations using basis sets of quadruple-zeta quality are compared to corresponding reference data obtained with scalar-relativistic energy-adjusted 5f-in-valence small-core pseudopotentials. The inclusion of core-polarization potentials in the 5f-in-core pseudopotential calculations and corrections of the basis set superposition error by the counterpoise correction leads to very good agreement between the 5f-in-valence and 5f-in-core pseudopotential results for bond lengths, bond angles and binding energies. Results from 5f-in-core pseudopotential calculations using different density functionals also show reasonable agreement with the more rigorous Coupled Cluster results. It is argued that the An 5f rather than the An f population is a useful criterion for the applicability of a specific An 5f-in-core pseudopotential.     

Water-soluble polymers as chelating agents for the deposition of Er<Superscript>3+</Superscript>/Yb<Superscript>3+</Superscript>:LiNbO<Subscript>3</Subscript> waveguiding films

Compared to other oxide materials, the sol-gel deposition of an optically transparent LiNbO₃ waveguiding film of sufficient thickness (approx. 1?μm) is complicated by the presence of a highly hydrolyzing Nb(V) in the starting solution. Thicker films require more concentrated solutions that are not easily achieved for such ions. This problem may be solved using strong chelating agents such as water-soluble polymers. To prepare a stable Er(III)/Yb(III)/Li(I)/Nb(V)/2-methoxyethanol solution with high metal concentration, we tested three such polymers: polyethylene glycol (PEG), polyacrylic acid (PAA) and polyvinyl alcohol (PVA), and compared them with already used polyvinylpyrrolidone (PVP). The solutions were spin-coated on crystalline sapphire substrates under a multi-step heating-deposition regime. Apart from Er³⁺/Yb³⁺ photoluminescence properties, we evaluated the influence of the film microstructure (SEM, AFM) on optical transparency and waveguiding ability in the UV/Vis/NIR region (transmission and m-line spectroscopy). Among the newly tested polymers, only PEG was able to prevent Nb(V) hydrolysis up to a maximum metal concentration of 0.6?mol/L. For PEG and PVP, the crystallization temperature of the deposited films (between 700?°C and 1000?°C) was compared. After further optimization of the heating-deposition process, we were able to prepare a transparent Er³⁺/Yb³⁺:LiNbO₃ film thick enough to guide an optical signal in the NIR region. Thus, the use of PEG results is one of the very few non-hydrolytic sol-gel methods suitable for the preparation of not only luminescent, but also waveguiding Er³⁺/Yb³⁺:LiNbO₃ structures.

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MS<Superscript>n</Superscript> characterization of protonated cyclic peptides and metal complexes

MSⁿ experiments involving low energy collisionally activated dissociation (CAD) in a quadrupole ion trap were used to characterize the fragmentation of alkali, alkaline earth and transition metal complexes of five cyclic peptides, and the results were compared with those obtained for protonated cyclic peptides. Complexes with metal ions produced enhanced abundances of the most diagnostic fragments for elucidating the primary structures. For cyclosporin A, nickel and lithium complexes gave additional sequence information compared with the protonated peptide. For depsipeptides, sodium and lead complexes were superior to the protonated peptide or other metal complexes for sequencing residues, and CAD of the lead complexes led to preferential cleavage of two residues at a time. For cyclic lipopeptides, complexes with silver, nickel and strontium ions provided enhanced abundances of key fragment ions.     

Distinctive and Complementary MS<Superscript>2</Superscript> Fragmentation Characteristics for Identification of Sulfated Sialylated <Emphasis Type="Italic">N</Emphasis>-Glycopeptides by nanoLC-MS/MS Workflow

High sensitivity identification of sulfated glycans carried on specific sites of glycoproteins is an important requisite for investigation of molecular recognition events involved in diverse biological processes. However, aiming for resolving site-specific glycosylation of sulfated glycopeptides by direct LC-MS² sequencing is technically most challenging. Other than the usual limiting factors such as lower abundance and ionization efficiency compared to analysis of non-glycosylated peptides, confident identification of sulfated glycopeptides among the more abundant non-sulfated glycopeptides requires additional considerations in the selective enrichment and detection strategies. Metal oxide has been applied to enrich phosphopeptides and sialylated glycopeptides, but its use to capture sulfated glycopeptides has not been investigated. Likewise, various complementary MS² fragmentation modes have yet to be tested against sialylated and non-sialylated sulfoglycopeptides due to limited appropriate sample availability. In this study, we have investigated the feasibility of sequencing tryptic sulfated N-glycopeptide and its MS² fragmentation characteristics by first optimizing the enrichment methods to allow efficient LC-MS detection and MS² analysis by a combination of CID, HCD, ETD, and EThcD on hybrid and tribrid Orbitrap instruments. Characteristic sulfated glyco-oxonium ions and direct loss of sulfite from precursors were detected as evidences of sulfate modification. It is anticipated that the technical advances demonstrated in this study would allow a feasible extension of our sulfoglycomic analysis to sulfoglycoproteomics.

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Measurements of <Superscript>210</Superscript>Po and <Superscript>210</Superscript>Pb in total diet samples: Estimate of dietary intakes of <Superscript>210</Superscript>Po and <Superscript>210</Superscript>Pb for Japanese

To estimate the dietary intakes of ²¹⁰Pb and ²¹⁰Po for the Japanese adults and their annual effective doses, ²¹⁰Pb and ²¹⁰Po were measured for 240 daily diet samples collected at two locations of Ishikawa Prefecture in Japan over three years by duplicate portion studies. No appreciable differences in intake rates of ²¹⁰Pb and ²¹⁰Po and their ²¹⁰Po/²¹⁰Pb ratios were seen among the years in each district, and between the two districts. The intake rates evaluated using 240 diet samples were 0.20 Bq/d/p for ²¹⁰Pb and 0.61 Bq/d/p for ²¹⁰Po as a median, respectively. Annual effective doses of ²¹⁰Pb and ²¹⁰Po for Japanese adults were estimated to be 0.050 and 0.053 mSv/y, respectively.     

1,9-Dicarbonyl-2,8-dioxo-butyne-ester Ferrocenophane: Synthesis,Structure and Recognition Properties for Co<Superscript>2+</Superscript> and Cu<Superscript>2+</Superscript> Ions

An efficient highly diluted synthetic approach to the synthesis of 1,9-dicarbonyl-2,8-dioxo-butyne ester ferrocenophane (L) has been developed. The title compound was characterized by IR, UV, FL, 1H NMR, spectroscopies, elemental analysis and so on. Further complex L shows fluorescence responses to Co²⁺ and Cu²⁺ in CH3OH, The results indicate that the complex could be applied in multianayte detection. The binding ability of receptor L CH3OH was tested for various cations (Co²⁺, Cu²⁺, Zn²⁺, and Ni²⁺ in water) and the binding constants for Co²⁺ and Cu²⁺ were the computed, having a distinct absorbance shift. The receptor is a very attractive array because its distinct absorbance shift profile in a semi-aqueous phase, making it applicable in the area of biology, environmental sciences and material chemistry.     

Sequential separation of <Superscript>99</Superscript>Tc, <Superscript>94</Superscript>Nb, <Superscript>55</Superscript>Fe, <Superscript>90</Superscript>Sr and <Superscript>59/63</Superscript>Ni from radioactive wastes

A sequential separation procedure has been developed for the determination of ⁹⁹Tc, ⁹⁴Nb, ⁵⁵Fe, ⁹⁰Sr and ^59/63Ni in various radioactive wastes generated from nuclear power plants. Ion exchange and extraction chromatography were adopted for individual separation of the radionuclides. Precipitation was supplementarily utilized for both purification of the individual radionuclides and preparation of the radionuclide sources for use in a radioactivity measurement. The chromatographic separation behavior of the radionuclides both from the sample matrix metals and from one another was investigated using stable metals, Re (as a surrogate of ⁹⁹Tc), Nb, Fe, Sr and Ni. The validity of the procedure for reliability and applicability was evaluated by measuring the recovery of the metal carriers added to synthetic radioactive waste solutions. The recoveries by the chromatographic separation were in the range of 84.8 to 102.2% with 2s of less than 8.6%, the recoveries by the precipitation being in the range of 84.3 to 97.3% with 2s of less than 10.9%.     

MS<Superscript>M</Superscript>, an Efficient Workflow for Metabolite Identification Using Hybrid Linear Ion Trap Orbitrap Mass Spectrometer

Identification of drug metabolites can often yield important information regarding clearance mechanism, pharmacologic activity, or toxicity for drug candidate molecules. Additionally, the identification of metabolites can provide beneficial structure-activity insight to help guide lead optimization efforts towards molecules with optimal metabolic profiles. There are challenges associated with detecting and identifying metabolites in the presence of complex biological matrices, and new LC-MS technologies have been developed to meet these challenges. In this report, we describe the development of an experimental approach that applies unique features of the hybrid linear ion trap Orbitrap mass spectrometer to streamline in vitro and in vivo metabolite identification experiments. The approach, referred to as MS^M, utilizes multiple collision cells, dissociation methods, mass analyzers, and detectors. With multiple scan types and different dissociation modes built into one experimental method, along with flexible post-acquisition analysis options, the MS^M workflow offers an attractive option to fast and reliable identification of metabolites in different kinds of in vitro and in vivo samples. The MS^M workflow was successfully applied to metabolite identification analysis of verapamil in both in vitro rat hepatocyte incubations and in vivo rat bile samples.     

Preparation of <Superscript>26</Superscript>Al, <Superscript>59</Superscript>Ni, <Superscript>44</Superscript>Ti, <Superscript>53</Superscript>Mn and <Superscript>60</Superscript>Fe from a proton irradiated copper beam dump

The station for pions cancer therapy was operated at PSI from 1980 to 1992. After a cooling time of 12 years it’s made of copper beam dump was cut and samples were taken for analytical purposes. The sampling collected about 500 g of high active copper chips that can be used for separation of exotic radionuclides. The analyses by gamma spectrometry, LSC and AMS showed main nuclides present to be ⁶⁰Co, ⁵⁴Mn, ²²Na, ⁶⁵Zn, ²⁶Al, ⁵³Mn, ⁵⁹Ni, ⁶³Ni, ⁵⁵Fe and ⁶⁰Fe and ⁴⁴Ti with a daughter nuclide ⁴⁴Sc. In the frame of ERAWAST project a procedure combining selective precipitation and ion exchange for the separation of the rare radionuclides from the copper beam dump was developed. The proposed separation procedure is easy for remote controlled implementation in a hot cell. The ion exchange separation of Ni, Al, Mg, Ti and Fe was complete and high decontamination factors for copper and cobalt were achieved. Based on the developed procedure a remotely controlled system for separation of exotic radionuclides from the copper chips was set up. The full scale system was installed in a hot cell where high activity levels can be handled. In order to evaluate the reliability and functionality of the system extensive tests have been done. During the test period 13.86 g in total of the proton irradiated copper beam dump were processed for separation of ²⁶Al, ⁵⁹Ni, ⁵³Mn, ⁴⁴Ti and ⁶⁰Fe. The results showed that the system was operational and the radionuclide separation was selective with high chemical yield. The procedure manages as well the generated liquid wastes containing high level of ⁶⁰Co activity.     

Disequilibrium of dissolved <Superscript>234</Superscript>U/<Superscript>238</Superscript>U and <Superscript>210</Superscript>Po/<Superscript>210</Superscript>Pb in Greek rivers

For the first time, a radiological study for the dissolved ²³⁸U, ²³⁴U, ²¹⁰Pb and ²¹⁰Po was held in major Greek rivers across the country. ²³⁴U/²³⁸U activity ratios are above one in all samples and ²¹⁰Po/²¹⁰Pb activity ratios are respectively below the unit indicating the disequilibrium in the samples. Quite satisfactory correlations were observed among ²³⁴U and ²³⁸U as well as among ²¹⁰Po and ²¹⁰Pb values. Uranium isotopes were separated by ion exchange and electroplated on stainless steel plates. ²¹⁰Po was spontaneously deposited on nickel plates, while ²¹⁰Pb was indirectly determined through the ingrowth of ²¹⁰Po. The sources were measured by a-spectrometry.     

Hydrolytic Behavior of La<Superscript>3+</Superscript> and Sm<Superscript>3+</Superscript> at Various Temperatures

The hydrolytic species of lanthanide ions, La³⁺ and Sm³⁺, in water at I = 0.1 mol·dm^?3 KCl ionic strength and temperatures of 298.15, 310.15 and 318.15 K were investigated by potentiometry. The hydrolytic species were modeled by the HySS simulation program. From the results, the hydrolytic species of each metal ion at different temperatures were calculated using the program HYPERQUAD2013. The hydrolysis constants (log₁₀ β) of [La(OH)]²⁺ and La(OH)₃ were calculated as ?8.52 ± 0.46, ?26.84 ± 0.48, and log₁₀ β values of [Sm(OH)]²⁺, [Sm(OH)₂]⁺, Sm(OH)₃ were calculated as ?7.11 ± 0.21, ?15.84 ± 0.25 and ?23.44 ± 0.52 in aqueous media at 298.15 K, respectively. The dependence of the hydrolysis constants on the temperature allowed us to calculate the enthalpy, entropy, and Gibbs energy of hydrolysis values of each species.     

Hydrothermal synthesis of core-shell structured PS@GdPO<Subscript>4</Subscript>:Tb<Superscript>3+</Superscript>/Ce<Superscript>3+</Superscript> spherical particles and their luminescence properties

Non-aggregated spherical polystyrene (PS) particles were coated with GdPO₄:Tb³⁺/Ce³⁺ phosphor layers by a conventional hydrothermal synthesis using poly(vinylpyrrolidone) (PVP) as an additive without further annealing treatment. X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), photoluminescence (PL), as well as luminescence decay experiments were used to characterise the resulting core-shell structured PS@GdPO₄:Tb³⁺/Ce³⁺ samples. The results of XRD indicated that the PS particles were successfully coated with the GdPO₄:Tb³⁺/Ce³⁺ phosphor layers, which could be further verified by the images of FESEM. Under ultraviolet excitation, the PS@GdPO₄:Tb³⁺/Ce³⁺ phosphors show Tb³⁺ characteristic emission, i.e. ⁵D₄-⁷F_J (J = {6, 5, 4, 3}) emission lines with green emission ⁵D₄-⁷F₅ (543 nm) as the most prominent group. The core-shell phosphors so obtained have potential applications in field emission display (FED) and plasma display panels (PDP).