Characterization of bis-carboxyethyl germanium sesquioxide and its complexes with amino acids using electrospray QqTOF mass spectrometry

This work deals with the application of electrospray ionization mass spectrometry (ESI-MS) with QqTOF analyzer for the characterization of Ge-132 complexes with different amino acids in aqueous solution with the emphasis on the determination of elemental composition. ESI mass spectra provide complementary structural information in both polarity modes. Some reaction products were suggested based on the interpretation of high resolution mass spectra. Moreover, the experimental isotopic distributions of ions were compared with theoretical calculated isotopic clusters. The superposition of many ion overlays was observed due to the wide isotopic distributions of studied polyisotopic complexes. The high resolution QqTOF analyzer enabled the discrimination of these ion signals differing at least by 0.12 mass units. The occurrence of overlaid signals from ions with smaller mass difference was successfully recognized based on the shift of isotopic distribution, and their elemental composition was verified using mass accuracies of non-overlaid isotopes at the borders of the isotopic cluster. Mass spectra obtained with ion trap and single quadrupole analyzers support QqTOF data.     

Isotopologs and isotopomers: New analytical aspects of isotopic mass spectrometry in biology

Metabolic products of biological systems in most cases are polyatomic molecular structures containing polyisotopic elements (hydrogen, carbon, nitrogen, oxygen, sulfur, chorine, etc.) that are different in genesis and biosynthetic pathways. In the molecules carrying two and more atoms of polyisotopic element in different positions (sites), the probability of detection of isotopes by sites in the pool (array) of analyzed molecules may be different, i.e., there is intramolecular isotopic heterogeneity by the specified element. Detection and quantitative estimation of isotopic heterogeneity of polyisotopic elements in molecules by the methods of isotopic mass spectrometry is a novel source of information about the processes involving the respective polyisotopic element. An isotopic equation has been proposed, the coefficients of which are normalized peak intensities of isotopically different molecular ions in the mass spectrum of the analyte. Solutions of this equation reflect the abundance ratios of isotopic atoms of polyisotopic element by its positions in molecules comprising the analyzed pool. During homogenous (equally probable) distribution of isotopic atoms of the element by all of its sites in molecules of the analyzed pool, solutions of the isotopic equation are equal to each other. In the case of non-homogenous isotope distribution of the polyisotopic element in the pool of molecules, solutions of the isotopic equation take on different values and may be presented by both real and complex numbers. Solutions of the isotopic equation reflect the peculiarities of distribution of element isotopes in a molecule and possible pathways of formation of a pool of analyzed molecules under laboratory and natural conditions.     

Interpretation of mass spectra

A computer programme is described which calculates the mass numbers and the relative intensities of each of the lines in the cluster formed in a mass spectrometer from a single type of fragment ion which contains one or more polyisotopic elements. Many elements such as B, C, S, Cl and Br possess more than one naturally occurring isotope, and the relative abundances of the various isotopes are known. A whole series of possible fragment ions may be calculated quite readily, and the results, which are printed numerically and in the form of a histogram, facilitate the interpretation of mass spectra. Trial data, a FORTRAN listing of the programme, and a sample of the output are given. The programme requires approximately 17K of fast core, and should be implemented without difficulty on any computer with a FORTRAN IV compiler.     

Advanced Mass Calibration and Visualization for FT-ICR Mass Spectrometry Imaging

Mass spectrometry imaging by Fourier transform ion cyclotron resonance (FT-ICR) yields hundreds of unique peaks, many of which cannot be resolved by lower performance mass spectrometers. The high mass accuracy and high mass resolving power allow confident identification of small molecules and lipids directly from biological tissue sections. Here, calibration strategies for FT-ICR MS imaging were investigated. Sub-parts-per-million mass accuracy is demonstrated over an entire tissue section. Ion abundance fluctuations are corrected by addition of total and relative ion abundances for a root-mean-square error of 0.158?ppm on 16,764 peaks. A new approach for visualization of FT-ICR MS imaging data at high resolution is presented. The ??Mosaic Datacube?? provides a flexible means to visualize the entire mass range at a mass spectral bin width of 0.001?Da. The high resolution Mosaic Datacube resolves spectral features not visible at lower bin widths, while retaining the high mass accuracy from the calibration methods discussed.     

Characterization of Ni(II) complexes of Schiff bases of amino acids and (S)-N-(2-benzoylphenyl)-1-benzylpyrrolidine-2-carboxamide using ion trap and QqTOF electrospray ionization tandem mass spectrometry

This work demonstrates the application of electrospray ionization mass spectrometry (ESI-MS) using two different mass analyzers, ion trap and hybrid quadrupole time-of-flight (QqTOF) mass analyzer, for the structural characterization of Ni(II) complexes of Schiff bases of (S)-N-(2-benzoylphenyl)-1-benzylpyrrolidine-2-carboxamide with different amino acids. ESI enables the determination of molecular weight on the basis of rather simple positive-ion ESI mass spectra containing only protonated molecules and adducts with sodium or potassium ions. Fragmentation patterns are characterized by tandem mass spectrometric experiments, where both tandem mass analyzers provide complementary information. QqTOF data are used for the determination of elemental composition of individual ions due to mass accuracies always better than 3 ppm with the external calibration, while multistage tandem mass spectra obtained by the ion trap are suitable for studying the fragmentation paths. The novel aspect of our approach is the combination of mass accuracies and relative abundances of all isotopic peaks in isotopic clusters providing more powerful data for the structural characterization of organometallic compounds containing polyisotopic elements. The benefit of relative and absolute mean mass accuracies is demonstrated on the example of studied Ni(II) complexes. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window (m/z) regardless of their abundance. This acquisition strategy overcomes the traditional data-dependent ion selection boosting data reproducibility and sensitivity. However, several tandem mass (MS/MS) spectra of the same precursor ion are acquired during chromatographic elution resulting in large data redundancy. Also, the significant number of chimeric spectra and the absence of accurate precursor ion masses hamper peptide identification. Here, we describe an algorithm to preprocess data-independent MS/MS spectra by filtering out noise peaks and clustering the spectra according to both the chromatographic elution profiles and the spectral similarity. In addition, we developed an approach to estimate the m/z value of precursor ions from clustered MS/MS spectra in order to improve database search performance. Data acquired using a small 3 m/z units precursor mass window and multiple injections to cover a m/z range of 400–1400 was processed with our algorithm. It showed an improvement in the number of both peptide and protein identifications by 8 % while reducing the number of submitted spectra by 18 % and the number of peaks by 55 %. We conclude that our clustering method is a valid approach for data analysis of these data-independent fragmentation spectra. The software including the source code is available for the scientific community.

Mass spectrometric study of aliphatic alpha-carbonyl azides

A series of derivatives of 2-azidoacetic acid and 2-azidoacetone were synthesized and their behaviour under electron ionization conditions was investigated. This paper reports the electron ionization fragmentation mechanisms for five aliphatic alpha-carbonyl azides, which were clarified by accurate mass measurements and B/E linked scans. The substituent influences the abundance and the nature of the ions resulting from the molecular ion fragmentation.     

Reinforcing Isotope and Atomic-Weight Concepts in General Chemistry Using Internet-Based Mass-Spectral Data

This paper describes how isotope and atomic-weight concepts are enhanced for students using mass-spectral data from interactive Internet sites. The class considers mass spectra for compounds containing only monoisotopic elements and later for polyisotopic elements. Students calculate molecular weights based on data they acquire from mass spectra on the Internet.     

Performance optimisation of a new-generation orthogonal-acceleration quadrupole-time-of-flight mass spectrometer

Orthogonal-acceleration quadrupole time-of-flight (oa-QTOF) mass spectrometers, employed for accurate mass measurement, have been commercially available for well over a decade. A limitation of the early instruments of this type was the narrow ion abundance range over which accurate mass measurements could be made with a high degree of certainty. Recently, a new generation of oa-QTOF mass spectrometers has been developed and these allow accurate mass measurements to be recorded over a much greater range of ion abundances. This development has resulted from new ion detection technology and improved electronic stability or by accurate control of the number of ions reaching the detector. In this report we describe the results from experiments performed to evaluate the mass measurement performance of the Bruker micrOTOF-Q, a member of the new-generation oa-QTOFs. The relationship between mass accuracy and ion abundance has been extensively evaluated and mass measurement accuracy remained stable (+/-1.5 m m/z units) over approximately 3-4 orders of magnitude of ion abundance. The second feature of the Bruker micrOTOF-Q that was evaluated was the SigmaFit function of the software. This isotope pattern-matching algorithm provides an exact numerical comparison of the theoretical and measured isotope patterns as an additional identification tool to accurate mass measurement. The smaller the value, the closer the match between theoretical and measured isotope patterns. This information is then employed to reduce the number of potential elemental formulae produced from the mass measurements. A relationship between the SigmaFit value and ion abundance has been established. The results from the study for both mass accuracy and SigmaFit were employed to define the performance criteria for the micrOTOF-Q. This provided increased confidence in the selection of elemental formulae resulting from accurate mass measurements.     

Reproducible product-ion tandem mass spectra on various liquid chromatography/mass spectrometry instruments for the development of spectral libraries

The results of the comparison of product-ion tandem mass (MS/MS) spectra recorded on three ion trap mass spectrometers, a triple quadrupole mass spectrometer and a Fourier transform ion cyclotron resonance mass spectrometer are reported. The spectra were recorded in accordance with a simple experimental protocol, which involved the collision-induced dissociation (CID) attenuation of the abundance of the [M+H]+ ion to between 10 and 50% of its original abundance.The degree of similarity between the spectra from four of the mass spectrometers was calculated off-line by comparing the five most abundant ions from the spectrum on each instrument. A percentage fit value (20% for each ion that matches) was calculated by comparing each spectrum against the spectra recorded for the same compound on each instrument. The percentage of the inter-library pairwise comparisons (total = 434) that matched to > or = 60% ranged from 64-89%, depending on the instrument pair. A blind trial was also undertaken using five unknown compounds resulting in 1670 pairwise comparisons with the library entries. The blind trial produced no false positives and correct identifications in all cases. The results of the study have established the basis for the construction of a transferable product-ion MS/MS library.     

Characterization of 4-Aryl-5-ethoxycarbonyl-6-methyl-3,4-dihydro- pyrimidin-2 （1H）-thiones by EI-TOF Mass Spectrometry

IntroductionIn1893,Pietro Biginelli reported the first synthe-sis(termed the Biginelli reaction)of3,4-dihydropyrim-idinone(denoted as“oxo-orO-Biginelli compound”in-cluding its derivatives,type A in Scheme1).In thelast decade,interest in these compounds …     

Structure Analysis and Ion Abundance in CID- MS- MS Spectra of Isomeric Oligosaccharides Using Quadrupole Time-of- flight Mass Spectrometry: Distinguishing between Isomeric Oligosaccharides

N - Linked oligosaccharide were analyzed by using electrospray ionization (ESI) quadrupole time - of- fight mass spectrometry(Q - Tof MS).The isomers showed the same MS and collisioninduced desociation(CID) MS - MS spectra in the m/z values because the sequence of the sugar residues was the same.But the relative ion abundance of the specific fragment ion was greatly different between the isomers.So, the isomeric oligosacchariedes were distinguished by using the ion abundance in their CID -MS - MS spectra.Discussing the ion abundance in accurate level, quantitative analysis of the mixtures of isomers were also performed.     

Mass spectrometry of the trimethylsilyl derivatives of medicinal barbiturates

The electron ionization mass spectra of the trimethylsilyl derivatives of a number of medicinal barbiturates have been examined. The trimethylsilyl derivatives are useful in the identification of barbiturates by gas liquid chromatography/mass spectrometry (g.l.c.-m.s.). Mass spectra of these derivatives are characterized by abundant high mass ions which permit the ready distinction of one barbiturate from another. The prominent and characteristic [M - 15] ion is an effective monitor of molecular weight, while other unique fragmentations and/or varying patterns of relative abundance serve to differentiate isomers.     

Mass spectra of some azoles

The principal electron-impact fragmentation patterns of 3,4,5-triphenyl-1,2,4-triazole, 2,5-diphenyl-1,3,4-thiadiazole, their perfluorinated analogues and 2,5-di(pentafluorophenyl)-1,3,4-oxadiazole have been established from metastable ion evidence and precise mass measurements. Although ions produced by expulsion of nitrogen from the molecular-ions of these compounds are of low abundance, the simultaneous expulsion of nitrogen and a C₇X₅ radical (X = H or F) gives rise to abundant ions.     

Mechanism of production of ions in electrospray mass spectrometry

A mechanism for the production of multiply charged molecular ion species in electrospray mass spectrometry (ES-MS) is still required. A concise discussion of a recently published ionic solution equilibrium model offering a partial mechanism is presented. That publication proposed that the ion abundance–charge profile could be fitted by one or a series of superimposed Gaussian functions, in accord with a solution equilibrium model. It is shown that indeed a simulated mass spectrum based on a solution odel can compare well with the observed spectrum. However, some new and recently published experimental evidence is presented which shows that the ES mass spectra of many proteins give rise to multiply charged molecular ions which carry higher charges than those calculated by the model. Further, the ion abundance–charge profile is very sensitive to some experimental parameters, e.g. cone voltage; it does not necessarily reflect the solution or gaseous ion populations in the mass spectrometer source. Therefore, the concept that gaseous multi-charged ions originate from equivalently charged solvated ions in electrically neutral solution must be treated with caution.     

实时直接分析高分辨质谱技术研究碳硼烷类化合物

该文运用高分辨质谱技术对实时直接分析(Direct analysis in real time,DART)离子化条件下碳硼烷化合物的质谱行为进行了研究,对碳硼烷化合物DART高分辨质谱中所得到的同位素峰簇进行了表征与归属。研究结果表明,选取的碳硼烷化合物在DART负离子条件下均能得到较好的质谱信号,这可能与硼笼结构的“缺电性”有关。含10个B原子的碳硼烷化合物形成的离子同位素峰簇信号中,通常情况下相对丰度最高的同位素峰中含2个10B以及8个11B。将碳硼烷化合物高分辨质谱分析的精确m/z数据信息与图谱中同位素峰轮廓分析相结合,是碳硼烷化合物有效的质谱定性分析与表征策略。     

Factorial Experimental Designs Elucidate Significant Variables Affecting Data Acquisition on a Quadrupole Orbitrap Mass Spectrometer

Instrument parameter values for a quadrupole Orbitrap mass spectrometer were optimized for performing global proteomic analyses. Fourteen factors were evaluated for their influence on data-dependent acquisition with an emphasis on both the rate of sequencing and spectral quality by maximizing two individually tested response variables (unique peptides and protein groups). Of the 14 factors, 12 factors were assigned significant contrast values (P?<?0.05) for both response variables. Fundamentally, when optimizing parameters, a balance between spectral quality and duty cycle needs to be reached in order to maximize proteome coverage. This is especially true when using a data-dependent approach for sequencing complex proteomes. For example, maximum ion injection time, automatic gain control settings, and minimum threshold settings for triggering MS/MS isolation and activation all heavily influence ion signal, the number of spectra collected, and spectral quality. To better assess the effect these parameters have on data acquisition, all MS/MS data were parsed according to ion abundance by calculating the percent of the AGC target reached for each MS/MS event and then compared with successful peptide-spectrum matches. This proved to be an effective approach for understanding the effect of ion abundance on successful peptide-spectrum matches and establishing minimum ion abundance thresholds for triggering MS/MS isolation and activation.

IR-MALDESI Mass Spectrometry Imaging of Biological Tissue Sections Using Ice as a Matrix

Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging of biological tissue sections using a layer of deposited ice as an energy-absorbing matrix was investigated. Dynamics of plume ablation were first explored using a nanosecond exposure shadowgraphy system designed to simultaneously collect pictures of the plume with a camera and collect the Fourier transform ion cyclotron resonance FT-ICR mass spectrum corresponding to that same ablation event. Ablation of fresh tissue analyzed with and without using ice as a matrix were compared using this technique. Effect of spot-to-spot distance, number of laser shots per pixel, and tissue condition (matrix) on ion abundance were also investigated for 50 μm-thick tissue sections. Finally, the statistical method called design of experiments was used to compare source parameters and determine the optimal conditions for IR-MALDESI of tissue sections using deposited ice as a matrix. With a better understanding of the fundamentals of ablation dynamics and a systematic approach to explore the experimental space, it was possible to improve ion abundance by nearly one order of magnitude.

Mass spectra of substituted uracils

The mechanisms for the major fragmentations obtained with selected substituted uracils are discussed. Interpretation of data was facilitated by use of metastable peaks, high-resolution data, and low-voltage spectra. The major fragmentation obtained with N-alkyl substituted uracils, when the alkyl group contains 2 or more carbons, is due to cleavage of the alkyl substituent. This cleavage is accompanied by a rearrangement of 1 or 2 hydrogens from the alkyl group to the uracil ring. Possible mechanisms for the rearrangements are discussed. It was found that the molecular ion of 1- and 3-alkyl substituted uracils (where the alkyl group has 2 or more carbons) does not undergo the expected ‘retro Diels-Alder Reaction’. Instead, the odd-electron ion formed by loss of the alkyl substituent with a single hydrogen rearrangement undergoes this reaction (loses HNCO). Since it is formed as a secondary reaction product, the relative abundance of the ‘retro Diels-Alder’ fragment is low compared to what is obtained in the spectra of the simple uracils. The ‘retro Diels-Alder Reaction’ can be used to differentiate between 2- and 4-thiouracils, and between 1- and 3-methyl and phenyl substituted uracils. It was found that 1- and 3-alkyl substituted uracils (alkyl group of 2 or more carbons) can be differentiated by the mass of the M-alkyl fragment since the 3-substituted compounds give predominantly a double hydrogen rearrangement and the 1-substituted compound gives mainly a single hydrogen rearrangement. In addition the intensity of the molecular ion, relative to the M-alkyl ion, is considerably stronger in the 1-substituted uracils.