European Journal of Mass Spectrometry最新文献

{"title":"Evaluation of an integrative Bayesian peptide detection approach on a combinatorial peptide library.","authors":"Miroslav Hruska,&nbsp;Dusan Holub","doi":"10.1177/14690667211066725","DOIUrl":"https://doi.org/10.1177/14690667211066725","url":null,"abstract":"<p><p>Detection of peptides lies at the core of bottom-up proteomics analyses. We examined a Bayesian approach to peptide detection, integrating match-based models (fragments, retention time, isotopic distribution, and precursor mass) and peptide prior probability models under a unified probabilistic framework. To assess the relevance of these models and their various combinations, we employed a complete- and a tail-complete search of a low-precursor-mass synthetic peptide library based on oncogenic KRAS peptides. The fragment match was by far the most informative match-based model, while the retention time match was the only remaining such model with an appreciable impact--increasing correct detections by around 8 %. A peptide prior probability model built from a reference proteome greatly improved the detection over a uniform prior, essentially transforming <i>de novo</i> sequencing into a reference-guided search. The knowledge of a correct sequence tag in advance to peptide-spectrum matching had only a moderate impact on peptide detection unless the tag was long and of high certainty. The approach also derived more precise error rates on the analyzed combinatorial peptide library than those estimated using PeptideProphet and Percolator, showing its potential applicability for the detection of homologous peptides. Although the approach requires further computational developments for routine data analysis, it illustrates the value of peptide prior probabilities and presents a Bayesian approach for their incorporation into peptide detection.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39790849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical description of electric fields in three-dimensional multipole ion traps.","authors":"Maxim Vasilyev,&nbsp;Semyon Rudyi,&nbsp;Yuri Rozhdestvensky","doi":"10.1177/14690667211047918","DOIUrl":"https://doi.org/10.1177/14690667211047918","url":null,"abstract":"<p><p>In this paper, the principle of forming the spatial distribution of the potential in multipole three-dimensional ion traps of a general type is considered. A matrix method for describing the electric fields in ion traps for the <math><mi>n</mi></math>th order of multipole is proposed. Typical electrode geometries for hexapole and octupole traps are considered.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39570583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Poly(2-vinylpyridine) as a reference compound for mass calibration in positive-ion matrix-assisted laser desorption/ionization-mass spectrometry on different instrumental platforms.","authors":"Jürgen H Gross","doi":"10.1177/14690667211055701","DOIUrl":"https://doi.org/10.1177/14690667211055701","url":null,"abstract":"<p><p>Butyl-terminated poly(2-vinylpyridine) (P2VP), C₄H₉(C₇H₇N)<i>_n</i>H, is evaluated for use as an external and internal mass calibrant in positive-ion matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). P2VP oligomers covering the <i>m/z</i> 450-4500 range are employed to calibrate a time-of-flight (TOF) mass spectrometer in linear and reflector mode, an ion mobility-quadrupole-time-of-flight (IM-Q-TOF) mass spectrometer, and a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The proton affinity of P2VPs introduced by the numerous pyridyl groups leads to the almost exclusive formation of [M + H]⁺ ions with common acidic matrices like α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) as well as with the non-acidic and aprotic matrices 1,8-dihydroxy-10<i>H</i>-anthracen-9-on (dithranol) and 2-[(2<i>E</i>)-3-(4-<i>tert</i>-butylphenyl)-2-methylprop-2-enylidene]malonitrile (DCTB). This prevalence of [M + H]⁺ ions evenly spaced at Δ(<i>m/z</i>) = 105.0578 renders butyl-terminated P2VP oligomers as convenient mass calibrants. The mass accuracies achieved across various <i>m/z</i> ranges with different mass analyzers and modes of operation are evaluated by using established standard compounds. Results as obtained by internal or external calibration are presented. Further, the compilation of mass reference lists tailored to suit the respective analyzer modes is discussed and those reference files are provided.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8586192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39592845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Joseph John Thomson investigates the paranormal.","authors":"Kevin M Downard","doi":"10.1177/14690667211050599","DOIUrl":"https://doi.org/10.1177/14690667211050599","url":null,"abstract":"<p><p>Joseph John Thomson is best known for detecting two isotopes of neon within cathode ray tubes that lay the foundation of the field of mass spectrometry. He was awarded the 1906 Nobel Prize in Physics for the discovery of the electron and for his work on the conduction of electricity in gases in the same devices. He is less known for his strong religious beliefs and his interest in psychical research and the paranormal. Thomson served as a member of the Society for Psychical Research for over 50 years and even became its Vice President. During this time, he attended a number of séances and demonstrations by professed psychics and mediums. This article traces those who influenced his interest in the paranormal, from Balfour Stewart to Lord Rayleigh and William Crookes. It reports and illustrates his beliefs and experiences investigating the paranormal in his own words.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39493740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vacuum ultraviolet photoionization and dissociative photoionization of toluene: Experimental and theoretical insights.","authors":"Yujie Zhao,&nbsp;Pei Huang,&nbsp;Li Li,&nbsp;Yousheng Zhan,&nbsp;Ke Wang,&nbsp;Haohang Yang,&nbsp;Jianhui Jin,&nbsp;Yuqian Chen,&nbsp;Yibao Liu,&nbsp;Liusi Sheng,&nbsp;Jun Chen,&nbsp;Maoqi Cao","doi":"10.1177/14690667211042707","DOIUrl":"https://doi.org/10.1177/14690667211042707","url":null,"abstract":"<p><p>The photoionization and dissociative photoionization of toluene have been studied using synchrotron radiation vacuum ultraviolet light with photon energy in the range of 8.50-25.50 eV. The ionization energies (8.82 eV) and double ionization energies (23.80 eV) of toluene as well as the appearance energies for its major fragments C₇H₇⁺ (11.17/10.71 eV), C₆H₅⁺ (13.73 eV), C₅H₆⁺ (13.58/12.50 eV), C₅H₅⁺ (16.23 eV), C₄H₅⁺ (15.64 eV), C₄H₄⁺ (16.10 eV) and C₄H₃⁺ (17.11 eV) are determined, respectively by using photoionization efficiency spectrometry. With the help of experimental and theoretical results, seven dissociative photoionization channels have been proposed: C₇H₇⁺ + H, C₆H₅⁺ + CH₃, C₅H₆⁺ + C₂H₂, C₅H₅⁺ + C₂H₂ + H, C₄H₅⁺ + C₃H₃, C₄H₄⁺ + C₃H₄ and C₄H₃⁺ + C₃H₄ + H. In addition, the geometries of the intermediates, transition states and products involved in these photoionization and dissociative photoionization processes have been performed at the B3LYP/6-311++G(d, p) level. The mechanisms of dissociative photoionization of toluene and the intermediates and transition states involved are discussed in detail. Generally speaking, the experimental results are in agreement with theoretical calculations in this work and published literature results. Especially the mechanisms of dissociative photoionization to C₄H₅⁺, C₄H₄⁺ and C₄H₃⁺ were discussed for the first time in this work. This investigation may provide useful information on understanding the photoionization and dissociative photoionization of toluene.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39512923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-resolution mass spectrometry reveals a complex ganglioside pattern and novel polysialylated structures associated with the human motor cortex.","authors":"Raluca Ica,&nbsp;Cristian Va Munteanu,&nbsp;Zeljka Vukelic,&nbsp;Alina D Zamfir","doi":"10.1177/14690667211040912","DOIUrl":"https://doi.org/10.1177/14690667211040912","url":null,"abstract":"<p><p>We have developed here a superior methodology based on high-resolution mass spectrometry for screening and fragmentation analysis of gangliosides extracted and purified from the human motor cortex . The experiments, conducted on a nanoelectrospray Orbitrap mass spectroscope in the negative ion mode, allowed the discrimination in the native mixture extracted from human motor cortex of no less than 83 different gangliosides, which represents the highest number of structures identified so far in this brain region. The spectral data, acquired in high-resolution mass spectrometry mode with a remarkable sensitivity and an average mass accuracy of 4.48 ppm, also show that the gangliosidome of motor cortex is generally characterized by species exhibiting a much higher degree of sialylation than previously known. Motor cortex was found dominated by complex structures with a sialylation degree ≥3, exhibiting long saccharide chains, in the G1 class. Fucogangliosides and species with the glycan chain elongated by either <i>O</i>-acetylation and/or acetate anion attachments were also detected; the later modification was for the first time discovered in this brain region. Of major significance is the identification of hepta and octasialylated species of GS1 and GO1 type, which are among the structures with the longest oligosaccharide chain discovered so far in the human brain. In the last stage of research, tandem mass spectrometry performed by higher energy collision dissociation provided structural data documenting the occurrence of GT1b (d18:1/20:0) isomer in the human motor cortex.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39411933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proximity Effects in Mass Spectra of Benzanilides.","authors":"Nathan W Fenwick,&nbsp;Amie Saidykhan,&nbsp;Yasser Nazir,&nbsp;Richard Telford,&nbsp;Binyaameen Masood,&nbsp;William H C Martin,&nbsp;Richard T Gallagher,&nbsp;Richard D Bowen","doi":"10.1177/14690667211054152","DOIUrl":"https://doi.org/10.1177/14690667211054152","url":null,"abstract":"<p><p>The analytical value of peaks arising by a proximity effect in the electron ionization mass spectra of benzanilides has been established by examining the spectra of numerous examples of general structure XC₆H₄NHCOC₆H₄Y. Significant [M-X]⁺ signals are observed only when X = Cl, Br, I or CH₃O in the 2-position. The presence of strong [M-X]⁺ signals, but negligibly weak [M-Y]⁺ peaks, even when the C-Y bond would be expected to break more readily than the C-X bond, indicates that these diagnostically useful signals do not arise by simple cleavage. Similarly, the presence of an appreciable [M-Cl]⁺ signal, but no [M-Br]⁺ signal, in the spectra of representative examples of 4-Br-2ClC₆H₃NHCOC₆H₄Y, reveals that loss of a substituent from the 2-position occurs much more rapidly than fission of a weaker bond to a substituent in the 4-position. These trends are interpreted in terms of cyclization of the ionized 2-substituted benzanilide, followed by elimination of the substituent originally in the 2-position, to form a protonated 2-arylbenzoxazole.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b1/ba/10.1177_14690667211054152.PMC8586190.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39699764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Certain Properties of a Generalized Class of Analytic Functions Involving Some Convolution Operator","authors":"F.S.A. Malik, Nusrat Ahmed Dar, Chitaranjan Sharma","doi":"10.34198/EJMS.7121.4976","DOIUrl":"https://doi.org/10.34198/EJMS.7121.4976","url":null,"abstract":"We use the concept of convolution to introduce and study the properties of a unified family \u0000 $mathcal{TUM}_gamma(g,b,k,alpha)$, \u0000 $(0leqgammaleq1,,kgeq0)$, \u0000 consisting of uniformly $k$-starlike and $k$-convex functions of \u0000 complex order $binmathbb{C}setminus{0}$ \u0000 and type $alphain[0,1)$.\u0000 The family $mathcal{TUM}_gamma(g,b,k,alpha)$ is a generalization of several other families of analytic functions available in literature.\u0000 Apart from discussing the coefficient bounds, sharp radii estimates, extreme points and the subordination theorem for this family, we settle down the Silverman's conjecture for integral means inequality. Moreover, invariance of this family under certain well-known integral operators is also established in this paper. Some previously known results are obtained as special cases.","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49519356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling of Extreme Crude Oil Price using the Generalized Pareto Distribution: Brent and West Texas Benchmark Price","authors":"Ngozi J. Amachukwu, H. Obiora-Ilouno, E. I. Obisue","doi":"10.34198/EJMS.6221.359374","DOIUrl":"https://doi.org/10.34198/EJMS.6221.359374","url":null,"abstract":"Background and objective: Crude oil is an essential commodity in many countries of the world. This work studies the risk involved in the extreme crude oil price, using the daily crude oil price of the Brent and the West Texas benchmark from year 1990 to 2019. Materials and methods: The Peak Over Threshold (POT) approach of the Generalized Pareto Distribution (GPD) was used to model the extreme crude oil price while the value at risk and the expected shortfall was used to quantify the risk involved in extreme price of crude oil. The GPD, using the Q-Q plot was found to be a good model for the extreme values of the crude oil price. Results: The Value at Risk (VaR) and the Expected Shortfall (ES) calculated at 90%, 95% and 99% with the Maximum Likelihood estimators of GPD parameters and the threshold values were found to decrease with increase in quantile for both benchmark. This shows that risk involved in extreme crude oil price will be borne only by the investors and public. Conclusion: It was also found that the VaR and ES of the Brent are higher than that of West Texas. This implies that it is safer to invest in West Texas crude oil.","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49305655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Third Hankel Determinant Problem for Certain Subclasses of Analytic Functions Associated with Nephroid Domain","authors":"Muhammad Ghaffar Khan, B. Ahmad, W. K. Mashwani, T. G. Shaba, Muhammad Arif","doi":"10.34198/EJMS.6221.293308","DOIUrl":"https://doi.org/10.34198/EJMS.6221.293308","url":null,"abstract":"In this research article we consider two well known subclasses of starlike and bounded turning functions associated with nephroid domain. Our aims to find third Hankel determinant for these classes.","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43760078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}