European Journal of Mass Spectrometry最新文献

{"title":"Fragmentation analysis of O-specific polysaccharide from bacteria Vibrio cholerae O139 by MALDI-TOF and LC/ESI-MS/MS","authors":"Filip Pančík, Z. Pakanová, Jana Mečárová, Alžbeta Čížová, S. Bystrický, S. Kozmon, P. Baráth","doi":"10.1177/14690667221099119","DOIUrl":"https://doi.org/10.1177/14690667221099119","url":null,"abstract":"Cholera is a life-threatening diarrhoeal disease caused by ingestion of Vibrio cholerae . There are at least 200 serogroups of V. cholerae but only two of them are causing epidemics – O1 and O139 serogroups. Fragmentation analysis of O-antigen, also known as O-specific polysaccharide (OSP), from lipopolysaccharide (LPS) is important to obtain new information about its structure, such as fragmentation patterns and fragment structures. In the present study, OSP and core (OSPc) structure from V. cholerae O139 was studied using matrix-assisted laser desorption ionization (MALDI)-time of flight (TOF) and direct injection electrospray ionization (ESI)-MS methods. MALDI-TOF analysis was performed in positive-ion reflectron mode, while ESI-MS was performed in negative ionization mode. ESI-MS analysis was followed by ESI-MS/MS analysis. Using this analytical approach, we managed to obtain two possible fragmentation pathways of OSP from V. cholerae O139 . Mutual sign of these two pathways is shortening the length of the oligosaccharide by neutral loss of monosaccharide residues. Additionally, liquid chromatography-MS analysis was performed to separate depicted molecular forms of OSPc.","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":"28 1","pages":"47 - 55"},"PeriodicalIF":1.3,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41838695","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":"GC-MS based metabolite fingerprinting of serous ovarian carcinoma and benign ovarian tumor","authors":"E. Eroglu, U. Kucukgoz Gulec, M. Vardar, S. Paydaş","doi":"10.1177/14690667221098520","DOIUrl":"https://doi.org/10.1177/14690667221098520","url":null,"abstract":"The aim of this study is to identify urinary metabolomic profile of benign and malign ovarian tumors patients. Samples were analyzed using gas chromatography-mass spectrometry (GC-MS) and metabolomic tools to define biomarkers that cause differentiation between groups. 7 metabolites were found to be different in patients with ovarian cancer (OC) and benign tumors (BT). R2Y and Q2 values were found to be 0.670 and 0.459, respectively. L-tyrosine, glycine, stearic acid, turanose and L-threonine metabolites were defined as prominent biomarkers. The sensitivity of the model was calculated as 90.72% and the specificity as 82.09%. In the pathway analysis, glutathione metabolism, aminoacyl-tRNA biosynthesis, glycine serine and threonine metabolic pathway, primary bile acid biosynthesis pathways were found to be important. According to the t-test, 29 metabolites were found to be significant in urine samples of OC patients and healthy controls (HC). R2Y and Q2 values were found to be 0.8170 and 0.749, respectively. These results showed that the model has high compatibility and predictive power. Benzoic acid, L-threonine, L-pyroglutamic acid, creatinine and 3,4-dihydroxyphenylacetic acid metabolites were determined as prominent biomarkers. The sensitivity of the model was calculated as 93.81% and the specificity as 98.59%. Glycine serine and threonine metabolic pathway, glutathione metabolism and aminoacyl-tRNA biosynthesis pathways were determined important in OC patients and HC. The R2Y, Q2, sensitivity and specificity values in the urine samples of BT patients and HC were found to be 0.869, 0.794, 91.75, 97.01% and 97.18%, respectively. L-threonine, L-pyroglutamic acid, benzoic acid, creatinine and pentadecanol metabolites were determined as prominent biomarkers. Valine, leucine and isoleucine biosynthesis and aminoacyl-tRNA biosynthesis were significant. In this study, thanks to the untargeted metabolomic approach and chemometric methods, every group was differentiated from the others and prominent biomarkers were determined.","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":"28 1","pages":"12 - 24"},"PeriodicalIF":1.3,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43743155","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 dipolar excitation for quadrupole mass filter","authors":"A. Konenkov, N. Konenkov, A. Sysoev","doi":"10.1177/14690667221087515","DOIUrl":"https://doi.org/10.1177/14690667221087515","url":null,"abstract":"The results of modeling AC and DC dipole excitation of ion oscillations in a quadrupole mass filter are presented. The simulation is done by numerical integration of the ion motion equations, ions’ initial coordinates and velocities are distributed normally. For AC dipole excitation the instability bands on the (a, q) stability diagram follow along the isolines β x / 2 and β y / 2 , creating regular dips on the transmission contour. We show that AC excitation at frequency Ω/2 makes it possible to control the resolution of the mass filter by either changing the AC amplitude or phase. Instability bands can be used for mass selective excitation in a linear ion trap. Options for the joint use of DC and AC dipole excitation to form the mass peak shape are considered.","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":"28 1","pages":"65 - 72"},"PeriodicalIF":1.3,"publicationDate":"2022-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43415810","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":"Elucidating the Fragmentation Mechanism of Protonated Lewis A Trisaccharide using MSⁿ CID.","authors":"Volker Iwan,&nbsp;Jürgen Grotemeyer","doi":"10.1177/14690667211069033","DOIUrl":"https://doi.org/10.1177/14690667211069033","url":null,"abstract":"<p><p>Lewis blood group antigens are a prominent example of isomeric oligosaccharides with biological activity. Understanding the fragmentation mechanism in the gas phase is essential for their identification and assignment by mass spectrometric methods such as ESI-MS. In this work, the [M + H]⁺ species of Lewis A trisaccharide and Lewis A trisaccharide methyl glycoside were studied by ESI-MS with FT-ICR as mass analyzer with respect to their fragmentation mechanism. The comparison between the underivatized and the methylated species has shown that the reducing end plays a key role in this mechanism. The results of this study question the existence of Z-type fragment ions after activation of the protonated species. The main product of the fragmentation are Y-type fragment ions and a combination of Y-type fragmentation and the loss of water at the reducing end instead of Z-type fragmentation. C-type fragment ions could not be detected. MS³ measurements also reveal that each fragment ion only occurs with the participation of a mobile proton and the possibility of glycosidic bond cleavage after fragmentation has already occurred at the reducing end as B₂ fragment ion.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":"27 6","pages":"256-265"},"PeriodicalIF":1.3,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39872685","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":"Development and validation of ultra performance liquid chromatography-tandem mass spectrometry method for the simultaneous estimation of dolutegravir, lamivudine and tenofovir in bulk and tablet dosage form.","authors":"Vyshali Veerareddy,&nbsp;Sireesha Dodda,&nbsp;Kiran Gangarapu","doi":"10.1177/14690667211058564","DOIUrl":"https://doi.org/10.1177/14690667211058564","url":null,"abstract":"<p><p>A simple, selective and rapid ultra performance liquid chromatography-tandem mass spectrometry method was developed and validated for the simultaneous estimation of dolutegravir, lamivudine and tenofovir in bulk and tablet dosage form. Chromatographic separation was attained on Acquity Ethylene Bridged Hybrid (BEH) C18 column (50 × 2.1 mm, 3.5 µm), using a mixture of acetonitrile and 0.1% formic acid in water (60:40, v/v) as a mobile phase at a flow rate of 0.12 mL/min. The total run time of analysis was 3.5 min. The analytes were detected using tandem mass spectrometry, operating in positive ionization and multiple reaction monitoring modes. The method's linearity was determined to be in the range of 10-150 ng/mL with <i>r</i>² > 0.99. The proposed method was validated as per the International Council for Harmonization (ICH) guidelines, and the results were found well within the acceptance limits. The method was successfully applied for the simultaneous quantification of all the three analytes in the combined tablet dosage form.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":"27 6","pages":"249-255"},"PeriodicalIF":1.3,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39681394","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":"BeerMIMS: Exploring the Use of Membrane-Inlet Mass Spectrometry (MIMS) Coupled to KNIME for the Characterization of Danish Beers.","authors":"Sean Sebastian Hughes,&nbsp;Marcus M K Nielsen,&nbsp;Rasmus Voersaa Jonsbo,&nbsp;Carsten Uhd Nielsen,&nbsp;Frants Roager Lauritsen,&nbsp;Bala Krishna Prabhala","doi":"10.1177/14690667211073317","DOIUrl":"https://doi.org/10.1177/14690667211073317","url":null,"abstract":"<p><p>Beer is a complex mix of more than 7700 compounds, around 800 of which are volatile. While GC-MS has been actively employed in the analysis of the volatome of beer, this method is challenged by the complex nature of the sample. Herein, we explored the possible of using membrane-inlet mass spectrometry (MIMS) coupled to KNIME to characterize local Danish beers. KNIME stands for Konstanz Information Miner and is a free open-source data processing software which comes with several prebuilt nodes, that, when organized, result in data processing workflows allowing swift analysis of data with outputs that can be visualized in the desired format. KNIME has been shown to be promising in automation of large datasets and requires very little computing power. In fact, most of the computations can be carried out on a regular PC. Herein, we have utilized a KNIME workflow for data visualization of MIMS data to understand the global volatome of beers. Feature identification was not possible as of now but with a combination of MIMS and a KNIME workflow, we were able to distinguish beers from different micro-breweries located in Denmark, laying the foundation for the use of MIMS in future analysis of the beer volatome.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":"27 6","pages":"266-271"},"PeriodicalIF":1.3,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39650291","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":"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":"27 6","pages":"217-234"},"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":"Discovery of metabolomic biomarkers for discriminating platinum-sensitive and platinum-resistant ovarian cancer by using GC-MS.","authors":"Evren C Eroglu,&nbsp;Sule Tunug,&nbsp;Omer Faruk Geckil,&nbsp;Umran Kucukgoz Gulec,&nbsp;Mehmet Ali Vardar,&nbsp;Semra Paydas","doi":"10.1177/14690667211057996","DOIUrl":"https://doi.org/10.1177/14690667211057996","url":null,"abstract":"<p><p>This study aims to determine ovarian cancer (OC) patients with platinum resistance for alternative treatment protocols by using metabolomic methodologies. Urine and serum samples of platinum-resistant and platinum-sensitive OC were analyzed using GC-MS. After data processing of GC-MS raw data, multivariate analyses were performed to interpret complex data for biologically meaningful information and to identify the biomarkers that cause differences between two groups. The biomarkers were verified after univariate, multivariate, and ROC analysis. Finally, metabolomic pathways related to group separations were specified. The results of biomarker analysis showed that 3,4-dihydroxyphenylacetic acid, 4-hydroxybutyric acid, L-threonine, D- mannose, and sorbitol metabolites were potential biomarkers in urine samples. In serum samples, L-arginine, linoleic acid, L-glutamine, and hypoxanthine were identified as important biomarkers. R2Y, Q2, AUC, sensitivity and specificity values of platinum-resistant and sensitive OC patients' urine and serum samples were 0.85, 0.545, 0.844, 91.30%, 81.08 and 0.570, 0.206, 0.743, 77.78%, 74.28%, respectively. In metabolic pathway analysis of urine samples, tyrosine metabolism and fructose and mannose metabolism were found to be statistically significant (p < 0.05) for the discrimination of the two groups. While 3,4-dihydroxyphenylacetic acid, L-tyrosine, and fumaric acid metabolites were effective in tyrosine metabolism. D-sorbitol and D-mannose metabolites were significantly important in fructose and mannose metabolism. However, seven metabolomic pathways were significant (p < 0.05) in serum samples. In terms of <i>p-</i>value, L-glutamine in the nitrogen metabolic pathway from the first three pathways; L-glutamine and pyroglutamic acid metabolites in D-glutamine and D-glutamate metabolism. In the arginine and proline metabolic pathway, L-arginine, L-proline, and L-ornithine metabolites differed significantly between the two groups.</p>","PeriodicalId":12007,"journal":{"name":"European Journal of Mass Spectrometry","volume":"27 6","pages":"235-248"},"PeriodicalIF":1.3,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39913230","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":"27 5","pages":"158-165"},"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":"27 5","pages":"191-204"},"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}