Journal of the American Society for Mass Spectrometry最新文献

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Studying Structural Details in Complex Samples. I. Combining two Chromatographic Separation Methods with Ultrahigh Resolution Mass Spectrometry
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-18 DOI: 10.1021/jasms.4c0022610.1021/jasms.4c00226
Jens Dreschmann, Lilla Molnarne Guricza and Wolfgang Schrader*, 
{"title":"Studying Structural Details in Complex Samples. I. Combining two Chromatographic Separation Methods with Ultrahigh Resolution Mass Spectrometry","authors":"Jens Dreschmann,&nbsp;Lilla Molnarne Guricza and Wolfgang Schrader*,&nbsp;","doi":"10.1021/jasms.4c0022610.1021/jasms.4c00226","DOIUrl":"https://doi.org/10.1021/jasms.4c00226https://doi.org/10.1021/jasms.4c00226","url":null,"abstract":"<p >The analysis of complex mixtures poses a challenge due to the high number of compounds present in a mixture, which often exceed the capabilities of analytical methods and instruments. Even more challenging is understanding the structural details of compounds within a complex sample. Most analytical methods provide just bulk information on complex samples, and individual structural details cannot be observed. High-resolution mass spectrometry, the best method to analyze complex samples, suffers from inherent problems for structural studies in complex systems because collision-induced fragmentation (CID) measurements cannot provide data from individual compounds alone. The combination of different steps of chromatographic separation, here the combination of size exclusion chromatography with argentation chromatography, provides sufficient reduction in complexity to implement a method that allows gaining structural details of individual compounds within a complex mixture. The combination of offline size exclusion chromatography followed by online argentation chromatography effectively creates fractions based on the respective properties of the compounds in the mixture (size and number of π-bonds and heteroatoms) and reduces matrix effects to a great extent. Mass spectrometry with ultrahigh resolution provides basic chemical information for each detected compound and also provides the opportunity to gain structural information from MS/MS experiments. The results indicate effectively separated sample fractions yielded by the chromatographic steps with tremendously decreased total numbers of compounds. Especially, argentation chromatography proved to be a valuable separation tool when it comes to heteroatom-containing constituents. In the end, the fragmentation experiments indicated high-quality data due to the clean ion isolation enabled by prior separation. The structural elucidations provided deep insights into the carbon space of crude oil.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"2859–2868 2859–2868"},"PeriodicalIF":3.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00226","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Identity Algorithm: How the Most Popular Electron Ionization Mass Spectral Library Search Engine Actually Works
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-18 DOI: 10.1021/jasms.4c0035010.1021/jasms.4c00350
Andrey Samokhin*, 
{"title":"The Identity Algorithm: How the Most Popular Electron Ionization Mass Spectral Library Search Engine Actually Works","authors":"Andrey Samokhin*,&nbsp;","doi":"10.1021/jasms.4c0035010.1021/jasms.4c00350","DOIUrl":"https://doi.org/10.1021/jasms.4c00350https://doi.org/10.1021/jasms.4c00350","url":null,"abstract":"<p >The Identity algorithm implemented in the MS Search (NIST) software is widely used for library searches of gas chromatography/mass spectrometry data against electron ionization mass spectral databases. It has been available to researchers since 1993, with the release of MS Search 1.5a. Despite its extensive use, the operational details of the algorithm have remained ambiguous. Attempts to replicate the algorithm have been unsuccessful because, as found in this research, the description in the manual is neither fully complete nor accurate. The main novelty of this work is the development of a unique approach for deconstructing the Identity algorithm. It is purely based on analyzing library search results obtained from several groups of synthetic mass spectra, each tailored to isolate and examine specific components of the algorithm. This approach facilitated a comprehensive understanding of the Identity algorithm and led to the development of a custom implementation that fully replicates the results obtained from the original MS Search software. The custom implementation of the Identity algorithm is now available in the <span>mssearchr</span> R package, enhancing accessibility for researchers.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3178–3183 3178–3183"},"PeriodicalIF":3.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Strategies for Using Postcolumn Infusion of Standards to Correct for Matrix Effect in LC-MS-Based Quantitative Metabolomics
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-15 DOI: 10.1021/jasms.4c0040810.1021/jasms.4c00408
Anne-Charlotte Dubbelman*, Bo van Wieringen, Lesley Roman Arias, Michael van Vliet, Roel Vermeulen, Amy C. Harms and Thomas Hankemeier*, 
{"title":"Strategies for Using Postcolumn Infusion of Standards to Correct for Matrix Effect in LC-MS-Based Quantitative Metabolomics","authors":"Anne-Charlotte Dubbelman*,&nbsp;Bo van Wieringen,&nbsp;Lesley Roman Arias,&nbsp;Michael van Vliet,&nbsp;Roel Vermeulen,&nbsp;Amy C. Harms and Thomas Hankemeier*,&nbsp;","doi":"10.1021/jasms.4c0040810.1021/jasms.4c00408","DOIUrl":"https://doi.org/10.1021/jasms.4c00408https://doi.org/10.1021/jasms.4c00408","url":null,"abstract":"<p >The matrix effect limits the accuracy of quantitation of the otherwise popular metabolomics technique liquid chromatography coupled to mass spectrometry (LC-MS). The gold standard to correct for this phenomenon, whereby compounds coeluting with the analyte of interest cause ionization enhancement or suppression, is to quantify an analyte based on the peak area ratio with an isotopologue added to the sample as an internal standard. However, these stable isotopes are expensive and sometimes unavailable. Here, we describe an alternative approach: matrix effect correction and quantifying analytes using a signal ratio with a postcolumn infused standard (PCIS). Using an LC-MS/MS method for eight endocannabinoids and related metabolites in plasma, we provide strategies to select, optimize, and evaluate PCIS candidates. Based on seven characteristics, the structural endocannabinoid analogue arachidonoyl-2′-fluoroethylamide was selected as a PCIS. Three methods to evaluate the PCIS correction vs no correction showed that PCIS correction improved values for the matrix effect, precision, and dilutional linearity of at least six of the analytes to within acceptable ranges. PCIS correction also resulted in parallelization of calibration curves in plasma and neat solution, for six of eight analytes even with higher accuracy than peak area ratio correction with their stable isotope labeled internal standard, i.e., the gold standard. This enables quantification based on neat solutions, which is a significant step toward absolute quantification. We conclude that PCIS has great, but so far underappreciated, potential in accurate LC-MS quantification.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3286–3295 3286–3295"},"PeriodicalIF":3.1,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00408","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Actinide Elemental Ratios of Spent Nuclear Fuel Samples by Resonance Ionization Mass Spectrometry
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-13 DOI: 10.1021/jasms.4c0037110.1021/jasms.4c00371
Manuel Raiwa*, Michael R. Savina, Autumn G. Roberts, Danielle Z. Shulaker and Brett H. Isselhardt, 
{"title":"Actinide Elemental Ratios of Spent Nuclear Fuel Samples by Resonance Ionization Mass Spectrometry","authors":"Manuel Raiwa*,&nbsp;Michael R. Savina,&nbsp;Autumn G. Roberts,&nbsp;Danielle Z. Shulaker and Brett H. Isselhardt,&nbsp;","doi":"10.1021/jasms.4c0037110.1021/jasms.4c00371","DOIUrl":"https://doi.org/10.1021/jasms.4c00371https://doi.org/10.1021/jasms.4c00371","url":null,"abstract":"<p >While resonance ionization mass spectrometry (RIMS) has demonstrated utility in measuring isotopic compositions of elements in complex matrices without the need for chemical separation to remove isobaric interferences, it has had limited application in measuring elemental compositions. The ability to determine elemental compositions via an in situ method like RIMS would be an exceptional asset in spent nuclear fuel analysis, where they are important in assessing reactor histories and whose chemical separation presents a radiological hazard. However, quantitative elemental analysis by RIMS requires special considerations because each element is ionized by its own set of lasers tuned to element specific resonant ionization wavelengths. We present the first comprehensive study of measuring elemental ratios by RIMS in spent nuclear fuel. All actinides produced by neutron capture are enhanced significantly radially from the center to the edge of a fuel pellet. This edge effect is not readily accessible by conventional bulk measurements.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3233–3241 3233–3241"},"PeriodicalIF":3.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00371","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Measuring 15N and 13C Enrichment Levels in Sparsely Labeled Proteins Using High-Resolution and Tandem Mass Spectrometry
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-12 DOI: 10.1021/jasms.4c0023710.1021/jasms.4c00237
Elijah T. Roberts, Jonathan Choi, Jeremy Risher, Paul G. Kremer, Adam W. Barb and I. Jonathan Amster*, 
{"title":"Measuring 15N and 13C Enrichment Levels in Sparsely Labeled Proteins Using High-Resolution and Tandem Mass Spectrometry","authors":"Elijah T. Roberts,&nbsp;Jonathan Choi,&nbsp;Jeremy Risher,&nbsp;Paul G. Kremer,&nbsp;Adam W. Barb and I. Jonathan Amster*,&nbsp;","doi":"10.1021/jasms.4c0023710.1021/jasms.4c00237","DOIUrl":"https://doi.org/10.1021/jasms.4c00237https://doi.org/10.1021/jasms.4c00237","url":null,"abstract":"<p >Isotope labeling of both <sup>15</sup>N and <sup>13</sup>C in selected amino acids in a protein, known as sparse labeling, is an alternative to uniform labeling and is particularly useful for proteins that must be expressed using mammalian cells, including glycoproteins. High levels of enrichment in the selected amino acids enable multidimensional heteronuclear NMR measurements of glycoprotein three-dimensional structure. Mass spectrometry provides a means to quantify the degree of enrichment. Mass spectrometric measurements of tryptic peptides of a selectively labeled glycoprotein expressed in HEK293 cells revealed complicated isotope patterns which consisted of many overlapping isotope patterns from intermediately labeled peptides, which complicates the determination of the label incorporation. Two challenges are uncovered by these measurements. Metabolic scrambling of amino groups can reduce the <sup>15</sup>N content of enriched amino acids or increase the <sup>15</sup>N in nontarget amino acids. Also, undefined, unlabeled medium components may dilute the enrichment level of labeled amino acids. The impact of this unexpected metabolic scrambling was overcome by simulating isotope patterns for all isotope-labeled peptide states and generating linear combinations to fit to the data. This method has been used to determine the percent incorporation of <sup>15</sup>N and <sup>13</sup>C labels and has identified several metabolic scrambling effects that were previously undetected in NMR experiments. Ultrahigh mass resolution is also utilized to obtain isotopic fine structure, from which enrichment levels of <sup>15</sup>N and <sup>13</sup>C can be assigned unequivocally. Finally, tandem mass spectrometry can be used to confirm the location of heavy isotope labels in the peptides.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"2877–2889 2877–2889"},"PeriodicalIF":3.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deciphering Isotopic Fine Structures of Silylated Compounds in Gas Chromatography–Vacuum Photoionization Orbitrap Mass Spectrometry of Bio-Oils
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-12 DOI: 10.1021/jasms.4c0038310.1021/jasms.4c00383
Silvia Juliana Vesga Martínez, Christopher P. Rüger*, Paul Kösling, Julian Schade, Sven Ehlert, Yury O. Tsybin and Ralf Zimmermann, 
{"title":"Deciphering Isotopic Fine Structures of Silylated Compounds in Gas Chromatography–Vacuum Photoionization Orbitrap Mass Spectrometry of Bio-Oils","authors":"Silvia Juliana Vesga Martínez,&nbsp;Christopher P. Rüger*,&nbsp;Paul Kösling,&nbsp;Julian Schade,&nbsp;Sven Ehlert,&nbsp;Yury O. Tsybin and Ralf Zimmermann,&nbsp;","doi":"10.1021/jasms.4c0038310.1021/jasms.4c00383","DOIUrl":"https://doi.org/10.1021/jasms.4c00383https://doi.org/10.1021/jasms.4c00383","url":null,"abstract":"<p >We introduce vacuum resonance-enhanced multiphoton ionization (REMPI) with high-resolution Orbitrap Fourier transform mass spectrometry (FTMS) for analyzing silylated polar compounds. UV laser radiation at 248 nm sensitively and selectively targets aromatic constituents, while high-resolution mass spectrometry (HRMS) enables high-performance mass spectrometric detection. This workflow enhances the detection confidence of polar constituents by identifying unique isotopologue patterns, including at the isotopic fine structure (IFS) level, in analytical standards and complex bio-oils. A direct and derivatized gas chromatography (GC) procedure on a polar standard component mixture allowed us to explore the general ionization and detection characteristics of REMPI FTMS. HRMS enabled the examination of the complex isotopologue profiles, revealing distinct patterns for the CHO<sub><i>x</i></sub>Si<sub><i>y</i></sub>-class compounds. Particularly in complex mixtures, this isobaric/isonucleonic complexity exceeded the classical mass resolution capabilities of the employed Orbitrap D30 series and prompted the usage of prolonged transients via an external data acquisition system. This procedure substantially improved mass spectrometric results by recording the unreduced time-domain transient data for up to 2 s. Notably, the ability to distinguish diagnostic isotopic pairs, such as <sup>12</sup>C/<sup>29</sup>Si vs <sup>13</sup>C/<sup>28</sup>Si with a mass split of ∼3.79 mDa and <sup>13</sup>C<sup>12</sup>C/<sup>28</sup>Si<sup>29</sup>Si vs <sup>13</sup>C<sub>2</sub>/<sup>28</sup>Si<sub>2</sub>, with an approximate mass difference of ∼3.32 mDa, demonstrates a significant and expected performance improvement. Finally, we benchmark the GC HRMS methodology to identify silylated oxygenated and nitrogen-containing constituents in ultracomplex bio-oil samples. The presented approach of utilizing the silicon isotope pattern and unique isotopologue mass splits for increasing attribution confidence can be applied beyond bio-oils toward the general GC analyses of polar oxygenates.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3242–3255 3242–3255"},"PeriodicalIF":3.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Systematic Workflow for Fragmentation Identification of Therapeutic Antibodies by Liquid Chromatography–Mass Spectrometry
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-11 DOI: 10.1021/jasms.4c0023910.1021/jasms.4c00239
Xiaoxu Zhang, Yanpeng Xu*, Liqi Xie, Pengcheng Shen, Jing Han, Xinyi Wang, Limeng Wang, Lei Zhang, Yuan Fang and Zhongli Zhang*, 
{"title":"A Systematic Workflow for Fragmentation Identification of Therapeutic Antibodies by Liquid Chromatography–Mass Spectrometry","authors":"Xiaoxu Zhang,&nbsp;Yanpeng Xu*,&nbsp;Liqi Xie,&nbsp;Pengcheng Shen,&nbsp;Jing Han,&nbsp;Xinyi Wang,&nbsp;Limeng Wang,&nbsp;Lei Zhang,&nbsp;Yuan Fang and Zhongli Zhang*,&nbsp;","doi":"10.1021/jasms.4c0023910.1021/jasms.4c00239","DOIUrl":"https://doi.org/10.1021/jasms.4c00239https://doi.org/10.1021/jasms.4c00239","url":null,"abstract":"<p >Fragmentation is a phenomenon ubiquitously observed during research and development of therapeutic antibodies. The clear identification of the cleavage site is vital for comprehending fragmentation mechanisms and optimizing processes. Capillary electrophoresis-sodium dodecyl sulfate (CE-SDS) is now widely used to detect and quantify fragments, while its peak identification is hindered by immature capillary electrophoresis-sodium dodecyl sulfate coupled with mass spectrometry techniques. In this study, we developed a systematic workflow for fragment characterization, which integrated direct identification, fragment enrichment, and fragmentation confirmation using multiple techniques, such as microscale peptide mapping (PM), PM of N-termini labeled sample, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in-gel extraction for molecular weight (MW) and PM measurements. By employing this innovative workflow, we successfully identified the cleavage sites of two therapeutic antibodies. In the first case, through direct liquid chromatography–mass spectrometry (LC-MS) characterization, the cleavages leading to the loss of biological function were identified on the linker of a bispecific antibody. In the second case involving a tetravalent antibody, direct LC-MS analysis failed. However, more sophisticated analysis nailed down the critical cleavage at the LC/HC: G<sub>105</sub>-R<sub>106</sub> site in the CDR3 region of the antibody. Our systematic workflow provides a clear and accessible method for identifying cleavage sites with broad applicability across pharmaceutical laboratories.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"2890–2899 2890–2899"},"PeriodicalIF":3.1,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Obtaining 20 μm Spatial Resolution with a 2940 nm Laser by IR-MALDESI Mass Spectrometry Imaging
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-08 DOI: 10.1021/jasms.4c0027610.1021/jasms.4c00276
Seth M. Eisenberg, Alena N. Joignant, Kevan T. Knizner, Jeffrey G. Manni and David C. Muddiman*, 
{"title":"Obtaining 20 μm Spatial Resolution with a 2940 nm Laser by IR-MALDESI Mass Spectrometry Imaging","authors":"Seth M. Eisenberg,&nbsp;Alena N. Joignant,&nbsp;Kevan T. Knizner,&nbsp;Jeffrey G. Manni and David C. Muddiman*,&nbsp;","doi":"10.1021/jasms.4c0027610.1021/jasms.4c00276","DOIUrl":"https://doi.org/10.1021/jasms.4c00276https://doi.org/10.1021/jasms.4c00276","url":null,"abstract":"<p >High spatial resolution is a key parameter in mass spectrometry imaging (MSI), enabling a greater understanding of system biology and cellular processes. Using a novel IR laser with good Gaussian beam quality (<i>M</i><sup>2</sup> = 4) coupled with spatial filtering and a reflective objective, 20 μm spatial resolution was obtained by IR-MALDESI. The optical train was optimized on burn paper before demonstrating feasibility for imaging of liver tissue. Finally, a mouse brain was analyzed using nested regions of interest at 20 and 140 μm spatial resolution, detecting neurotransmitters and lipids with high spatial resolution on the corpus callosum and surrounding brain tissue.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"2942–2949 2942–2949"},"PeriodicalIF":3.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Peak-Based Machine Learning for Plastic Type Classification in Time-of-Flight Secondary Ion Mass Spectrometry
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-08 DOI: 10.1021/jasms.4c0032510.1021/jasms.4c00325
Jin Gyeong Son*, Hyun Kyong Shon, Ji-Eun Kim, In−Ho Lee and Tae Geol Lee*, 
{"title":"Peak-Based Machine Learning for Plastic Type Classification in Time-of-Flight Secondary Ion Mass Spectrometry","authors":"Jin Gyeong Son*,&nbsp;Hyun Kyong Shon,&nbsp;Ji-Eun Kim,&nbsp;In−Ho Lee and Tae Geol Lee*,&nbsp;","doi":"10.1021/jasms.4c0032510.1021/jasms.4c00325","DOIUrl":"https://doi.org/10.1021/jasms.4c00325https://doi.org/10.1021/jasms.4c00325","url":null,"abstract":"<p >Time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurement data and machine learning were used in this work to classify six different types of plastics. In order to take into account the characteristics of the measurement data, the local maxima of the measurement data were first examined in a preprocessing step. Several machine learning methods were then implemented to create a model that could successfully classify the plastics. To visualize the data distribution, we applied a dimensionality reduction method, namely, principal component analysis. Finally, to distinguish between the six types of plastics, we conducted an ensemble analysis using four tree-based algorithms: decision tree, random forest, gradient boosting, and LIGHTGBM. This approach can identify the feature importance of plastic samples and allow the inference of the chemical properties of each plastic type. In this way, ToF-SIMS data could be utilized to successfully classify plastics and enhance explainability.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3107–3115 3107–3115"},"PeriodicalIF":3.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assignment of Disulfide Bonds in HNTX-XXI by Double-Enzymatic Digestion and Edman Degradation
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-08 DOI: 10.1021/jasms.4c0031910.1021/jasms.4c00319
Bo Chen, Juan He, Zhaotun Hu and Xiongzhi Zeng*, 
{"title":"Assignment of Disulfide Bonds in HNTX-XXI by Double-Enzymatic Digestion and Edman Degradation","authors":"Bo Chen,&nbsp;Juan He,&nbsp;Zhaotun Hu and Xiongzhi Zeng*,&nbsp;","doi":"10.1021/jasms.4c0031910.1021/jasms.4c00319","DOIUrl":"https://doi.org/10.1021/jasms.4c00319https://doi.org/10.1021/jasms.4c00319","url":null,"abstract":"<p >HNTX-XXI, a peptide toxin derived from the venom of the spider <i>Ornithoctonus hainana</i>, comprises a 64-amino-acid protein architecture that notably incorporates eight cysteine residues positioned at positions 2, 10, 14, 16, 17, 23, 36, and 63. The close spatial proximity of Cys16 and Cys17 poses a challenge in resolving their disulfide bridge configurations using standard methodologies. In this study, we introduce an innovative and highly efficient approach for delineating disulfide pairings in peptides containing adjacent cysteines. Our methodology integrates a two-step proteolytic digestion strategy utilizing trypsin and Glu-specific staphylococcal V8 protease coupled with a subsequent round of Edman degradation. This multifaceted approach enables the precise characterization of the disulfide bonds within the peptide. Specifically, targeted proteolysis by trypsin and V8, followed by reversed-phase HPLC separation of the resulting peptides, facilitated the unambiguous identification of disulfide linkages between Cys10-Cys23 and Cys14-Cys63. For the fragment containing the four remaining cysteines, a single cycle of Edman degradation was employed, strategically breaking the peptide bond between the adjacent cysteines. This pivotal step enabled the isolation and analysis of the resulting fragments. Subsequently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was utilized, revealing the presence of two additional disulfide bonds: Cys2-Cys17 and Cys16-Cys36. Collectively, these findings allow for the definitive assignment of the four disulfide linkages in HNTX-XXI as Cys2-Cys17, Cys10-Cys23, Cys14-Cys63, and Cys16-Cys36. This rapid and sensitive methodology represents a significant advancement in the structural characterization of peptide toxins with complex disulfide bond patterns, underscoring its potential for broad application in the field of venom peptide research.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3089–3094 3089–3094"},"PeriodicalIF":3.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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