Journal of the American Society for Mass Spectrometry最新文献

{"title":"Studying Structural Details in Complex Samples. I. Combining two Chromatographic Separation Methods with Ultrahigh Resolution Mass Spectrometry.","authors":"Jens Dreschmann, Lilla Molnarne Guricza, Wolfgang Schrader","doi":"10.1021/jasms.4c00226","DOIUrl":"10.1021/jasms.4c00226","url":null,"abstract":"<p><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":" ","pages":"2859-2868"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646485","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}

{"title":"Measuring ¹⁵N and ¹³C Enrichment Levels in Sparsely Labeled Proteins Using High-Resolution and Tandem Mass Spectrometry.","authors":"Elijah T Roberts, Jonathan Choi, Jeremy Risher, Paul G Kremer, Adam W Barb, I Jonathan Amster","doi":"10.1021/jasms.4c00237","DOIUrl":"10.1021/jasms.4c00237","url":null,"abstract":"<p><p>Isotope labeling of both ¹⁵N and ¹³C 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 ¹⁵N content of enriched amino acids or increase the ¹⁵N 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 ¹⁵N and ¹³C 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 ¹⁵N and ¹³C 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":" ","pages":"2877-2889"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611841","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}

{"title":"Combined Quantification and Characterization of Dissolved Organic Matter by Liquid Chromatography-Mass Spectrometry Using Charged Aerosol Detection.","authors":"Stacey L Felgate, Elizabeth Jakobsson, Andrea Balderrama Subieta, Lars J Tranvik, Jeffrey A Hawkes","doi":"10.1021/jasms.4c00255","DOIUrl":"10.1021/jasms.4c00255","url":null,"abstract":"<p><p>Dissolved organic matter (DOM) is a complex mixture of thousands of molecular formulas comprised of an unknown number of chemical compounds, the concentration and composition of which are critical to ecosystem function and biogeochemical cycling. Despite its importance, our understanding of the DOM composition is lacking. This is principally due to its molecular complexity, which means that no single method is capable of describing DOM in its entirety. Quantification is typically done by proxy (e.g., relative to carbon content) and does not necessarily match well to compositional data, due to incomplete analytical windows and selectivity of different analytical methods. We present an integrated liquid chromatography (LC)-diode array detector (DAD)-charged aerosol detector (CAD)-mass spectrometry (MS) pipeline designed to both characterize and quantify solid-phase extractable DOM (SPE-DOM) in a single analysis. We applied this method to a set of eight Swedish water bodies sampled in the summer and winter. Chromophoric SPE-DOM was proportionally higher in samples with higher SPE-DOM concentrations but remained relatively consistent between sampling occasions. Ionizable SPE-DOM was relatively consistent across sites but was proportionally higher in summer. Overall, the carbon content of DOM was very consistently ∼40% across sites in both summer and winter. These findings suggest that SPE-DOM concentration at these sites is driven by (presumably allochthonous) chromophoric inputs, with an increased relative contribution in summer of material that is more ionizable and less chromophoric and may be either autochthonous or selectively enriched from allochthonous sources. Thus, with minimal additional effort, this method provided further compositional insights not attained by any single analysis in isolation.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"2910-2917"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378926","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}

{"title":"Editorial: Special Issue on Computational Mass Spectrometry","authors":"Aivett Bilbao,&nbsp;Devin Schweppe and Lingjun Li*,&nbsp;","doi":"10.1021/jasms.4c0045410.1021/jasms.4c00454","DOIUrl":"https://doi.org/10.1021/jasms.4c00454https://doi.org/10.1021/jasms.4c00454","url":null,"abstract":"","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"2743–2745 2743–2745"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760943","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}

{"title":"A Rapid Analysis Method for Determination of Hydrocarbon Types in Aviation Turbine Fuel by Gas Chromatography-Mass Spectrometry.","authors":"Naixin Wang, Yanqiang Shi, Yue Zhao, Wei Wang, Xin Jin, Yingrong Liu, Zelong Liu, Guangtong Xu","doi":"10.1021/jasms.4c00301","DOIUrl":"10.1021/jasms.4c00301","url":null,"abstract":"<p><p>A rapid analysis method for determination of hydrocarbon types in aviation turbine fuel was investigated in this study. A kind of reversible adsorption material packed as an unsaturated trap was used to separate saturated hydrocarbons and unsaturated hydrocarbons in the GC-MS system. No manual process or organic reagent was needed during the entire analysis process. The contents of 13 kinds of hydrocarbons, including paraffins, monocycloparaffins, dicycloparaffins, tricycloparaffins, monoolefins, cycloolefins, alkylbenzenes, C_<i>n</i>H_2<i>n</i>-8 aromatics, C_<i>n</i>H_2<i>n</i>-10 aromatics, naphthalenes, C_<i>n</i>H_2<i>n</i>-14 aromatics, C_<i>n</i>H_2<i>n</i>-16 aromatics, and C_<i>n</i>H_2<i>n</i>-18 aromatics were calculated by the characteristic mass fragments detected by MS with the modified matrices of ASTM D2425. The overall analysis time was less than 10 min. The precision of this test method has been conducted with 8 laboratories attended and 16 samples analyzed. The performance of this new method was demonstrated by comparing the results tested by ASTM D1319, ASTM D2425, and ASTM D6379. This rapid analysis method can provide hydrocarbon compositions of aviation turbine fuels or other liquid hydrocarbon samples within the same distillation range.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3010-3018"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492610","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}

{"title":"A Systematic Workflow for Fragmentation Identification of Therapeutic Antibodies by Liquid Chromatography-Mass Spectrometry.","authors":"Xiaoxu Zhang, Yanpeng Xu, Liqi Xie, Pengcheng Shen, Jing Han, Xinyi Wang, Limeng Wang, Lei Zhang, Yuan Fang, Zhongli Zhang","doi":"10.1021/jasms.4c00239","DOIUrl":"10.1021/jasms.4c00239","url":null,"abstract":"<p><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: G₁₀₅-R₁₀₆ 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":" ","pages":"2890-2899"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611777","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}

{"title":"Deciphering Isotopic Fine Structures of Silylated Compounds in Gas Chromatography-Vacuum Photoionization Orbitrap Mass Spectrometry of Bio-Oils.","authors":"Silvia Juliana Vesga Martínez, Christopher P Rüger, Paul Kösling, Julian Schade, Sven Ehlert, Yury O Tsybin, Ralf Zimmermann","doi":"10.1021/jasms.4c00383","DOIUrl":"10.1021/jasms.4c00383","url":null,"abstract":"<p><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_<i>x</i>Si_<i>y</i>-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 ¹²C/²⁹Si vs ¹³C/²⁸Si with a mass split of ∼3.79 mDa and ¹³C¹²C/²⁸Si²⁹Si vs ¹³C₂/²⁸Si₂, 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":" ","pages":"3242-3255"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611817","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}

{"title":"Enrichable Protein Footprinting for Structural Proteomics.","authors":"Jamison D Wolfer, Benjamin B Minkoff, Heather L Burch, Michael R Sussman","doi":"10.1021/jasms.4c00362","DOIUrl":"10.1021/jasms.4c00362","url":null,"abstract":"<p><p>Protein footprinting is a useful method for studying protein higher order structure and conformational changes induced by interactions with various ligands via addition of covalent modifications onto the protein. Compared to other methods that provide single amino acid-level structural resolution, such as cryo-EM, X-ray diffraction, and NMR, mass spectrometry (MS)-based methods can be advantageous as they require lower protein amounts and purity. As with other MS-based proteomic methods, such as post-translational modification analysis, enrichment techniques have proven necessary for both optimal sensitivity and sequence coverage when analyzing highly complex proteomes. Currently used reagents for footprinting via covalent labeling, such as hydroxyl radicals and carbodiimide-based methods, do not yet have a suitable enrichment method, limiting their applicability to whole proteome analysis. Here, we report a method for enrichable covalent labeling built upon the GEE/EDC system commonly used to covalently label aspartic acid and glutamic acid residues. Novel labeling reagents containing alkynyl functionality can be \"clicked\" to any azido-containing molecule with copper-catalyzed azide-alkyne cycloaddition (CuAAC), allowing for enrichment or further labeling. Multiple azide- and alkyne-containing GEE-like molecules were tested, and the most efficient method was determined to be the EDC-facilitated coupling of glycine propargyl amide (GPA) to proteins. The pipeline we report includes clicking via CuAAC to a commercially available biotin-azide containing a photocleavable linker, followed by enrichment using a streptavidin resin and subsequent cleavage under ultraviolet light. The enrichment process was optimized through the screening of clickable amines, coupling reagents, and enrichment scaffolds and methods with pure model proteins and has also been applied to complex mixtures of proteins isolated from the model plant, <i>Arabidopsis thaliana</i>, suggesting that our method may ultimately be used to measure protein conformation on a proteomic scale.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3192-3202"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680474","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}

{"title":"Improving Top-Down Sequence Coverage with Targeted Fragment Matching.","authors":"Matthew T Robey, Kenneth R Durbin","doi":"10.1021/jasms.4c00161","DOIUrl":"10.1021/jasms.4c00161","url":null,"abstract":"<p><p>Top-down mass spectrometry (TDMS) of intact proteins and antibodies enables direct determination of truncations, sequence variants, post-translational modifications, and disulfides without the need for any proteolytic cleavage. While mass deconvolution of top-down tandem mass spectra is typically used to identify fragment masses for matching to candidate proteoforms, larger molecules such as monoclonal antibodies can produce many fragment ions, making spectral interpretation challenging. Here, we explore an alternative approach for proteoform spectral matching that is better suited for larger protein analysis. This workflow uses direct matching of theoretical proteoform isotopic distributions to TDMS spectra, avoiding drawbacks of mass deconvolution such as poor sensitivity and problems differentiating overlapping distributions. Using a data set that analyzed an intact NIST monoclonal antibody across different fragmentation modes, we show that this isotope fitting strategy increased the sequence coverage of both light and heavy chain sequences >3-fold. We further found that isotope fitting is particularly amenable to identifying large fragments, including those near the hinge region that have been traditionally difficult to analyze by top-down methods. These advances in proteoform spectral matching can greatly increase the power of top-down analyses for intact biotherapeutics and other large molecules.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3296-3300"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492612","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}

{"title":"Atmospheric Pressure Photoionization with Halogen Anion Attachment for Mass Spectrometric Analysis of Hydrocarbons and Hydrocarbon-Based Polymers.","authors":"Essi Rytkönen, Juha Rouvinen, Janne Jänis, Marko Mäkinen","doi":"10.1021/jasms.4c00331","DOIUrl":"10.1021/jasms.4c00331","url":null,"abstract":"<p><p>Aliphatic hydrocarbons and hydrocarbon-based synthetic polymers are of interest in many fields, but their characterization by mass spectrometric methods is generally limited due to their poor ionizability. Recently, atmospheric pressure photoionization (APPI), combined with halogen anion attachment in negative-ion mode, has drawn attention as a potential method for ionizing various polymers without extensive fragmentation or other unwanted side reactions. In this work, the applicability of halogen anion attachment with APPI was studied using several synthetic polymers, including polyethylene, polypropylene, polyisoprene, and polystyrene, as well as simple <i>n</i>-alkanes of various chain lengths. For hydrocarbon-based polymers, the method produced clear distributions of intact polymer adduct ions when different halogen anions were used. It was found that increasing the halogen anion size decreased ionization efficiency, particularly in the absence of π-bonds in the polymer structure. Testing with simple <i>n</i>-alkanes showed that only molecules containing fifty or more carbon atoms formed detectable halogen adducts, possibly due to the low gas-phase stabilities of the lighter <i>n</i>-alkane adduct ions. In conclusion, halogen anion attachment with negative-ion APPI appears to be a highly promising method for polymer analysis, providing structural data and clean polymer mass spectra with minimal fragmentation, which can be useful for the identification of unknown samples.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3147-3156"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581620","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}