{"title":"Ultrahigh-Resolution Mass Spectrometry Advances for Biogeochemical Analysis: From Seafloor Sediments to Petroleum and Marine Oil Spills.","authors":"Jagoš R Radović, Renzo C Silva","doi":"10.1021/jasms.4c00266","DOIUrl":"https://doi.org/10.1021/jasms.4c00266","url":null,"abstract":"<p><p>This Perspective explores the transformative impact of ultrahigh-resolution mass spectrometry (UHR-MS), particularly Fourier transform ion cyclotron resonance (FT-ICR-MS), in the characterization of complex environmental and petroleum samples. UHR-MS has significantly advanced our ability to identify molecular formulas in complex mixtures, revolutionizing the study of biogeochemical processes and organic matter evolution on wide time scales. We start by briefly reviewing the main technological advances of UHR-MS in the context of petroleum and environmental applications, highlighting some of the challenges of the technology such as quantitation and structural identification. We then showcase a selection of impactful applications published in the last 20+ years. In the field of environmental lipidomics, high-resolution analysis of lipids in sediments enables multiproxy studies and provides novel insights into past environmental conditions. UHR-MS has also facilitated the characterization of kerogen, a complex, poorly soluble mixture formed from sedimented organic matter over geological time scales, and the identification of polar compounds within its fractions. In petroleum (geo)chemistry, UHR-MS has enabled the identification of biomarkers such as petroporphyrins, asphaltenes, and high-molecular-weight naphthenic acids, shedding light on the molecular complexity of crude oil. The application of UHR-MS in oil spill science has revealed significant molecular transformations during weathering processes, such as photo-oxidation, which are crucial for assessing the environmental impact of past spills and improving the preparedness for future spills. These advancements underscore the role of this maturing analytical technology in deepening our understanding of geochemical processes and biogeochemical cycles, highlighting its potential for future research directions in organic geochemistry.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799044","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}
Weikai Cao, Phillip Y Chu, Merlin L Bruening, Rachel Liuqing Shi, Hilda Hernandez-Barry, John C Tran
{"title":"Efficient, Low-Cost, and High-Throughput Sodium Dodecyl Sulfate (SDS) Removal from Protein Digests Using Weak-Anion Exchange.","authors":"Weikai Cao, Phillip Y Chu, Merlin L Bruening, Rachel Liuqing Shi, Hilda Hernandez-Barry, John C Tran","doi":"10.1021/jasms.4c00304","DOIUrl":"https://doi.org/10.1021/jasms.4c00304","url":null,"abstract":"<p><p>Sodium dodecyl sulfate (SDS) plays a pivotal role in protein denaturation, tissue extraction, and protein mass-based electrophoretic separations. However, even modest concentrations of SDS can cause column overpressure, retention time shifts, and ionization signal suppression during liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. Thus, SDS removal is a critical step for LC-MS/MS analysis of protein digests containing SDS. This study describes an inexpensive and high-throughput method to remove SDS from protein digests using weak-anion exchange (WAX) resins in 96-well filter plates. Requiring less than 3 min, this method can reduce SDS concentrations from 0.1-0.4% to less than 5 ppm and from 0.6-1% to less than 100 ppm. After SDS removal, the recoveries of unmodified tryptic peptides and phosphorylated peptides (at 94.3 nM) were ∼90% and ∼70%, respectively. Additionally, when using aqueous 1% SDS to solubilize trastuzumab-spiked mouse serum and subsequently removing the SDS using the WAX resin, quantitation of trastuzumab exhibited excellent linearity (<i>R</i><sup>2</sup> = 0.9996) together with a low coefficient of variation (<10%). Calculated concentrations were within 20% of the expected value for spiked standard samples (0.5, 1, and 2 μg/mL trastuzumab in mouse serum). The method is about 20× more cost-effective versus commercialized SDS removal kits and both the resin and filter plate are readily available, so the method should easily transfer to other laboratories.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799001","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}
Mudita Vats, Bryn Flinders, Theodoros Visvikis, Corinna Dawid, Thomas F Hofmann, Eva Cuypers, Ron M A Heeren
{"title":"Mass Spectrometry Imaging for Spatial Ingredient Classification in Plant-Based Food.","authors":"Mudita Vats, Bryn Flinders, Theodoros Visvikis, Corinna Dawid, Thomas F Hofmann, Eva Cuypers, Ron M A Heeren","doi":"10.1021/jasms.4c00353","DOIUrl":"https://doi.org/10.1021/jasms.4c00353","url":null,"abstract":"<p><p>Mass spectrometry imaging (MSI) techniques enable the generation of molecular maps from complex and heterogeneous matrices. A burger patty, whether plant-based or meat-based, represents one such complex matrix where studying the spatial distribution of components can unveil crucial features relevant to the consumer experience or production process. Furthermore, the MSI data can aid in the classification of ingredients and composition. Thin sections of different burger samples and vegetable constituents (carrot, pea, pepper, onion, and corn) were prepared for matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) MSI analysis. MSI measurements were performed on all samples, and the data sets were processed to build three machine learning models aimed at detecting meat adulteration in vegetable burger samples, identifying individual ingredients within the vegetable burger matrix, and discriminating between burgers from different manufacturers. Ultimately, the successful detection of adulteration and differentiation of various burger recipes and their constituent ingredients were achieved. This study demonstrates the potential of MSI coupled with building machine learning models to enable the comprehensive characterization of burgers, addressing critical concerns for both the food industry and consumers.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790831","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":"Roughhousing with Ions: Surface-Induced Dissociation and Electron Capture Dissociation as Diagnostics of Q-Cyclic IMS-TOF Instrument Tuning Gentleness.","authors":"Andrew J Arslanian, Vicki H Wysocki","doi":"10.1021/jasms.4c00417","DOIUrl":"https://doi.org/10.1021/jasms.4c00417","url":null,"abstract":"<p><p>Native mass spectrometry can characterize a range of biomolecular features pertinent to structural biology, including intact mass, stoichiometry, ligand-bound states, and topology. However, when an instrument's ionization source is tuned to maximize signal intensity or adduct removal, it is possible that the biomolecular complex's tertiary and quaternary structures can be rearranged in a way that no longer reflect its native-like conformation. This could affect downstream ion activation experiments, leading to erroneous conclusions about the native-like structure. One activation strategy is surface-induced dissociation (SID), which generally causes native-like protein complexes to dissociate along the weakest subunit interfaces, revealing critical information about the complex's native-like topology and subunit connectivity. If the quaternary structure has been disturbed, then the SID fingerprint will shift as well. Thus, SID was used to diagnose source-induced quaternary structure rearrangement and help tune an instrument's source and other upstream transmission regions to strike the balance between signal intensity, adduct removal, and conserving the native-like structure. Complementary to SID, electron-capture dissociation (ECD) can also diagnose rearranged quaternary structures and was used after in-source activation to confirm that the subunit interfaces were rearranged, opening the structure to electron capture and subsequent dissociation. These results provide a valuable guide for new practitioners of native mass spectrometry and highlight the importance of using standard protein complexes when tuning new instrument platforms for optimal native mass spectrometry performance.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790834","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}
Kayla Williams-Pavlantos, McKenna J Redding, Oluwapelumi O Kareem, Mark A Arnould, Scott M Grayson, Chrys Wesdemiotis
{"title":"Tandem Mass Spectrometry Reflects Architectural Differences in Analogous, Bis-MPA-Based Linear Polymers, Hyperbranched Polymers, and Dendrimers.","authors":"Kayla Williams-Pavlantos, McKenna J Redding, Oluwapelumi O Kareem, Mark A Arnould, Scott M Grayson, Chrys Wesdemiotis","doi":"10.1021/jasms.4c00330","DOIUrl":"10.1021/jasms.4c00330","url":null,"abstract":"<p><p>The growing use of branched polymers in various industrial and technological applications has prompted significant interest in understanding their properties, for which accurate structure determination is vital. This work is the first instance where the macromolecular structures of dendrimers, linear polymers, and hyperbranched polymers with analogous 2,2-bis(hydroxymethyl)propionic acid (bis-MPA) backbone groups were synthesized and analyzed via tandem mass spectrometry (MS/MS). When comparing the fragmentation pathways of these polymers, some unique and interesting patterns emerge that provide insight into the primary structures and architectures of each of these materials. As expected, the linear polymer undergoes multiple random backbone cleavages resulting in several fragment ion distributions that vary in size and end group composition. The hyperbranched polymer dissociates preferentially at branching sites; however, differently branched isomers exist for each oligomer size, thus giving rise again to several fragment distributions. In contrast, the dendrimer presents a unique fragmentation pattern comprising key fragment ions of high molecular weight; this unique characteristic stands out as a signature for identifying dendrimer structures. Overall, dendrimers, hyperbranched polymers, and linear polymers display individualized fragmentation behaviors, which are caused by differences in primary structure. As a result, tandem mass spectrometry fragmentation is a particularly useful analytical tool for distinguishing such macromolecular architectures.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3135-3146"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602840","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}
Xiaoxiao Huang, Xin Wang, Victoria C Cotham, David Bramhall, Jieqiang Zhong, Yimeng Zhao, Haibo Qiu, Shunhai Wang, Ning Li
{"title":"Development of a Novel Label-Free Subunit HILIC-MS Method for Domain-Specific Free Thiol Identification and Quantitation in Therapeutic Monoclonal Antibodies.","authors":"Xiaoxiao Huang, Xin Wang, Victoria C Cotham, David Bramhall, Jieqiang Zhong, Yimeng Zhao, Haibo Qiu, Shunhai Wang, Ning Li","doi":"10.1021/jasms.4c00308","DOIUrl":"10.1021/jasms.4c00308","url":null,"abstract":"<p><p>Cysteine residues are crucial for the formation of conserved disulfide bonds in therapeutic monoclonal antibodies (mAbs), which are essential for their folding and structural stability. The presence of free thiols in mAbs can indicate incomplete disulfide bond formation, potentially impacting the molecule's conformational stability. Free thiol quantitation has been achieved using labeling-based strategies such as maleimide and haloalkyl derivatives at both intact and peptide levels. However, intact-level measurement only provides total free thiol levels, while peptide-level measurement is time-consuming and more prone to assay-induced artifacts. In this study, we present a novel label-free HILIC-MS method that separates free thiol species at the subunit level, followed by free thiol localization by the MS2 fragmentation pattern. This allows for facile identification and quantitation of intrachain free thiols at domain-specific resolution. Compared to bottom-up approaches, this subunit HILIC-MS method excels in simpler sample preparation and higher throughput and enables chain-specific free thiol analysis for bispecific mAbs. This method can be readily applied for screening mAb candidates with elevated levels of free thiols in early-stage developability assessment and facilitating an effective comparability evaluation of mAb samples during process development.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3019-3027"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542808","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, Devin Schweppe, Lingjun Li","doi":"10.1021/jasms.4c00454","DOIUrl":"https://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"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765244","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":"Assessment of the Migration of Polar Compounds from Petroleum-Contaminated Soil Using a Column Leaching Experiment.","authors":"Jianwen Wang, Yufu Han, Zibin Zhao, Chao Ma, Guanghui Yu, Yulin Qi","doi":"10.1021/jasms.4c00305","DOIUrl":"10.1021/jasms.4c00305","url":null,"abstract":"<p><p>When petroleum leaks into soil, the polar compounds exhibit strong biological toxicity, causing serious damage to soil animals, plants, and microorganisms and potentially threatening human health. However, the systematic comprehension of the migration of polar compounds in petroleum-contaminated soil remains limited. Herein, we employed elemental analysis, stable carbon isotope analysis, and high-resolution mass spectrometry techniques to study the migration of polar compounds in petroleum-contaminated soil using a column leaching experiment. The results indicate that petroleum migration ability in soil is limited, and the compounds are primarily concentrated in the soil above 40 cm. The C/N, C/H, and δ<sup>13</sup>C ratios of organic matter in soils are highly affected by petroleum contamination. Meanwhile, the different compound classes show varying migration abilities, with N<sub>1</sub> and N<sub>1</sub>O<sub>1</sub> compounds exhibiting stronger adsorption capacity on soil, while oxygen-containing compounds are more likely to migrate with water to deeper soil. Additionally, molecular polarity, unsaturation degree, and size are key factors affecting the migration of polar compounds in petroleum within the soil. This simulation experiment offers valuable insights into comprehending migration of polar compounds in petroleum-contaminated soil and their potential impacts for soil ecological environment.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3037-3048"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338952","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":"Hierarchical Biclustering of Mouse Pancreas Mass Spectrometry Imaging Data Using Recursive Rank-2 Non-negative Matrix Factorization.","authors":"Melanie Nijs, Etienne Waelkens, Bart De Moor","doi":"10.1021/jasms.4c00268","DOIUrl":"10.1021/jasms.4c00268","url":null,"abstract":"<p><p>One of the main challenges in mass spectrometry imaging data analysis remains the analysis of <i>m</i>/<i>z</i>-spectra displaying a low signal-to-noise ratio caused by their low abundance, sample preparation, matrix effects, fragmentation, and other artifacts. Additionally, we observe that molecules with a high abundance suppress those with lower intensities and misdirect classical tools for MSI data analysis, such as principal component analysis. As a result, the observed significance of a molecule may not always be directly related to its abundance. In this work, we present a recursive rank-2 non-negative matrix factorization (rr2-NMF) algorithm that automatically returns spectral and spatial visualization of colocalized molecules, both highly and lowly abundant. Using this hierarchical decomposition, our method finds spatial and spectral correlations on different levels of abundances. The quality of the analysis is evaluated on MALDI-TOF data of healthy mouse pancreatic tissue for the annotation of molecules of interest in the lower abundances. The results show interesting findings regarding the functioning and colocalization of certain molecules.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"2934-2941"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387185","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}
Simon Höving, Hao Song, Luisa Speicher, Arthur Schiller, Joachim Franzke
{"title":"Compact Plasma Ionization for Ion Mobility Spectrometry Using a 4.3 MHz Miniature Tesla Coil.","authors":"Simon Höving, Hao Song, Luisa Speicher, Arthur Schiller, Joachim Franzke","doi":"10.1021/jasms.4c00360","DOIUrl":"10.1021/jasms.4c00360","url":null,"abstract":"<p><p>In this study, a low-cost 4.3 MHz plasma ionization source for ion mobility spectrometry (IMS), utilizing a miniaturized Tesla coil, is presented. This compact design, combined with a 3D printed cyclic olefin copolymer (COC) housing, delivers a stable and directed plasma suitable for ionization in IMS applications. The 3D printed housing ensures chemical resistance and low off-gassing, which are crucial for maintaining sample integrity. The Tesla coil produces a consistent sine wave at 4.3 MHz, and when connected to stainless steel screw electrodes it generates a stable plasma capable of ionizing analytes such as limonene, MTBE, nicotine, 2-octanone, and propofol. Measurements were conducted in both positive and negative ion modes. The results demonstrate the Tesla coil's effectiveness as a low-cost and reliable ionization source for IMS, offering comparable performance to traditional Ni<sup>63</sup> β-emitters. This advancement in plasma ionization technology could facilitate more accessible and flexible IMS systems for diverse analytical applications. The integration of 3D printing in the development of this ionization source underscores the potential for customized, low-cost analytical instrumentation, promoting innovation in laboratory environments and commercial applications.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3214-3220"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581623","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}