Journal of Mass Spectrometry最新文献

{"title":"The path forward for protein footprinting, covalent labeling, and mass spectrometry-based protein conformational analyses","authors":"Nicholas B. Borotto","doi":"10.1002/jms.5064","DOIUrl":"10.1002/jms.5064","url":null,"abstract":"<p>Mass spectrometry-based approaches to assess protein conformation have become widely utilized due to their sensitivity, low sample requirements, and broad applicability to proteins regardless of size and environment. Their wide applicability and sensitivity also make these techniques suitable for the analysis of complex mixtures of proteins, and thus, they have been applied at the cell and even the simple organism levels. These works are impressive, but they predominately employ “bottom-up” workflows and require proteolytic digestion prior to analysis. Once digested, it is not possible to distinguish the proteoform from which any single peptide is derived and therefore, one cannot associate distal—in primary structure—concurrent post-translational modifications (PTMs) or covalent labels, as they would be found on separate peptides. Thus, analyses via bottom-up proteomics report the average PTM status and higher-order structure (HOS) of all existing proteoforms. Second, these works predominately employ promiscuous reagents to probe protein HOS. While this does lead to improved conformational resolution, the formation of many products can divide the signal associated with low-copy number proteins below signal-to-noise thresholds and complicate the bioinformatic analysis of these already challenging systems. In this perspective, I further detail these limitations and discuss the positives and negatives of top-down proteomics as an alternative.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hardware and software solutions for implementing nanospray desorption electrospray ionization (nano-DESI) sources on commercial mass spectrometers","authors":"Li-Xue Jiang,&nbsp;Ryan T. Hilger,&nbsp;Julia Laskin","doi":"10.1002/jms.5065","DOIUrl":"10.1002/jms.5065","url":null,"abstract":"<p>Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization mass spectrometry imaging (MSI) approach that enables spatial mapping of biological and environmental samples with high spatial resolution and throughput. Because nano-DESI has not yet been commercialized, researchers develop their own sources and interface them with different commercial mass spectrometers. Previously, several protocols focusing on the fabrication of nano-DESI probes have been reported. In this tutorial, we discuss different hardware requirements for coupling the nano-DESI source to commercial mass spectrometers, such as the safety interlock, inlet extension, and contact closure. In addition, we describe the structure of our custom software for controlling the nano-DESI MSI platform and provide detailed instructions for its usage. With this tutorial, interested researchers should be able to implement nano-DESI experiments in their labs.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.5065","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analyzing noncovalent interactions between notoginseng saponins and lysozyme by deposition scanning intensity fading MALDI-TOF mass spectrometry","authors":"Xintong Zhao,&nbsp;Juan Ren,&nbsp;Ze Wang,&nbsp;Xiangfeng Chen","doi":"10.1002/jms.5058","DOIUrl":"10.1002/jms.5058","url":null,"abstract":"<p>Analysis of noncovalent interactions between natural products and proteins is important for rapid screening of active ingredients and understanding their pharmacological activities. In this work, the intensity fading MALDI-TOF mass spectrometry (IF-MALDI-MS) method with improved reproducibility was implemented to investigate the binding interactions between saponins from <i>Panax notoginseng</i> and lysozyme. The benchmark IF-MALDI-MS experiment was established using <i>N</i>,<i>N</i>′,<i>N</i>″-triacetylchitotriose-lysozyme as a model system. The reproducibility of ion intensities in IF-MALDI-MS was improved by scanning the whole sample deposition with a focused laser beam. The relative standard deviation (RSD) of deposition scanning IF-MALDI-MS is 5.7%. Similar decay trends of the relative intensities of notoginseng saponins against increasing amounts of lysozyme were observed for all six notoginseng saponins. The half-maximal fading concentration (FC₅₀) was calculated to quantitatively characterize the binding affinity of each ligand based on the decay curve. According to the FC₅₀ values obtained, the binding affinities of the six notoginseng saponins were evaluated in the following order: notoginsenoside S &gt; notoginsenoside Fc &gt; ginsenoside Rb1 &gt; ginsenoside Rd &gt; notoginsenoside Ft1 &gt; ginsenoside Rg1. The binding order was in accordance with molecular docking studies, which showed hydrogen bonding might play a key role in stabilizing the binding interaction. Our results demonstrated that deposition scanning IF-MALDI-MS can provide valuable information on the noncovalent interactions between ligands and proteins.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mass spectrometry imaging-based multi-omics approaches to understand drug metabolism and disposition","authors":"Nav Raj Phulara,&nbsp;Herana Kamal Seneviratne","doi":"10.1002/jms.5042","DOIUrl":"10.1002/jms.5042","url":null,"abstract":"","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phytochemical investigation and characterisation of methanolic extract of Glycine max seeds using LCMS/MS and in silico studies for wound healing activity","authors":"Madhusmita Sahu,&nbsp; Kamakshi,&nbsp;Jyotirmaya Sahoo,&nbsp;Sudhansu Ranjan Swain,&nbsp;Manisha Chauhan,&nbsp;Riya Goyal,&nbsp;Sakshi Gupta,&nbsp;Komalpreet Kaur","doi":"10.1002/jms.5045","DOIUrl":"https://doi.org/10.1002/jms.5045","url":null,"abstract":"<p>Soybean is scientifically known as <i>Glycine max</i>. It belongs to the Fabaceae family. It consists of a lot of bioactive phytochemicals like saponin, phenolic acid, flavonoid, sphingolipids and phytosterols. It also owns excellent immune-active effects in the physiological system. Soy and its phytochemicals have been found to have pharmacological properties that include anticancer, antioxidant, anti-hypercholesterolaemic, anti-diabetic, oestrogenic, anti-hyperlipidaemic, anti-inflammatory, anti-obesity, anti-hypertensive, anti-mutagenic, immunomodulatory, anti-osteoporotic, antiviral, hepatoprotective, antimicrobial, goitrogenic anti-skin ageing, wound healing, neuroprotective and anti-photoageing activities. Present study has been designed to set standard pharmacognostical extraction method, complexation of compounds, qualitative evaluation through phytochemical screening, identification by TLC, physicochemical properties, solubility profile, total phenolic, flavonoid content as well as analytical evaluation or characterisation like UV and FT-IR of methanolic extract of <i>G. max</i>. The final observations like physicochemical properties such as total ash value, LOD and pH were recorded. Phytochemical screenings show the presence of flavonoid, alkaloid, saponin, carbohydrate, tannins, protein, gums and mucilage, fixed oils and fats. The results were found significant. Further in silico studies proved creatinine and euparin to be potent wound healing agents.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141251467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glycoproteomics: Charting new territory in mass spectrometry and glycobiology By Stacy A. Malaker","authors":"Malaker","doi":"10.1002/jms.5061","DOIUrl":"https://doi.org/10.1002/jms.5061","url":null,"abstract":"<p>\u0000 \u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.5061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141245535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrospray ionization tandem mass spectrometry of 4-aryl-3,4-dihydrocoumarins","authors":"Herbert J. Dias,&nbsp;William H. Santos,&nbsp;Luis C. S. Filho,&nbsp;Eduardo J. Crevelin,&nbsp;J. Scott McIndoe,&nbsp;Ricardo Vessecchi,&nbsp;Antônio E. M. Crotti","doi":"10.1002/jms.5062","DOIUrl":"10.1002/jms.5062","url":null,"abstract":"<p>We have investigated the gas-phase fragmentation reactions of 11 synthetic 4-aryl-3,4-dihydrocoumarins by electrospray ionization tandem mass spectrometry (ESI-MS/MS) on a quadrupole-time-of flight (Q-TOF) hybrid mass spectrometer. We have also estimated thermochemical data for the protonated coumarins (precursor ion <b>A</b>) and product ion structures by computational chemistry at a B3LYP level of theory to establish the ion structures and to rationalize the fragmentation pathways. The most abundant ions in the product ion spectra of coumarins <b>1–11</b> resulted from C₈H₈O₂, CO₂, C₄H₄O₃, C₈H₁₀O₃, C₈H₈O₂, and CH₃OH eliminations through retro-Diels–Alder (RDA) reactions, remote hydrogen rearrangements (β-eliminations), and β-lactone ring contraction. Although the investigated coumarins shared most of the fragmentation pathways, formation of a benzylic product ion and its corresponding tropylium ion was diagnostic of the substituents at ring C. The thermochemical data revealed that the nature and position of the substituents at ring C played a key role in the formation of this product ion and determined its relative intensity in the product ion spectrum. The results of this study contribute to knowledge of the gas-phase ion chemistry of this important class of organic compounds.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tandem mass spectrometry of homologous 3-hydroxyfurazan and nitrile amino acids: Analysis of cooperative interactions and fragmentation processes","authors":"J. Stuart Grossert,&nbsp;Andrew M. J. Crowell,&nbsp;Donatella Boschi,&nbsp;Marco L. Lolli,&nbsp;Robert L. White","doi":"10.1002/jms.5043","DOIUrl":"10.1002/jms.5043","url":null,"abstract":"<p>The assignment of structure by tandem mass spectrometry (MS/MS) relies on the interpretation of the fragmentation behavior of gas-phase ions. Mass spectra were acquired for a series of heterocyclic mimetics of acidic amino acids and a related series of nitrile amino acids. All amino acids were readily protonated or deprotonated by electrospray ionization (ESI), and distinctive fragmentation processes were observed when the ions were subjected to collision-induced dissociation (CID). The deprotonated heterocycles showed bond cleavages of the 3-hydroxyfurazan ring with formation of oxoisocyanate and the complementary deprotonated nitrile amino acid. Further fragmentation of the deprotonated nitrile amino acids was greatly dependent on the length of the alkyl nitrile side chain. Competing losses of CO₂ versus HCN occurred from α-cyanoglycinate (shortest chain), whereas water was lost from 2-amino-5-cyanopentanoate (longest chain). Interestingly, loss of acrylonitrile by a McLafferty-type fragmentation process was detected for 2-amino-4-cyanobutanoate, and several competing processes were observed for β-cyanoalanate. In one process, cyanide ion was formed either by consecutive losses of ammonia, carbon dioxide, and acetylene or by a one-step decarboxylative elimination. In another, complementary ions were obtained from β-cyanoalanate by loss of acetonitrile or HN=CHCO₂H. Fragmentation of the protonated 3-hydroxyfurazan and nitrile amino acids resulted in the cumulative loss (H₂O + CO), a loss that is commonly observed for protonated aliphatic α-amino acids. Overall, the distinct fragmentation behavior of the multifunctional 3-hydroxyfurazan amino acids correlated with the charged site, whereas fragmentations of the deprotonated nitrile amino acids showed cooperative interactions between the nitrile and the carboxylate groups.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.5043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141093495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the fate of protonated chloroformates in the gas phase: a competition between forming HCl and chloroformic acid","authors":"Malick Diedhiou,&nbsp;Paul M. Mayer","doi":"10.1002/jms.5044","DOIUrl":"10.1002/jms.5044","url":null,"abstract":"<p>Chloroformates are prevalent in the atmosphere due to their utilization as fuel additives and industrial solvents. These species may undergo interactions with atmospheric water resulting in protonated chloroformates. This study delves into the gas-phase dissociation of these protonated species. Tandem mass spectrometry was employed to scrutinize the unimolecular dissociation of protonated methyl (<b>1</b>), ethyl (<b>2</b>), neopentyl (<b>3</b>), and phenyl chloroformate (<b>4</b>). Notably, <b>1</b> and <b>4</b> exhibited HCl loss, yielding CH₃OCO⁺ and C₆H₅OCO⁺, respectively, with <b>1</b> additionally generating neutral methanol and ClCO⁺. <b>4</b> additionally loses CO and CO₂. In contrast, <b>2</b> and <b>3</b> each only exhibit a single fragmentation channel, with <b>2</b> losing C₂H₄ to generate protonated chloroformic acid and <b>3</b> generating protonated 2-methylbutene by losing neutral chloroformic acid. Density functional theory at the B3LYP/6-311+G(d,p) level of theory was employed to explore minimum energy reaction pathways for each ion, and CBS-QB3 single-point energy calculations were added to provide reliable energetics. The Rice–Ramsperger–Kassel–Marcus (RRKM) calculations of the rate constants for selected competing processes were carried out to link theory and experiment. One common unimolecular process observed was the 1,3-H shift of the proton from the carbonyl oxygen to the ester oxygen before dissociation.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.5044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Charge-solvated versus protonated salt forms of cyclodepsipeptide toxins in electrospray: Dissociation of alkali-cationized forms enables straightforward sequencing of cereulide","authors":"Sophie Liuu,&nbsp;Kam eng Trinh,&nbsp;Ekaterina Darii,&nbsp;Chenqin Cao,&nbsp;Annelaure Damont,&nbsp;Yves Gimbert,&nbsp;François Fenaille,&nbsp;Yassine Makni,&nbsp;Chanthadary Inthavong,&nbsp;Gwenaëlle Lavison-Bompard,&nbsp;Jacques-Antoine Hennekinne,&nbsp;Olivier Firmesse,&nbsp;Jean-Claude Tabet","doi":"10.1002/jms.5037","DOIUrl":"10.1002/jms.5037","url":null,"abstract":"<p><i>Bacillus cereus</i> is responsible for foodborne outbreaks worldwide. Among the produced toxins, cereulide induces nausea and vomiting after 30 min to 6 h following the consumption of contaminated foods. Cereulide, a cyclodepsipeptide, is an ionophore selective to K⁺ in solution. In electrospray, the selectivity is reduced as [M + Li]⁺; [M + Na]⁺ and [M + NH₄]⁺ can also be detected without adding corresponding salts. Two forms are possible for alkali-cationized ions: <i>charge-solvated</i> (CS) that exclusively dissociates by releasing a bare alkali ion and <i>protonated salt</i> (PS), yielding alkali product ions by covalent bond cleavages (CBC) promoted by mobile proton. Based on a modified peptide cleavage nomenclature, the PS product ion series (<b>b</b>, <b>a</b>, [<b>b</b> + H₂O] and [<b>b</b> + C_nH_2nO] [<i>n</i> = 4, 5]) are produced by Na⁺/Li⁺/K⁺-cationized cereulide species that specifically open at ester linkages followed by proton mobilization promoting competitive ester CBC as evidenced under resonant collision activation. What is more, unlike the sodiated or lithiated cereulide, which regenerates little or no alkali cation, the potassiated forms lead to an abundant K⁺ regeneration. This occurs by splitting of (i) the potassiated CS forms with an appearance threshold close to that of the PS first fragment ion generation and (ii) eight to four potassiated residue product ions from the PS forms. Since from Na⁺/Li⁺-cationized cereulide, (i) the negligible Na⁺/Li⁺ regeneration results in a higher sensibility than that of potassiated forms that abundantly releasing K⁺, and (ii) a better sequence recovering, the use of Na⁺ (or Li⁺) should be more pertinent to sequence isocereulides and other cyclodepsipeptides.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.5037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}