Mass spectrometry最新文献

{"title":"Interpretation of α-Pinene Mass Spectra in APCI-Like Ambient Mass Spectrometry Using GC-Coupled Atmospheric Pressure Corona Discharge Ionization.","authors":"Ren Ishihara, Daisuke Fukuyama, Kanako Sekimoto","doi":"10.5702/massspectrometry.A0190","DOIUrl":"10.5702/massspectrometry.A0190","url":null,"abstract":"<p><p>Ambient mass spectrometry (AMS) enables real-time analysis without sample preparation, yet atmospheric pressure corona discharge ionization (APCI)-like ion sources can oxidize analytes in-source, obscuring spectral interpretation. We investigated α-pinene using atmospheric pressure corona discharge ionization mass spectrometry (APCDI-MS; one of APCI-like AMS) and, when needed, coupled gas chromatography (GC) to separate pre-existing oxidation products from species formed inside the ion source. By comparing adduct formation and product-ion patterns, we show that oxygenated ions from primary (pre-source) and secondary (in-source) oxidation display similar ion formation behavior, notably ready NH₄ ⁺-adduct formation, whereas fragment ions rarely form NH₄ ⁺ adducts. GC-based characterization of in-source oxidation provides features that assist interpretation of APCI-like AMS spectra acquired without chromatography.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0190"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12930354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147290244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Native Mass Spectrometry Enables Direct Detection of Endogenous Protein Complexes from Crude Lysates of Cultured Human Cells.","authors":"Michiko Tajiri, Yusuke Tateishi, Qiuyi Wang, Hiroko Morinaga, Hiroyuki Miura, Yoshinori Arita, Masaru Nishiguchi, Daisuke Okumura, Tsuyoshi Konuma, Satoko Akashi","doi":"10.5702/massspectrometry.A0198","DOIUrl":"10.5702/massspectrometry.A0198","url":null,"abstract":"<p><p>Native mass spectrometry (MS) enables the direct observation of non-covalent protein interactions while preserving the higher-order structures of protein complexes. We previously developed direct native MS approaches for analyzing overexpressed protein complexes from crude lysates and single human cells, retaining their interactions with small molecules and drugs. Here, we demonstrate that this strategy can be extended to endogenous protein complexes, which are present at substantially lower abundance than the overexpressed protein complexes analyzed in previous direct native MS studies, by directly analyzing crude lysates of cultured human HEK293T cells without prior purification or buffer exchange. Although crude human cell lysates contain salts and matrix compounds that typically cause peak broadening and signal suppression, we successfully observed the endogenous ~145-kDa glyceraldehyde-3-phosphate dehydrogenase (GAPDH) tetramer directly from unpurified human cell lysates, including its NAD⁺-bound forms. These results demonstrate the feasibility of directly detecting an endogenous high-molecular-weight protein complex and its cofactor-binding states from crude human cultured cell lysates, providing a basis for extending this approach to other endogenous protein assemblies and future single-cell native MS analyses.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0198"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13461571/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148725391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of LC/MS Methods for Hydrophilic Metabolites to Enable Integration of Human Blood Metabolome Data.","authors":"Yuri Imado, Masatomo Takahashi, Yuki Soma, Shunsuke Aburaya, Kohta Nakatani, Taizo Hanai, Takeshi Bamba, Yoshihiro Izumi","doi":"10.5702/massspectrometry.A0188","DOIUrl":"10.5702/massspectrometry.A0188","url":null,"abstract":"<p><p>Information on candidate biomarker metabolites identified in recent disease biomarker discovery research is expected to play a key role in the future of personalized and precision medicine. Liquid chromatography mass spectrometry (LC/MS) is a powerful method for metabolomic analysis due to its comprehensive coverage and high detection sensitivity. However, the suitability of LC/MS methods for the identification and quantification of hydrophilic metabolites remains debatable. Here, we evaluated the performance of LC/MS methods combining four types of LC [hydrophilic interaction chromatography (HILIC), ion chromatography (IC) with an anion-exchange (AEX) column (AEX-IC), reversed-phase LC (RPLC) with a pentafluorophenylpropyl (PFPP) column (PFPP-RPLC), and unified-hydrophilic interaction AEX LC (unified-HILIC/AEX)], using the same Orbitrap mass spectrometer, with the aim of integrating future human plasma metabolome data. First, we conducted a qualitative performance evaluation of four LC/MS methods, HILIC/MS, AEX-IC/MS, PFPP-RPLC/MS, and unified-HILIC/AEX/MS, by analyzing 511 hydrophilic metabolite standards and NIST Standard Reference Material (SRM) 1950 (Metabolites in Frozen Human Plasma). The evaluation focused on metabolome coverage, peak width, sensitivity, and separation performance of isomers. Next, we thoroughly evaluated the quantitative performance of the four analytical methods for 63 hydrophilic metabolites in SRM 1950 using a stable isotope-labeled internal standard (SILIS) mixture derived from ¹³C-labeled <i>Escherichia coli</i> extracts. Furthermore, we successfully estimated new concentration values for 29 metabolites without certified values in SRM 1950 using quantitative data from the four LC/MS methods. We objectively evaluated the performance of the four LC/MS methods and demonstrated that absolute quantification using SILIS is effective for integrating hydrophilic metabolite data in metabolomics.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0188"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12887570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146166046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Signatures in Extracellular Vesicles as Predictive Markers of Neural and Cardiac Differentiation from Human iPSCs.","authors":"Mei Mikami, Eri Katsuno, Shunsuke Hoshina, Kansei Takashita, Daisuke Takakura, Nana Kawasaki","doi":"10.5702/massspectrometry.A0197","DOIUrl":"10.5702/massspectrometry.A0197","url":null,"abstract":"<p><p>Human induced pluripotent stem cell (iPSC)-derived neural cells (NCs) and cardiomyocytes (CMs) show significant promise for clinical applications in regenerative medicine. Because the manufacturing of iPSC-derived products faces challenges in quality reproducibility, cost, and manufacturing time, closed automated culture systems have been developed. Recently, an efficient and noninvasive cell monitoring system based on extracellular markers secreted by cells represents a new strategy for closed systems. Extracellular vesicles (EVs), secreted by cells, contain proteins involved in stem cell differentiation; however, EV proteins in the cell culture medium are difficult to analyze because of their low abundance. Thus, their changes during cell differentiation, and the relationship between EV and cell proteins, remain unclear. In this study, we investigated the changes in EV proteins during iPSC differentiation into NCs and CMs using data-independent acquisition LC/MS/MS (DIA-MS), a highly comprehensive and quantitative approach. We observed significant positive correlations between the EV protein abundance and cellular protein expression levels during differentiation on days 0-7, and identified signature proteins characteristic of NCs and CMs. Among these, trophoblast glycoprotein (TPBG) for NC differentiation and keratin, type I cytoskeletal 19 (KRT19) for CM differentiation were particularly increased in both cells and EVs. Moreover, TPBG and KRT19 levels at day 7 showed similar trends to the differences in differentiation observed among the cell lines, as determined by flow cytometry. These findings suggest that these EV proteins may serve as predictive markers for monitoring differentiation into NC and CM.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0197"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13386156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Atmospheric Pressure Corona Discharge Ionization of <i>n</i>-Heptane (I): Formation of the Molecular Ion M^+• and Dehydrogenated Ions [M - 2H]^+• and [M - <i>n</i>H]⁺ (<i>n</i> = 1, 3, 5).","authors":"Daisuke Fukuyama, Masahiro Hashimoto, Masaaki Ubukata, Kanako Sekimoto, Mitsuo Takayama","doi":"10.5702/massspectrometry.A0193","DOIUrl":"10.5702/massspectrometry.A0193","url":null,"abstract":"<p><p>The formation of M^+∙, [M - 2H]^+∙, and [M - <i>n</i>H]⁺ (<i>n</i> = 1, 3, 5) ions has been reported by using atmospheric pressure corona discharge (APCD) of <i>n</i>-heptane. The M^+∙ and [M - H]⁺ ions can be produced by high-electric field tunnel ionization (HEFTI) and hydride abstraction reactions, respectively. It has been proposed that the [M - 2H]^+∙, [M - 3H]⁺, and [M - 5H]⁺ ions are produced by the loss of hydrogen atoms from the [M - H]⁺ ion. The geometric and electronic configurations of the M^+∙, [M - 2H]^+∙, and [M - <i>n</i>H]⁺ (<i>n</i> = 1, 3, 5) ions were determined by quantum chemical calculations (QCCs). The product ions resulting from higher-energy collisional dissociation (HCD) of the M^+∙ ion can be characterized by the loss of alkyl radicals and alkanes, while those of the [M - 2H]^+∙ ion can be characterized by the loss of alkyl radicals and alkenes. The HCD product ions of the [M - <i>n</i>H]⁺ (<i>n</i> = 1, 3, 5) ions can be fundamentally characterized by the loss of alkenes. The product ions present in the HCD spectra can be supported by the geometric and electronic configurations determined by the QCCs. The fragment ions observed in the APCD mass spectrum are likely attributable to the result of collisional interactions between the M^+· ion and the air components such as N₂, O₂, and Ar, or to the result of the HEF-induced cracking reaction leading to the alkyl fragments.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0193"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13132661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147816862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Use of the Peptide Barcode Method for Efficient Screening of mRNA Expression Control Sequence.","authors":"Shun Kumano, Kazuki Tanaka, Akihiro Nojima","doi":"10.5702/massspectrometry.A0196","DOIUrl":"10.5702/massspectrometry.A0196","url":null,"abstract":"<p><p>The precise control of specific protein expression in target cells remains a critical challenge for the advancement of messenger RNA (mRNA) therapeutics. While incorporating regulatory sequences, such as microRNA-responsive RNA switches, is a promising approach for cell-type-specific targeting, optimizing these sequences requires extensive and time-consuming screening using conventional evaluation methods. In this study, we applied a multiplexed evaluation methodology utilizing peptide barcodes coupled with liquid chromatography-mass spectrometry (LC-MS) to improve the screening and design efficiency of mRNA expression control sequences. We designed mRNAs equipped with cell-specific expression control sequences and fused unique peptide barcodes to the encoded target proteins. By comparing conventional individual transfections with simultaneous co-transfections, we demonstrated that our LC-MS-based method can successfully distinguish and quantify protein expression derived from individual mRNA candidates within a single mixed sample. The simultaneous evaluation using peptide barcodes yielded results equivalent to the individual evaluations but required a reduced number of samples. This multiplexed technology would accelerate the screening process for regulatory sequences and is expected to enhance the development of mRNA therapeutics with high targeting specificity.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0196"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13333580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148436967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reply to Comment on \"Identification of Negative Ion at <i>m/z</i> 20 Produced by Atmospheric Pressure Corona Discharge Ionization under Ambient Air\".","authors":"Mitsuo Takayama","doi":"10.5702/massspectrometry.A0185","DOIUrl":"10.5702/massspectrometry.A0185","url":null,"abstract":"","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0185"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12765808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145912130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enantioselective Determination of Carnitine Enantiomers in Food and Supplement Samples by Chiral Liquid Chromatography-Tandem Mass Spectrometry.","authors":"Aogu Furusho, Yutaro Nakayama, Hiroki Mizuno, Eiji Sugiyama, Kenji Kojima, Kenichiro Todoroki","doi":"10.5702/massspectrometry.A0191","DOIUrl":"10.5702/massspectrometry.A0191","url":null,"abstract":"<p><p>Carnitine (CAR) is an essential compound for animals and plays several physiological roles related to energy production. These functions are possessed by only the l-forms, while the d-forms are known to inhibit the uptake of the l-forms, thus causing a CAR deficiency. Therefore, it is required to determine dl-CAR in various samples such as foods, supplements, and drugs by an enantioselective analytical method. In this study, we developed a chiral liquid chromatography-tandem mass spectrometry (LC-MS/MS) method using derivatization. The CAR enantiomers derivatized with 4-nitrophenylhydrazine were successfully separated on a CHIRALPAK ZWIX (-) column (resolution = 1.64) and detected with high sensitivity and selectivity by MS/MS. The developed method was well validated and applied to the analysis of eight kinds of foods and an l-CAR supplement. Only the l-forms were found in all the tested food samples and were abundant in meat, milk, and yogurt. The system was also applicable for a supplement sample and could detect the d-CAR contamination at the 2.5% level, suggesting its potential for use in the purity test of CAR preparations.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0191"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12964190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147377355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Practical Workflow for Reliable MALDI-Based Hydrogen/Deuterium Exchange Mass Spectrometry.","authors":"Tatsuya Yamamoto, Honoo Satake","doi":"10.5702/massspectrometry.A0200","DOIUrl":"10.5702/massspectrometry.A0200","url":null,"abstract":"<p><p>Matrix-assisted laser desorption/ionization-based hydrogen/deuterium exchange mass spectrometry (MALDI-HDX-MS) can provide peptide-level information on protein conformational dynamics without any specialized liquid chromatography (LC)-HDX instrumentation. Accurate interpretation of structure-dependent deuterium incorporation and reproducible MALDI-HDX measurements require minimization of unintended exchange and spectral variability during MALDI sample preparation and acquisition. Appropriate control of matrix crystallization, humidity, and spectral acquisition timing is therefore essential for reliable MALDI-HDX analysis. In this Technical Report, we describe a practical workflow for reliable MALDI-HDX measurements using human adenylate kinase 1 (AK1) as a model protein. The workflow includes humidity-controlled spotting on a precooled MALDI plate, preparation of a precooled α-cyano-4-hydroxycinnamic acid matrix solution, rapid vacuum-assisted drying, and time-controlled spectral acquisition. Precooling of the matrix solution induced visible two-layer separation, and use of the lower layer produced relatively uniform, small crystal clusters and favorable MALDI spectra. The influence of acquisition timing after matrix drying was evaluated using AK1 peptic fragments. For a peptide fragment sensitive to post-drying forward exchange, a small but detectable increase in deuterium incorporation was observed at 15 min after the start of matrix drying, whereas no substantial change was observed at 10 min compared with 5 min. Importantly, the increase caused by delayed acquisition was smaller than the difference in deuterium incorporation between structurally distinct peptide regions, indicating that structure-dependent HDX information was retained within the defined acquisition window. Establishment of practical matrix crystallization and spectral acquisition conditions will facilitate the reliable application of MALDI-HDX-MS to biological studies of protein conformational dynamics.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0200"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13586138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149008686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How to Use Quantum Chemistry for Analyzing Mass Spectrometry Data.","authors":"Kim Greis","doi":"10.5702/massspectrometry.A0195","DOIUrl":"10.5702/massspectrometry.A0195","url":null,"abstract":"<p><p>The gas-phase environment of a mass spectrometer is the ideal system to benchmark advanced computational methods, as the properties of ionic species derived from mass spectrometry experiments are identical to the target of (quantum) computational predictions. This is particularly applicable for gas-phase ion spectroscopy techniques, where lasers are interfaced with mass spectrometers to gain further information about isolated ions. Complementing experimental results with computational findings allows one to increase the value of the results and to better interpret the data. The calculation of isolated particles in the gas phase is straightforward and requires fewer approximations than more complex systems. This review serves to give a brief overview of where quantum chemistry and mass spectrometry mutually benefit each other. The main topics covered in this review include fragmentation methods, ion-molecule reactions, ion mobility-mass spectrometry, and ion spectroscopy methods.</p>","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"A0195"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13333582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148436940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}