Journal of the American Society for Mass Spectrometry最新文献_第3页

Improved Rapid Equilibrium Dialysis-Mass Spectrometry (RED-MS) Method for Measuring Small Molecule-Protein Complex Binding Affinities in Solution. 改进的快速平衡透析-质谱法 (RED-MS) 用于测量溶液中的小分子-蛋白质复合物结合亲和力。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-04 DOI: 10.1021/jasms.4c00334

Bryan Choi, Calvin Han, Jonathan R LaRochelle, Warintra Pitsawong, Damian Houde

{"title":"Improved Rapid Equilibrium Dialysis-Mass Spectrometry (RED-MS) Method for Measuring Small Molecule-Protein Complex Binding Affinities in Solution.","authors":"Bryan Choi, Calvin Han, Jonathan R LaRochelle, Warintra Pitsawong, Damian Houde","doi":"10.1021/jasms.4c00334","DOIUrl":"https://doi.org/10.1021/jasms.4c00334","url":null,"abstract":"Rapid equilibrium dialysis (RED) is predominantly used for the characterization of drug absorption, distribution, metabolism, and excretion (ADME) properties in plasma and biological fluids. We describe herein improvements in the use of RED in conjunction with mass spectrometry (RED-MS) to enable robust binding affinity measurements of small molecules for recombinant proteins and complexes from a single dialysis data set. The affinities calculated from RED-MS correlated well with measurements by both surface plasmon resonance (SPR) and affinity selection mass spectrometry (AS-MS). The method was particularly useful for quantifying the binding of small molecules to large protein complexes that were not amendable by common biophysical characterization techniques. Compound pooling and integration with automated liquid handling increased assay throughput and enabled the analysis of hundreds of measurements per week. RED-MS offers a viable option for measuring compound binding in solution and may facilitate small molecule affinity optimization toward difficult-to-drug protein complexes.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Infrared Laser Ablation and Capture of Formalin-Fixed Paraffin-Embedded Tissue. 红外线激光烧蚀和捕获福尔马林固定的石蜡包埋组织。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-04 DOI: 10.1021/jasms.4c00299

Blessing C Egbejiogu, Fabrizio Donnarumma, Kermit K Murray

{"title":"Infrared Laser Ablation and Capture of Formalin-Fixed Paraffin-Embedded Tissue.","authors":"Blessing C Egbejiogu, Fabrizio Donnarumma, Kermit K Murray","doi":"10.1021/jasms.4c00299","DOIUrl":"https://doi.org/10.1021/jasms.4c00299","url":null,"abstract":"Formalin-fixed paraffin-embedded (FFPE) tissue is a ubiquitous and invaluable resource for biomedical research and clinical applications. However, FFPE tissue proteomics is challenging due to protein cross-linking and chemical modification. Laser ablation sampling allows precise removal of material from tissue sections with high spatial control and reproducibility for offline proteomics by liquid chromatography coupled with tandem mass spectrometry. In this work, we used a pulsed mid-infrared laser for microsampling of rat liver tissue for subsequent identification and quantification of proteins. It was found that more proteins were identified by FFPE tissue laser ablation sampling compared to fresh frozen (FF) tissue laser ablation sampling and that more proteins were identified by laser ablation than by manual dissection of FFPE tissue. In contrast to previous studies, no loss of hydrophilic proteins due to residual cross-linking was observed. The efficient capture of proteins by laser ablation microsampling is attributed to efficient laser breakup of the tissue which facilitates downstream processing of the proteins.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative Analysis of Drugs in a Mimetic Tissue Model Using Nano-DESI on a Triple Quadrupole Mass Spectrometer. 在三重四极杆质谱仪上使用纳米 DESI 对模拟组织模型中的药物进行定量分析

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-01 DOI: 10.1021/jasms.4c00345

Alyssa M Moore, Andrew Bowman, Syeda Nazifa Wali, Miranda R Weigand, David Wagner, Junhai Yang, Julia Laskin

{"title":"Quantitative Analysis of Drugs in a Mimetic Tissue Model Using Nano-DESI on a Triple Quadrupole Mass Spectrometer.","authors":"Alyssa M Moore, Andrew Bowman, Syeda Nazifa Wali, Miranda R Weigand, David Wagner, Junhai Yang, Julia Laskin","doi":"10.1021/jasms.4c00345","DOIUrl":"https://doi.org/10.1021/jasms.4c00345","url":null,"abstract":"Mass spectrometry is a powerful analytical technique used at every stage of the pharmaceutical research process. A specialized branch of this method, mass spectrometry imaging (MSI), has emerged as an important tool for determining the spatial distribution of drugs in biological samples. Despite the importance of MSI, its quantitative capabilities are still limited due to the complexity of biological samples and the lack of separation prior to analysis. This makes the simultaneous quantification and visualization of analytes challenging. Several techniques have been developed to address this challenge and enable quantitative MSI. One such approach is the mimetic tissue model, which involves the incorporation of an analyte of interest into tissue homogenates at several concentrations. A calibration curve that accounts for signal suppression by the complex biological matrix is then created by measuring the signal of the analyte in the series of tissue homogenates. Herein, we use the mimetic tissue model on a triple quadrupole mass spectrometer (QqQ) in multiple reaction monitoring mode to demonstrate the quantitative abilities of nanospray desorption electrospray ionization (nano-DESI) and compare these results with those obtained using atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI). For the tested compounds, our findings indicate that nano-DESI achieves lower standard deviations than AP-MALDI, resulting in superior limits of detection for the studied analytes. Additionally, we discuss the limitations of the mimetic tissue model in the quantification of certain analytes and the challenges involved with the implementation of the model.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of a Novel Label-Free Subunit HILIC-MS Method for Domain-Specific Free Thiol Identification and Quantitation in Therapeutic Monoclonal Antibodies. 开发一种新型无标记亚基 HILIC-MS 方法，用于治疗性单克隆抗体中域特异性游离硫醇的鉴定和定量。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-10-30 DOI: 10.1021/jasms.4c00308

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":"https://doi.org/10.1021/jasms.4c00308","url":null,"abstract":"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.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single Cell MALDI-MSI Analysis of Lipids and Proteins within a Replicative Senescence Fibroblast Model. 对复制衰老成纤维细胞模型中的脂质和蛋白质进行单细胞 MALDI-MSI 分析。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-10-30 DOI: 10.1021/jasms.4c00095

Emily R Sekera, Lorena Rosas, Joseph H Holbrook, Quetzalli D Angeles-Lopez, Timur Khaliullin, Mauricio Rojas, Ana L Mora, Amanda B Hummon

{"title":"Single Cell MALDI-MSI Analysis of Lipids and Proteins within a Replicative Senescence Fibroblast Model.","authors":"Emily R Sekera, Lorena Rosas, Joseph H Holbrook, Quetzalli D Angeles-Lopez, Timur Khaliullin, Mauricio Rojas, Ana L Mora, Amanda B Hummon","doi":"10.1021/jasms.4c00095","DOIUrl":"10.1021/jasms.4c00095","url":null,"abstract":"In this study, we evaluate lipids and select proteins in human lung fibroblasts (hLFs) to interrogate changes occurring due to aging and senescence. To study single cell populations, a comparison of cells adhered onto slides using poly-d-lysine versus centrifugal force deposition was first analyzed to determine whether specific alterations were observed between preparations. The poly-d-lysine approach was then utilized to interrogate the lipidome of the cell populations and further evaluate potential applications of the MALDI-immunohistochemistry (IHC) platform for single-cell-level analyses. Two protein markers of senescence, vimentin and p21, were both observed within the fibroblast populations and quantified. Lipidomic analysis of the fibroblasts found 12 lipids significantly altered because of replicative senescence, including fatty acids, such as stearic acid, and ceramide phosphoethanolamine species (CerPE). Similar to previous reports, alterations were detected in putative fatty acid building blocks, ceramides, among other lipid species. Altogether, our results reveal the ability to detect lipids implicated in senescence and show alterations to protein expression between normal and senescent fibroblast populations, including differences between young and aged cells. This report is the first time that the MALDI-IHC system has been utilized at a single-cell level to analyze both protein expression and lipid profiles in cultured cells, with a particular focus on changes associated with aging and senescence.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Processing Next-Generation Mass Spectrometry Imaging Data: Principal Component Analysis at Scale. 处理下一代质谱成像数据：规模主成分分析

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-10-28 DOI: 10.1021/jasms.4c00314

Kasper Krijnen, Paul Blenkinsopp, Ron M A Heeren, Ian G M Anthony

{"title":"Processing Next-Generation Mass Spectrometry Imaging Data: Principal Component Analysis at Scale.","authors":"Kasper Krijnen, Paul Blenkinsopp, Ron M A Heeren, Ian G M Anthony","doi":"10.1021/jasms.4c00314","DOIUrl":"https://doi.org/10.1021/jasms.4c00314","url":null,"abstract":"Mass spectrometry imaging (MSI) is constantly improving in spatial resolving power, throughput and mass resolution. Although beneficial, these improvements increase data set size and content. The larger data requires correspondingly fast computer-based analyses. However, these analyses often do not scale well with increased data size. Principal component analysis (PCA) is an important analytical tool commonly used with MSI data; however, most PCA algorithms load and process the entire data set within random access memory (RAM) which is most often insufficient for large data sets. PCA algorithms that use less RAM than the data set exist but are usually much slower or sacrifice precision and are rarely used for MSI data processing. Incremental PCA (IPCA) is an alternative algorithm that avoids large RAM allocations while also preserving speed and analytical precision. Here, we demonstrate and benchmark the use of differing implementations of IPCA, PCA, and commercial software on large and often complex MSI data sets. We show that using an already-published Python-based IPCA algorithm, IPCA can be successfully applied to MSI data sets too large to fit with RAM. Furthermore, our benchmarks demonstrate that, contrary to expectations, IPCA is faster than all other tested PCA implementations on all large data sets that can be directly compared.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Conformation-Specific Approach to Native Top-down Mass Spectrometry. 原生自上而下质谱法的构象特异性方法

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-10-25 DOI: 10.1021/jasms.4c00361

Hannah M Britt, Aisha Ben-Younis, Nathanael Page, Konstantinos Thalassinos

引用次数: 0

The Application of a Random Forest Classifier to ToF-SIMS Imaging Data. 将随机森林分类器应用于 ToF-SIMS 成像数据。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-10-25 DOI: 10.1021/jasms.4c00324

Mariya A Shamraeva, Theodoros Visvikis, Stefanos Zoidis, Ian G M Anthony, Sebastiaan Van Nuffel

引用次数: 0

Fellgett Revisited: On the Nature of Noise in Two-Dimensional Mass Spectrometry. 费尔格特重访：论二维质谱法中噪音的性质》。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-10-25 DOI: 10.1021/jasms.4c00294

Callan Littlejohn, Meng Li, Pui Yiu Lam, Mark P Barrow, Peter B O'Connor

引用次数: 0

Photochemical and Collision-Induced Cross-Linking in Stereochemically Distinct Scaffolds of Peptides and Nitrile Imines in Gas-Phase Ions. 气相离子中肽和腈胺立体化学上不同支架的光化学和碰撞诱导交联。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-10-24 DOI: 10.1021/jasms.4c00317

Hongyi Zhu, Marianna Nytka, Tuan Ngoc Kim Vu, Karel Lemr, František Tureček

{"title":"Photochemical and Collision-Induced Cross-Linking in Stereochemically Distinct Scaffolds of Peptides and Nitrile Imines in Gas-Phase Ions.","authors":"Hongyi Zhu, Marianna Nytka, Tuan Ngoc Kim Vu, Karel Lemr, František Tureček","doi":"10.1021/jasms.4c00317","DOIUrl":"https://doi.org/10.1021/jasms.4c00317","url":null,"abstract":"Intramolecular cross-linking between peptides and nitrile-imine intermediates was studied in stereochemically distinct conjugates in which the reacting components were mounted on cis-1,2-cyclohexane and trans-1,4-cyclohexane scaffolds that we call 1,2-s-peptides and 1,4-s-peptides, respectively. The nitrile-imine intermediates were generated by N2 loss from 2,5-diaryltetrazole tags upon UV-photodissociation at 213 and 250 nm or by collision-induced dissociation, and further interrogated by CID and UVPD-MS3. Peptide fragment ion series originating from linear structures and macrocyclic cross-links were distinguished and used to quantify the cross-linking yields. The yields in MS2 varied between 27% for AAAG conjugates to 78% for GAAAK conjugates, depending on the peptide sequence. The CID-MS3 yields were in a 57-97% range, depending on the peptide sequence. Structures of 1,2-s-peptide and 1,4-s-peptide ions as well as several of their nitrile-imine intermediates and cross-links were investigated by high-resolution cyclic ion mobility in combination with Born-Oppenheimer molecular dynamics and density functional theory calculations. Matches between the experimental and calculated collision cross sections and ion relative Gibbs energies were used to assign peptide structures. Peptide conjugates C-terminated with Gly and Lys residues underwent cross-linking by the carboxyl group, as established by MS3 sequencing and corroborated by carboxyl blocking experiments that lowered the cross-linking yields. Peptide conjugates C-terminated with Arg also cross-linked via the side-chain guanidine group. A notable feature of the 1,4-s-peptide ions was the participation of low-energy twist-boat cyclohexane conformers that was enforced by strong hydrogen bonds between the peptide and nitrile imine.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0