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

Peak-Based Machine Learning for Plastic Type Classification in Time-of-Flight Secondary Ion Mass Spectrometry. 基于峰值的机器学习技术用于飞行时间二次离子质谱法中的塑料类型分类

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-11-08 DOI: 10.1021/jasms.4c00325

Jin Gyeong Son, Hyun Kyong Shon, Ji-Eun Kim, In Ho Lee, Tae Geol Lee

引用次数: 0

Subcellular Proteomic Mapping of Lysine Lactylation. 赖氨酸乳化的亚细胞蛋白质组图谱

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-11-21 DOI: 10.1021/jasms.4c00366

Qiuyu Bao, Ning Wan, Zimeng He, Ji Cao, Wenjie Yuan, Haiping Hao, Hui Ye

{"title":"Subcellular Proteomic Mapping of Lysine Lactylation.","authors":"Qiuyu Bao, Ning Wan, Zimeng He, Ji Cao, Wenjie Yuan, Haiping Hao, Hui Ye","doi":"10.1021/jasms.4c00366","DOIUrl":"10.1021/jasms.4c00366","url":null,"abstract":"Protein lactylation is a novel post-translational modification (PTM) involved in many important physiological processes such as macrophage polarization, immune regulation, and tumor cell growth. However, traditional methodologies for studying lactylation have predominantly relied on peptide enrichment from whole-cell lysates, which tend to favor the detection of high-abundance peptides, thus limiting the identification of low-abundance lactylated peptides. To address this limitation, here, we employed subcellular fractionation to separate proteins and map lactylated peptides from each isolated subcellular fraction using a model cell line. In brief, we identified 1,217 lysine lactylation (Kla) sites on 553 proteins across four subcellular fractions. Subsequent pathway enrichment analysis revealed that Kla proteins participate in distinct pathways depending on the subcellular contexts. In addition, this subcellular fractionation method enabled the discovery of 36 previously unreported Kla proteins and 223 novel Kla sites, many of which are present in low abundance. Notably, several proteins contain multiple newly identified Kla sites, exemplified by the transcriptional regulator ATRX. Furthermore, our results indicate the possibility of PTM crosstalk between Kla and other PTMs such as ubiquitination and sumoylation. In conclusion, subcellular fractionation facilitates the identification of Kla proteins that have been previously uncovered and could be overlooked by affinity enrichment of whole-cell lysates.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3221-3232"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680418","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 : 2024-12-04 Epub 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 : 2024-12-04 Epub Date: 2024-10-25 DOI: 10.1021/jasms.4c00324

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

{"title":"The Application of a Random Forest Classifier to ToF-SIMS Imaging Data.","authors":"Mariya A Shamraeva, Theodoros Visvikis, Stefanos Zoidis, Ian G M Anthony, Sebastiaan Van Nuffel","doi":"10.1021/jasms.4c00324","DOIUrl":"10.1021/jasms.4c00324","url":null,"abstract":"Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging is a potent analytical tool that provides spatially resolved chemical information on surfaces at the microscale. However, the hyperspectral nature of ToF-SIMS datasets can be challenging to analyze and interpret. Both supervised and unsupervised machine learning (ML) approaches are increasingly useful to help analyze ToF-SIMS data. Random Forest (RF) has emerged as a robust and powerful algorithm for processing mass spectrometry data. This machine learning approach offers several advantages, including accommodating nonlinear relationships, robustness to outliers in the data, managing the high-dimensional feature space, and mitigating the risk of overfitting. The application of RF to ToF-SIMS imaging facilitates the classification of complex chemical compositions and the identification of features contributing to these classifications. This tutorial aims to assist nonexperts in either machine learning or ToF-SIMS to apply Random Forest to complex ToF-SIMS datasets.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"2801-2814"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492614","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}

引用次数: 0

A Streamlined Workflow for Microscopy-Driven MALDI Imaging Mass Spectrometry Data Collection. 显微镜驱动 MALDI 成像质谱数据采集的简化工作流程。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-11-07 DOI: 10.1021/jasms.4c00365

Allison B Esselman, Megan S Ward, Cody R Marshall, Ellie L Pingry, Martin Dufresne, Melissa A Farrow, Matthew Schrag, Jeffrey M Spraggins

{"title":"A Streamlined Workflow for Microscopy-Driven MALDI Imaging Mass Spectrometry Data Collection.","authors":"Allison B Esselman, Megan S Ward, Cody R Marshall, Ellie L Pingry, Martin Dufresne, Melissa A Farrow, Matthew Schrag, Jeffrey M Spraggins","doi":"10.1021/jasms.4c00365","DOIUrl":"10.1021/jasms.4c00365","url":null,"abstract":"Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a rapidly advancing technology for biomedical research. As spatial resolution increases, however, so do acquisition time, file size, and experimental cost, which increases the need to perform precise sampling of targeted tissue regions to optimize the biological information gleaned from an experiment and minimize wasted resources. The ability to define instrument measurement regions based on key tissue features and automatically sample these specific regions of interest (ROIs) addresses this challenge. Herein, we demonstrate a workflow using standard software that allows for direct sampling of microscopy-defined regions by MALDI IMS. Three case studies are included, highlighting different methods for defining features from common sample types─manual annotation of vasculature in human brain tissue, automated segmentation of renal functional tissue units across whole slide images using custom segmentation algorithms, and automated segmentation of dispersed HeLa cells using open-source software. Each case minimizes data acquisition from unnecessary sample regions and dramatically increases throughput while uncovering molecular heterogeneity within targeted ROIs. This workflow provides an approachable method for spatially targeted MALDI IMS driven by microscopy as part of multimodal molecular imaging studies.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"2795-2800"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602787","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}

引用次数: 0

Identifying Process Differences with ToF-SIMS: An MVA Decomposition Strategy. 利用 ToF-SIMS 识别过程差异：一种 MVA 分解策略。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-10-04 DOI: 10.1021/jasms.4c00327

Nico Fransaert, Allyson Robert, Bart Cleuren, Jean V Manca, Dirk Valkenborg

{"title":"Identifying Process Differences with ToF-SIMS: An MVA Decomposition Strategy.","authors":"Nico Fransaert, Allyson Robert, Bart Cleuren, Jean V Manca, Dirk Valkenborg","doi":"10.1021/jasms.4c00327","DOIUrl":"10.1021/jasms.4c00327","url":null,"abstract":"In time-of-flight secondary ion mass spectrometry (ToF-SIMS), multivariate analysis (MVA) methods such as principal component analysis (PCA) are routinely employed to differentiate spectra. However, additional insights can often be gained by comparing processes, where each process is characterized by its own start and end spectra, such as when identical samples undergo slightly different treatments or when slightly different samples receive the same treatment. This study proposes a strategy to compare such processes by decomposing the loading vectors associated with them, which highlights differences in the relative behavior of the peaks. This strategy identifies key information beyond what is captured by the loading vectors or the end spectra alone. While PCA is widely used, partial least-squares discriminant analysis (PLS-DA) serves as a supervised alternative and is the preferred method for deriving process-related loading vectors when classes are narrowly separated. The effectiveness of the decomposition strategy is demonstrated using artificial spectra and applied to a ToF-SIMS materials science case study on the photodegradation of N719 dye, a common dye in photovoltaics, on a mesoporous TiO2 anode. The study revealed that the photodegradation process varies over time, and the resulting fragments have been identified accordingly. The proposed methodology, applicable to both labeled (supervised) and unlabeled (unsupervised) spectral data, can be seamlessly integrated into most modern mass spectrometry data analysis workflows to automatically generate a list of peaks whose relative behavior varies between two processes, and is particularly effective in identifying subtle differences between highly similar physicochemical processes.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3116-3125"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374951","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}

引用次数: 0

ToF-SIMS Investigation of Environmental Effects on Analyte Migration in Matrix Coatings for Mass Spectrometry Imaging Using a Newly Developed Vapor Deposition System. 利用新开发的气相沉积系统，ToF-SIMS 研究环境对质谱成像基质涂层中分析物迁移的影响。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-10-11 DOI: 10.1021/jasms.4c00340

Thorsten Adolphs, Michael Bäumer, Florian Bosse, Bart Jan Ravoo, Richard E Peterson, Heinrich F Arlinghaus, Bonnie J Tyler

{"title":"ToF-SIMS Investigation of Environmental Effects on Analyte Migration in Matrix Coatings for Mass Spectrometry Imaging Using a Newly Developed Vapor Deposition System.","authors":"Thorsten Adolphs, Michael Bäumer, Florian Bosse, Bart Jan Ravoo, Richard E Peterson, Heinrich F Arlinghaus, Bonnie J Tyler","doi":"10.1021/jasms.4c00340","DOIUrl":"10.1021/jasms.4c00340","url":null,"abstract":"High resolution mass spectrometry images are of increasing importance in biological applications, such as the study of tissues and single cells. Two promising techniques for this are matrix-enhanced secondary ion mass spectrometry (ME-SIMS) and matrix-assisted laser desorption/ionization (MALDI). For both techniques, the sample of interest must be coated with a matrix prior to analysis, and analytes must migrate into the matrix. The mechanisms involved in this migration and the factors that influence the migration are poorly understood, which lead to difficulties with reproducibility. In this work, a sublimation matrix coater with an effusion cell and sample cooling was developed and built in-house for controlled physical vapor deposition. In this system, sample transfer between the coater and mass spectrometer is possible without breaking vacuum, which facilitates the study of environmental influences on analyte migration. The influence of exposure to ambient air on the migration of two analytes (a lipid and a peptide), which were coated with the matrix α-cyano-4-hydroxycinnamic acid (CHCA), was studied using 3D-SIMS imaging. Although the distribution of analyte in the matrix changed very little after 21 h of storage in vacuum, significant redistribution of the analyte was observed after exposure to ambient air. The magnitude of the effect was greater for the lipid than for the peptide. Further work is needed to determine the role of humidity in the redistribution process and the impact of analyte redistribution on MALDI measurements.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3163-3169"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399037","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

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 : 2024-12-04 Epub 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":"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":" ","pages":"2785-2789"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","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

Automated Single Cell Phenotyping of Time-of-Flight Secondary Ion Mass Spectrometry Tissue Images. 飞行时间二次离子质谱组织图像的自动单细胞表型分析。

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-11-19 DOI: 10.1021/jasms.4c00328

Sweta Bajaj, Spencer Tolleson, Aida Zarfeshani, Monirath Hav, Sean C Pawlowski, Danielle E Lyons, Raghav Padmanabhan, Jay G Tarolli, Máté Levente Nagy

{"title":"Automated Single Cell Phenotyping of Time-of-Flight Secondary Ion Mass Spectrometry Tissue Images.","authors":"Sweta Bajaj, Spencer Tolleson, Aida Zarfeshani, Monirath Hav, Sean C Pawlowski, Danielle E Lyons, Raghav Padmanabhan, Jay G Tarolli, Máté Levente Nagy","doi":"10.1021/jasms.4c00328","DOIUrl":"10.1021/jasms.4c00328","url":null,"abstract":"Existing analytical techniques are being improved or applied in new ways to profile the tissue microenvironment (TME) to better understand the role of cells in disease research. Fully understanding the complex interactions between cells of many different types and functions is often slowed by the intense data analysis required. Multiplexed Ion Beam Imaging (MIBI) has been developed to simultaneously characterize 50+ cell types and their functions within the TME with a subcellular spatial resolution, but this results in complex data sets that are challenging to qualitatively analyze. Deep Learning (DL) techniques were used to build the MIBIsight workflow, which can process images containing thousands of cells into easily digestible reports and plots to enable researchers to easily summarize data sets in a study and make informed conclusions. Here we present the three types of DL models that have been trained with annotated MIBI images that have been pathologist validated as well as the associated workflow for the evolution of raw mass spectral data into actionable reports and plots.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3126-3134"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674740","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

Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome. 泛素化多肽的质谱特征分析为探索黑暗泛素组提供了启示

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-09-27 DOI: 10.1021/jasms.4c00213

Regina M Edgington, Damien B Wilburn

{"title":"Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome.","authors":"Regina M Edgington, Damien B Wilburn","doi":"10.1021/jasms.4c00213","DOIUrl":"10.1021/jasms.4c00213","url":null,"abstract":"Ubiquitylation is a structurally and functionally diverse post-translational modification that involves the covalent attachment of the small protein ubiquitin to other protein substrates. Trypsin-based proteomics is the most common approach for globally identifying ubiquitylation sites. However, we estimate that such methods are unable to detect ∼40% of ubiquitylation sites in the human proteome, i.e., \"the dark ubiquitylome\", including many important for human health and disease. In this meta-analysis of three large ubiquitylomic data sets, we performed a series of bioinformatic analyses to assess experimental features that could aid in uniquely identifying site-specific ubiquitylation events. Spectral predictions from Prosit were compared to experimental spectra of tryptic ubiquitylated peptides, revealing previously uncharacterized fragmentation of the diGly scar. Analysis of the LysC-derived ubiquitylated peptides reveals systematic, multidimensional peptide fragmentation, including diagnostic b-ions from fragmentation of the LysC ubiquitin scar. Comprehensively, these findings provide diagnostic spectral signatures of modification events that could be applied to new analysis methods for nontryptic ubiquitylomics.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"2849-2858"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338954","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}

引用次数: 0