Journal of Proteome Research最新文献_第9页

A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-21 DOI: 10.1021/acs.jproteome.4c0087110.1021/acs.jproteome.4c00871

Markus Schneider, Daniel P. Zolg, Patroklos Samaras, Samia Ben Fredj, Dulguun Bold, Agnes Guevende, Alexander Hogrebe, Michelle T. Berger, Michael Graber, Vishal Sukumar, Lizi Mamisashvili, Igor Bronsthein, Layla Eljagh, Siegfried Gessulat, Florian Seefried, Tobias Schmidt and Martin Frejno*,

{"title":"A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis","authors":"Markus Schneider, Daniel P. Zolg, Patroklos Samaras, Samia Ben Fredj, Dulguun Bold, Agnes Guevende, Alexander Hogrebe, Michelle T. Berger, Michael Graber, Vishal Sukumar, Lizi Mamisashvili, Igor Bronsthein, Layla Eljagh, Siegfried Gessulat, Florian Seefried, Tobias Schmidt and Martin Frejno*, ","doi":"10.1021/acs.jproteome.4c0087110.1021/acs.jproteome.4c00871","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00871https://doi.org/10.1021/acs.jproteome.4c00871","url":null,"abstract":"The exponential increase in proteomics data presents critical challenges for conventional processing workflows. These pipelines often consist of fragmented software packages, glued together using complex in-house scripts or error-prone manual workflows running on local hardware, which are costly to maintain and scale. The MSAID Platform offers a fully automated, managed proteomics data pipeline, consolidating formerly disjointed functions into unified, API-driven services that cover the entire process from raw data to biological insights. Backed by the cloud-native search algorithm CHIMERYS, as well as scalable cloud compute instances and data lakes, the platform facilitates efficient processing of large data sets, automation of processing via the command line, systematic result storage, analysis, and visualization. The data lake supports elastically growing storage and unified query capabilities, facilitating large-scale analyses and efficient reuse of previously processed data, such as aggregating longitudinally acquired studies. Users interact with the platform via a web interface, CLI client, or API, providing flexible, automated access. Readily available tools for accessing result data include browser-based interrogation and one-click visualizations for statistical analysis. The platform streamlines research processes, making advanced and automated proteomic workflows accessible to a broader range of scientists. The MSAID Platform is globally available via https://platform.msaid.io.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1241–1249 1241–1249"},"PeriodicalIF":3.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00871","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomics Reveals That Vitamin D Deficiency Leads to Immunoglobulin Abnormalities and Immune Dysregulation in Patients with Post-COVID-19 Condition

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-20 DOI: 10.1021/acs.jproteome.4c0112010.1021/acs.jproteome.4c01120

Wenrui Ji, Xiaomin Xie*, Guirong Bai, Yalei Fan, Yanting He, Li Zhang, Haiyan Zhou, Ling Li and Huan Li,

{"title":"Proteomics Reveals That Vitamin D Deficiency Leads to Immunoglobulin Abnormalities and Immune Dysregulation in Patients with Post-COVID-19 Condition","authors":"Wenrui Ji, Xiaomin Xie*, Guirong Bai, Yalei Fan, Yanting He, Li Zhang, Haiyan Zhou, Ling Li and Huan Li, ","doi":"10.1021/acs.jproteome.4c0112010.1021/acs.jproteome.4c01120","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01120https://doi.org/10.1021/acs.jproteome.4c01120","url":null,"abstract":"Vitamin D (VD) levels are closely related to the occurrence of post-COVID-19 conditions (PCCs), but the specific mechanism is still unclear. Here, a total of 50 PCC patient serum samples were divided into the VD sufficient group (VD ≥ 30 ng/mL), the VD insufficient group (20 ng/mL ≤ VD < 30 ng/mL), and the VD deficiency group (VD < 20 ng/mL) and then subjected to proteomic analysis. We identified 15 differential abundance proteins (DAPs) between the VD sufficient and VD insufficient groups, including 5 immunoglobulin proteins (JCHAJN, IGHV4–28, GHV4–34, IGHM, and IGLV2–11), which were significantly negatively correlated with VD levels in PCC patients. These DAPs were primarily enriched in immune-related pathways such as the TNF signaling pathway and the B cell receptor signaling pathway. Compared with the VD insufficient group, VD deficiency resulted in 4 proteins being upregulated and 8 proteins being downregulated. The declined abundance of IGLV1–47 negatively correlated with serum VD levels. Albumin (ALB) was in the center of the protein–protein interaction (PPI) network map of all DAPs and was negatively correlated with serum VD levels. In conclusion, VD insufficiency/deficiency leads to abnormalities in immunoglobulin heavy, light, and J chains, resulting in PCC syndrome. VD supplementation may be a potential therapeutic strategy to alleviate the symptoms of PCC.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1449–1461 1449–1461"},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Swift Universal Glycan Acquisition (SUGA) Enables Quantitative Glycan Profiling across Diverse Sample Types

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-20 DOI: 10.1021/acs.jproteome.4c0065710.1021/acs.jproteome.4c00657

Christopher Ashwood, Cecilia Voelcker and Richard D. Cummings*,

{"title":"Swift Universal Glycan Acquisition (SUGA) Enables Quantitative Glycan Profiling across Diverse Sample Types","authors":"Christopher Ashwood, Cecilia Voelcker and Richard D. Cummings*, ","doi":"10.1021/acs.jproteome.4c0065710.1021/acs.jproteome.4c00657","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00657https://doi.org/10.1021/acs.jproteome.4c00657","url":null,"abstract":"The ability to rapidly analyze complex mixtures of glycans derived from glycoproteins is important, but techniques are often laborious and require multiple glycan derivatization steps. Here, we describe an approach termed Swift Universal Glycan Acquisition (SUGA) in which the total released, nonreduced N-glycan samples are analyzed following direct injection and electrospray ionization in a mass spectrometer with a rapid 3 min run time for each sample. As electrospray ionization (ESI) can generate multiple charge states and adducts for the same glycan composition (MS1), deconvolution is performed to yield the relative intensity profile for each detected glycan composition; each annotated composition is supported by an annotated MS2 spectrum. This combination of MS1 and MS2 data enables confident glycan identification. The data obtained by SUGA are comparable to those obtained using permethylated N-glycans analyzed by matrix-assisted laser desorption/ionization (MALDI)-MS. The SUGA approach was applied to the analyses of several purified glycoproteins and N-glycans derived from cells and compared to spectra obtained following permethylation and analysis by MALDI-MS. This new approach will facilitate the rapid and high-throughput analysis of N-glycans from diverse biological samples.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1030–1038 1030–1038"},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00657","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

γ Irradiation Alters the Staphylococcus aureus Proteome and Enhances Pathogenicity

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-20 DOI: 10.1021/acs.jproteome.4c0101810.1021/acs.jproteome.4c01018

Jingjing Liu, Xinghua Jin, Jingxin Zhu, Jundong Feng, Jian Zhao, Yixuan Wang, Quan Wang and Xiaofeng Song*,

{"title":"γ Irradiation Alters the Staphylococcus aureus Proteome and Enhances Pathogenicity","authors":"Jingjing Liu, Xinghua Jin, Jingxin Zhu, Jundong Feng, Jian Zhao, Yixuan Wang, Quan Wang and Xiaofeng Song*, ","doi":"10.1021/acs.jproteome.4c0101810.1021/acs.jproteome.4c01018","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01018https://doi.org/10.1021/acs.jproteome.4c01018","url":null,"abstract":"Staphylococcus aureus (S. aureus) infection has become one of the most common and severe complications among cancer patients. The impact of γ radiation from radiotherapy on S. aureus’s growth and virulence is not yet fully understood. In this study, S. aureus was exposed to γ radiation at a dose of 100 Gy, and its descendants were cultured under normal conditions. Proteome alternations of unirradiated, irradiated, and descendants of irradiated S. aureus were identified by using data-independent acquisition (DIA) proteomic technology. To investigate the consequences of proteome alternations induced by γ irradiation in S. aureus, functional enrichment analysis, pathway enrichment analysis, and protein–protein interaction network analysis were performed. Differentially expressed proteins (DEPs) in the irradiated S. aureus and its descendants were primarily enriched in lipoteichoic acid biosynthesis, S. aureus infection, two-component system, and cationic antimicrobial peptide resistance, suggesting an enhanced infection ability. A strong infection ability is typically associated with increased biofilm formation. Both the proteome study and the biofilm assay indicate that γ irradiation enhances the infection ability of S. aureus, likely resulting in increased pathogenicity.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1373–1385 1373–1385"},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gemcitabine Alters Phosphatidylcholine Metabolism in Mouse Pancreatic Tumors

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-19 DOI: 10.1021/acs.jproteome.4c0083910.1021/acs.jproteome.4c00839

Nav Raj Phulara, Chiaki Tsuge Ishida, Peter John Espenshade and Herana Kamal Seneviratne*,

{"title":"Gemcitabine Alters Phosphatidylcholine Metabolism in Mouse Pancreatic Tumors","authors":"Nav Raj Phulara, Chiaki Tsuge Ishida, Peter John Espenshade and Herana Kamal Seneviratne*, ","doi":"10.1021/acs.jproteome.4c0083910.1021/acs.jproteome.4c00839","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00839https://doi.org/10.1021/acs.jproteome.4c00839","url":null,"abstract":"Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest diseases, despite advancements in elucidating tumor biology and developing novel therapeutics. Importantly, lipids, such as phospholipids, are crucial for the survival and proliferation of tumor cells. However, the impact of chemotherapeutic drugs on phospholipid metabolism in PDAC remains poorly understood. Gemcitabine (a nucleoside analogue) is a first-line drug in PDAC treatment, but its clinical effectiveness is limited by multiple factors. Herein, we employed matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) and proteomics approaches to investigate gemcitabine-induced lipid metabolism alterations in mouse pancreatic tumors following gemcitabine treatment (n = 3, control tumors; n = 3, gemcitabine-treated tumors). From MALDI MSI experiments, we observed elevated levels of several phosphatidylcholines (PCs), PC(30:0), PC(32:3), PC(34:2), PC(36:1), and PC(36:2), in gemcitabine-treated tumor tissues compared to the control. In addition, proteomics data revealed the differential abundance of several phospholipid-binding proteins in response to gemcitabine treatments. Furthermore, several endoplasmic reticulum stress-related proteins exhibited high expression in gemcitabine-treated tumor tissues. Altogether, our MALDI MSI and proteomics data provide important insights into alterations in PC metabolism in pancreatic tumors in response to gemcitabine treatment. Importantly, targeting the altered PC metabolism during gemcitabine therapy might help combat pancreatic cancer.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1209–1218 1209–1218"},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative Proteome and Phosphoproteome Profiling across Three Cell Lines Revealed Potential Proteins Relevant to Nasopharyngeal Carcinoma Metastasis

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-19 DOI: 10.1021/acs.jproteome.4c0100210.1021/acs.jproteome.4c01002

Jie Song, Yi Shen, Zhen Wu, Lin Huang, Yun Deng, Wei Yu*, Xiaoshen Wang* and Xumin Zhang*,

{"title":"Quantitative Proteome and Phosphoproteome Profiling across Three Cell Lines Revealed Potential Proteins Relevant to Nasopharyngeal Carcinoma Metastasis","authors":"Jie Song, Yi Shen, Zhen Wu, Lin Huang, Yun Deng, Wei Yu*, Xiaoshen Wang* and Xumin Zhang*, ","doi":"10.1021/acs.jproteome.4c0100210.1021/acs.jproteome.4c01002","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01002https://doi.org/10.1021/acs.jproteome.4c01002","url":null,"abstract":"Despite the substantial reduction in the mortality rates of nasopharyngeal carcinoma (NPC), metastasis remains the primary cause of death in NPC cases. To explore metastasis-related proteins, we conducted proteomic and phosphoproteomic analyses of three NPC cell lines: SUNE1 and its subclones, 5–8F (high metastatic potential) and 6–10B (low metastatic potential). Using TMT-based quantification, we identified 1231, 1524, and 166 differentially regulated proteins (DRPs), as well as 177, 270, and 20 differentially regulated phosphoproteins (DRpPs) in 5–8F/SUNE1, 6–10B/SUNE1 and 5–8F/6–10B, respectively. These were enriched in cancer metastasis-related pathways, including cell migration and PPAR and PI3K pathways. Notably, 5–8F and 6–10B showed greater proteomic and phosphoproteomic similarity. To identify key proteins involved in NPC metastasis, we focused on the top 10 DRPs in 5–8F/6–10B. Knockdown experiments revealed that eight of these proteins, CRABP2, DNAJC15, NACAD, MYL9, DPYSL3, MAOA, MCAM, and S100A2, significantly influenced cell migration or invasion, with CRABP2, NACAD, and DPYSL3 dramatically enhancing these processes. Notably, DNAJC15 and NACAD are identified for the first time as novel metastasis-related proteins. Our findings demonstrate the effectiveness of this approach in identifying NPC metastasis biomarker candidates and offer new insights into underlying metastasis mechanisms, thus laying the groundwork for future research endeavors.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1356–1372 1356–1372"},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epitope and Paratope Mapping of a SUMO-Remnant Antibody Using Cross-Linking Mass Spectrometry and Molecular Docking

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-18 DOI: 10.1021/acs.jproteome.4c0071710.1021/acs.jproteome.4c00717

Simon Comtois-Marotte, Éric Bonneil, Chongyang Li, Matthew J. Smith and Pierre Thibault*,

{"title":"Epitope and Paratope Mapping of a SUMO-Remnant Antibody Using Cross-Linking Mass Spectrometry and Molecular Docking","authors":"Simon Comtois-Marotte, Éric Bonneil, Chongyang Li, Matthew J. Smith and Pierre Thibault*, ","doi":"10.1021/acs.jproteome.4c0071710.1021/acs.jproteome.4c00717","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00717https://doi.org/10.1021/acs.jproteome.4c00717","url":null,"abstract":"The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity, and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often requiring exogenous gene expression in cells and immunoaffinity purification of SUMO-remnant peptides following tryptic digestion. Previously, an antibody was developed to enrich tryptic peptides containing the remnant NQTGG on the receptor lysine, although the specifics of the structural interaction motif remained unclear. This study integrates de novo sequencing, intact mass spectrometry, cross-linking mass spectrometry, and molecular docking to elucidate the structural interaction motifs of a SUMO-remnant antibody. Additional cross-linking experiments were performed using SUMOylated peptides and high-field asymmetric waveform ion mobility spectrometry (FAIMS) to enhance the sensitivity and confirm interactions at the paratope interface. This study establishes a robust framework for characterizing antibody–antigen interactions, offering valuable insights into the structural basis of SUMO-remnant peptide recognition.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1092–1101 1092–1101"},"PeriodicalIF":3.8,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Proteoform Program of Life: Deciphering Evolution at the Protein Level.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-18 DOI: 10.1021/acs.jproteome.5c00028

Neil L Kelleher

引用次数: 0

Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-17 DOI: 10.1021/acs.jproteome.4c0087410.1021/acs.jproteome.4c00874

Richard M. Searfoss, Emily Zahn, Zongtao Lin and Benjamin A. Garcia*,

{"title":"Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation","authors":"Richard M. Searfoss, Emily Zahn, Zongtao Lin and Benjamin A. Garcia*, ","doi":"10.1021/acs.jproteome.4c0087410.1021/acs.jproteome.4c00874","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00874https://doi.org/10.1021/acs.jproteome.4c00874","url":null,"abstract":"Top-down proteomics is the study of intact proteins and their post-translational modifications with mass spectrometry. Historically, this field is more challenging than its bottom-up counterpart because the species are much bigger and have a larger number of possible combinations of sequences and modifications; thus, there is a great need for technological development. With improvements in instrumentation and a multiplicity of fragmentation modes available, top-down proteomics is quickly gaining in popularity with renewed attention on increasing confidence in identification and quantification. Here, we systematically evaluated the Sciex ZenoTOF 7600 system for top-down proteomics, applying standards in the field to validate the platform and further experimenting with its capabilities in electron-activated dissociation and post-translational modification site localization. The instrument demonstrated robustness in standard proteins for platform QC, as aided by zeno trapping. We were also able to apply this to histone post-translational modifications, achieving high sequence coverage that allowed PTM’s site localization across protein sequences with optimized EAD fragmentation. We demonstrated the ability to analyze proteins spanning the mass range and included analysis of glycosylated proteins. This is a reference point for future top-down proteomics experiments to be conducted on the ZenoTOF 7600 system.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1230–1240 1230–1240"},"PeriodicalIF":3.8,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","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 Untargeted Lipidomics Using Liquid Chromatography Ion Mobility-Mass Spectrometry.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-14 DOI: 10.1021/acs.jproteome.4c00658

Jinyong Kim, Dong-Gi Mun, Husheng Ding, Erica Marie Forsberg, Sven W Meyer, Aiko Barsch, Akhilesh Pandey, Seul Kee Byeon

{"title":"Single Cell Untargeted Lipidomics Using Liquid Chromatography Ion Mobility-Mass Spectrometry.","authors":"Jinyong Kim, Dong-Gi Mun, Husheng Ding, Erica Marie Forsberg, Sven W Meyer, Aiko Barsch, Akhilesh Pandey, Seul Kee Byeon","doi":"10.1021/acs.jproteome.4c00658","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00658","url":null,"abstract":"Advancements in technology over the years have propelled omics analysis to the level of single cell resolution. Following the breakthroughs in single cell transcriptomics and genomics, single cell proteomics has recently rapidly progressed, aided by highly sensitive mass spectrometry instrumentation. However, there is currently a paucity of studies and methodologies for single cell lipidomics, aside from imaging-based approaches. Profiling lipids at the single cell level holds promise for providing novel insights into the complex heterogeneity of cells in various human disorders. Further, by integrating single cell lipidomics with other single cell omics including proteomics, it becomes possible to achieve single cell multiomics, enabling the discovery of novel molecular signatures. We developed untargeted single cell lipidomics using nanoflow liquid chromatography-ion mobility spectrometry-mass spectrometry. To enhance lipid coverage at the single cell level, the method was conducted in both positive and negative ion modes. We identified an average of 161 lipids spanning phospholipids, sphingolipids, cholesteryl esters, and glycerides in positive ion mode from single cells of human cholangiocarcinoma cells based on a rule-based lipid annotation. Additionally, an average of 20 species of phospholipids was identified in the negative ion mode. These preliminary data demonstrate a new methodology to profile lipids at a single or low input of cells.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0