Journal of Proteome Research最新文献_第2页

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.4c00839

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

{"title":"Gemcitabine Alters Phosphatidylcholine Metabolism in Mouse Pancreatic Tumors.","authors":"Nav Raj Phulara, Chiaki Tsuge Ishida, Peter John Espenshade, Herana Kamal Seneviratne","doi":"10.1021/acs.jproteome.4c00839","DOIUrl":"https://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":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456246","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.4c00717

Simon Comtois-Marotte, Éric Bonneil, Chongyang Li, Matthew J Smith, 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, Pierre Thibault","doi":"10.1021/acs.jproteome.4c00717","DOIUrl":"https://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":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447402","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.4c00874

Richard M Searfoss, Emily Zahn, Zongtao Lin, 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, Benjamin A Garcia","doi":"10.1021/acs.jproteome.4c00874","DOIUrl":"https://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":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143431968","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

Cloud-Enabled Scalable Analysis of Large Proteomics Cohorts.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-13 DOI: 10.1021/acs.jproteome.4c00771

Harendra Guturu, Andrew Nichols, Lee S Cantrell, Seth Just, Janos Kis, Theodore Platt, Iman Mohtashemi, Jian Wang, Serafim Batzoglou

{"title":"Cloud-Enabled Scalable Analysis of Large Proteomics Cohorts.","authors":"Harendra Guturu, Andrew Nichols, Lee S Cantrell, Seth Just, Janos Kis, Theodore Platt, Iman Mohtashemi, Jian Wang, Serafim Batzoglou","doi":"10.1021/acs.jproteome.4c00771","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00771","url":null,"abstract":"Rapid advances in depth and throughput of untargeted mass-spectrometry-based proteomic technologies enable large-scale cohort proteomic and proteogenomic analyses. As such, the data infrastructure and search engines required to process data must also scale. This challenge is amplified in search engines that rely on library-free match between runs (MBR) search, which enable enhanced depth-per-sample and data completeness. However, to date, no MBR-based search could scale to process cohorts of thousands or more individuals. Here, we present a strategy to deploy search engines in a distributed cloud environment without source code modification, thereby enhancing resource scalability and throughput. Additionally, we present an algorithm, Scalable MBR, that replicates the MBR procedure of popular DIA-NN software for scalability to thousands of samples. We demonstrate that Scalable MBR can search thousands of MS raw files in a few hours compared to days required for the original DIA-NN MBR procedure and demonstrate that the results are almost indistinguishable to those of DIA-NN native MBR. We additionally show that empirical spectra generated by Scalable MBR better approximates DIA-NN native MBR compared to semiempirical alternatives such as ID-RT-IM MBR, preserving user choice to use empirical libraries in large cohort analysis. The method has been tested to scale to over 15,000 injections and is available for use in the Proteograph Analysis Suite.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412372","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

Metabolic and Proteomic Divergence is Present in Spleens and Livers from Berkeley Sickle Cell Anemia and β-Thalassemia Mice. 伯克利镰状细胞贫血小鼠和β-地中海贫血小鼠的脾脏和肝脏存在代谢和蛋白质组差异

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-13 DOI: 10.1021/acs.jproteome.4c00814

Nishant K Rana, Christina Lisk, Francesca Cendali, Melissa J Lucero, Abby Grier, Saini Setua, Kiruphararan Thangaraju, Alamzeb Khan, Julie A Reisz, Monika Dzieciatkowska, David I Pak, Delaney Swindle, Mae X Danaher, Saqib Khan, Natalie Westover, Matthieu Carter, Kathryn Hassell, Rachelle Nuss, Gemlyn George, Paul W Buehler, Angelo D'Alessandro, David C Irwin

{"title":"Metabolic and Proteomic Divergence is Present in Spleens and Livers from Berkeley Sickle Cell Anemia and β-Thalassemia Mice.","authors":"Nishant K Rana, Christina Lisk, Francesca Cendali, Melissa J Lucero, Abby Grier, Saini Setua, Kiruphararan Thangaraju, Alamzeb Khan, Julie A Reisz, Monika Dzieciatkowska, David I Pak, Delaney Swindle, Mae X Danaher, Saqib Khan, Natalie Westover, Matthieu Carter, Kathryn Hassell, Rachelle Nuss, Gemlyn George, Paul W Buehler, Angelo D'Alessandro, David C Irwin","doi":"10.1021/acs.jproteome.4c00814","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00814","url":null,"abstract":"Sickle cell disease and β-Thalassemia are two of the most prevalent hemoglobinopathies worldwide. Both occur due to genetic mutations within the HBB gene and are characterized by red blood cell dysfunction, anemia, and end-organ injury. The spleen and liver are the primary organs where erythrophagocytosis, engulfing the red blood cells, occurs in these diseases. Understanding metabolism and protein composition within these tissues can therefore inform the extent of hemolysis and disease progression. We utilized a multiomics approach to highlight metabolomic and proteomic differences in the spleen and liver. The Berkley sickle cell disease (Berk-SS), heterozygous B1/B2 globin gene deletion (HbbTh3/+) a known β-Thalassemia model, and wildtype (WT, C57/Bl6) murine models were evaluated in this report. This analysis showed Berk-SS and HbbTh3/+ shared distinct antioxidant and immunosuppressive splenic phenotypes compared to WT mice with divergence in purine metabolism, gluconeogenesis, and glycolysis. In contrast, Berk-SS mice have a distinct liver pro-inflammatory phenotype not shared by HbbTh3/+ or WT mice. Together, these data emphasize that metabolic and proteomic reprogramming of the spleen and livers in Berk-SS and HbbTh3/+mice may be relevant to the individual disease processes.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412373","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

Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-12 DOI: 10.1021/acs.jproteome.4c01107

Xinyue Liu, Shane L Dawson, Steven P Gygi, Joao A Paulo

{"title":"Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer.","authors":"Xinyue Liu, Shane L Dawson, Steven P Gygi, Joao A Paulo","doi":"10.1021/acs.jproteome.4c01107","DOIUrl":"10.1021/acs.jproteome.4c01107","url":null,"abstract":"Comprehensive global proteome profiling that is amenable to high throughput processing will broaden our understanding of complex biological systems. Here, we evaluate two leading mass spectrometry techniques, Data Independent Acquisition (DIA) and Tandem Mass Tagging (TMT), for extensive protein abundance profiling. DIA provides label-free quantification with a broad dynamic range, while TMT enables multiplexed analysis using isobaric tags for efficient cross-sample comparisons. We analyzed 18 samples, including four cell lines (IHCF, HCT116, HeLa, MCF7) under standard growth conditions, in addition to IHCF treated with two H2O2 concentrations, all in triplicate. Experiments were conducted on an Orbitrap Astral mass spectrometer, employing Field Asymmetric Ion Mobility Spectrometry (FAIMS). Despite utilizing different acquisition strategies, both the DIA and TMT approaches achieved comparable proteome depth and quantitative consistency, with each method quantifying over 10,000 proteins across all samples, with marginally higher protein-level precision for the TMT strategy. Relative abundance correlation analysis showed strong agreement at both peptide and protein levels. Our findings highlight the complementary strengths of DIA and TMT for high-coverage proteomic studies, providing flexibility in method selection based on specific experimental needs.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397605","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

Deciphering Proteoform Landscape of Mammary Carcinoma by Top-Down Proteomics.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-12 DOI: 10.1021/acs.jproteome.4c01044

Samantha J Knott, Trisha Tucholski, Harini Josyer, David Inman, Andreas Friedl, Yanlong Zhu, Ying Ge, Suzanne M Ponik

{"title":"Deciphering Proteoform Landscape of Mammary Carcinoma by Top-Down Proteomics.","authors":"Samantha J Knott, Trisha Tucholski, Harini Josyer, David Inman, Andreas Friedl, Yanlong Zhu, Ying Ge, Suzanne M Ponik","doi":"10.1021/acs.jproteome.4c01044","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01044","url":null,"abstract":"Defining the proteoform landscape of breast cancer can provide unique insights into the signaling pathways driving disease progression. While bottom-up proteomics has been utilized to profile breast cancer, it lacks the ability to capture intact proteoforms that may underpin the disease. Top-down proteomics is ideally suited to characterize intact proteoforms; however, most top-down proteomics studies have been limited to low molecular weight (MW) proteins (<50 kDa). Herein, we employed a two-dimensional (2D) liquid chromatography combining size exclusion chromatography (SEC) with reverse phase chromatography (RPC) followed by high-resolution mass spectrometry (MS) to expand the coverage for high MW proteoforms. Using this 2D-SEC-RPC-MS approach, we observed a 5-fold increase in the detection of high MW proteoforms (>50 kDa) compared to the conventional 1D-RPC-MS. SEC separation significantly enhanced the detection of high MW proteoforms (>104 kDa), including intermediate filament proteins, vimentin and keratins. Based on accurate mass measurements and MS/MS data, we identified 775 proteoforms from both TFA and HEPES extracts and detected PTMs, such as acetylation, glutathionylation, and myristoylation. Pathway analysis uncovered many proteoforms involved in processes dysregulated in cancer progression. Overall, our findings illustrate the power of top-down proteomics in defining the proteoform landscape of breast carcinoma.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397603","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

Myosin Light Chain 12b and MASP1 as Novel Biomarker Candidates in Active Juvenile Idiopathic Arthritis─A Combined Proteomics/Bioinformatics Approach.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-11 DOI: 10.1021/acs.jproteome.4c01054

Vanditha Mohan, Sajitha Krishnan, Suma Balan, Sonu Das, Jerry Earali, Evelyn Maria, Devaki Nair, Mathew John

引用次数: 0