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Vocabulary Matters: An Annotation Pipeline and Four Deep Learning Algorithms for Enzyme Named Entity Recognition J. Proteome Res. (IF 4.4) Pub Date : 2024-05-11 Meiqi Wang, Avish Vijayaraghavan, Tim Beck, Joram M. Posma
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Systematic Assessment of Deep Learning-Based Predictors of Fragmentation Intensity Profiles J. Proteome Res. (IF 4.4) Pub Date : 2024-05-10 Mehdi B. Hamaneh, Aleksey Y. Ogurtsov, Oleg I. Obolensky, Yi-Kuo Yu
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Proteomic Analysis of Idiopathic Nephrotic Syndrome Triggered by Primary Podocytopathies in Adults: Regulatory Mechanisms and Diagnostic Implications J. Proteome Res. (IF 4.4) Pub Date : 2024-05-10 Qiaoling Chen, Jiaming Xu, Lifang Liu, Qiuping Ye, Wanjun Lin, Yonggen Liao, Ruiyu Gao, Xinyu Zhang, Ruoyan Chen, Yunfeng Xiong, Sihui Chen, Xiaoyi Ye, Lixin Wei
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Effect of Acupuncture on Tear Proteomics in Patients with Video Display Terminal-Related Dry Eye J. Proteome Res. (IF 4.4) Pub Date : 2024-05-09 Na Tang, Lewei Tang, Jiacheng Lyu, Xiaohan Jiang, Yan Li, Chen Ding, Shengjin Xiang
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Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues J. Proteome Res. (IF 4.4) Pub Date : 2024-05-08 Shengbo Wang, Andrew Collins, Ananth Prakash, Silvie Fexova, Irene Papatheodorou, Andrew R. Jones, Juan Antonio Vizcaíno
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Global Proteomic Analysis Reveals Alterations in Differentially Expressed Proteins between Cardiopathic Lamin A/C Mutations J. Proteome Res. (IF 4.4) Pub Date : 2024-05-08 Corey L. Anderson, Kyle A. Brown, Ryan J. North, Janay K. Walters, Sara T. Kaska, Mathew R. Wolff, Timothy J. Kamp, Ying Ge, Lee L. Eckhardt
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Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags J. Proteome Res. (IF 4.4) Pub Date : 2024-05-07 Trenton M. Peters-Clarke, Yiran Liang, Keaton L. Mertz, Kenneth W. Lee, Michael S. Westphall, Joshua D. Hinkle, Graeme C. McAlister, John E. P. Syka, Ryan T. Kelly, Joshua J. Coon
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The Future of Proteomics is Up in the Air: Can Ion Mobility Replace Liquid Chromatography for High Throughput Proteomics? J. Proteome Res. (IF 4.4) Pub Date : 2024-05-07 Yuming Jiang, Daniel DeBord, Heidi Vitrac, Jordan Stewart, Ali Haghani, Jennifer E. Van Eyk, Justyna Fert-Bober, Jesse G. Meyer
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Comparative Proteomics Identified EXOSC1 as a Target Protein of Anticancer Peptide LVTX-8 in Nasopharyngeal Carcinoma Cells J. Proteome Res. (IF 4.4) Pub Date : 2024-05-03 Ganghua Zhu, Lingxiang Wang, Xingyao Wang, Xiaoping Dong, Shu Yang, Jiaqi Wang, Siyuan Xu, Yong Zeng
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Longitudinal Fluctuations in Protein Concentrations and Higher-Order Structures in the Plasma Proteome of Kidney Failure Patients Subjected to a Kidney Transplant J. Proteome Res. (IF 4.4) Pub Date : 2024-05-03 Sofia Kalaidopoulou Nteak, Franziska Völlmy, Marie V. Lukassen, Henk van den Toorn, Maurits A. den Boer, Albert Bondt, Sjors P. A. van der Lans, Pieter-Jan Haas, Arjan D. van Zuilen, Suzan H. M. Rooijakkers, Albert J. R. Heck
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Machine Learning Reveals Serum Glycopatterns as Potential Biomarkers for the Diagnosis of Nonalcoholic Fatty Liver Disease (NAFLD) J. Proteome Res. (IF 4.4) Pub Date : 2024-05-02 Xiaocheng Li, Yaqing Xiao, Xinhuan Chen, Yayun Zhu, Haoqi Du, Jian Shu, Hanjie Yu, Xiameng Ren, Fan Zhang, Jing Dang, Chen Zhang, Shi Su, Zheng Li
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Single-Cell Proteomics Accelerates toward Proteoforms J. Proteome Res. (IF 4.4) Pub Date : 2024-05-03 Sarah N. Sipe, Nikolai Slavov
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Discovery and Verification of Sjögren’s Syndrome Protein Biomarkers in Tears by Targeted LC-MRM J. Proteome Res. (IF 4.4) Pub Date : 2024-04-29 Maggy Lépine, Marie-Claude Robert, Lekha Sleno
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Optimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples J. Proteome Res. (IF 4.4) Pub Date : 2024-05-01 Christa P. Baker, Roland Bruderer, James Abbott, J. Simon C. Arthur, Alejandro J. Brenes
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eLIMS: Ensemble Learning-Based Spatial Segmentation of Mass Spectrometry Imaging to Explore Metabolic Heterogeneity J. Proteome Res. (IF 4.4) Pub Date : 2024-05-01 Mudassir Shah, Lei Guo, Xiangnan Xu, Lingli Deng, Keyi Lu, Jiyang Dong, Chao Zhao, Jingjing Xu
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Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod J. Proteome Res. (IF 4.4) Pub Date : 2024-05-01 Emma Timmins-Schiffman, Amy E. Maas, Rayhan Khanna, Leocadio Blanco-Bercial, Eric Huang, Brook L. Nunn
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Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples J. Proteome Res. (IF 4.4) Pub Date : 2024-05-01 Michal Greguš, Antonius Koller, Somak Ray, Alexander R. Ivanov
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Endogenous Protein–Protein Interaction Network of the NPC Cholesterol Transporter 1 in the Cerebral Cortex J. Proteome Res. (IF 4.4) Pub Date : 2024-04-30 Roshan Javanshad, Thu T. A. Nguyen, Ruth D. Azaria, Wenping Li, Daisy Edmison, Liang-Wei Gong, Swetha Gowrishankar, Andrew P. Lieberman, Mark L. Schultz, Stephanie M. Cologna
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Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry J. Proteome Res. (IF 4.4) Pub Date : 2024-04-30 Jack Freestone, William Stafford Noble, Uri Keich
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MassDash: A Web-Based Dashboard for Data-Independent Acquisition Mass Spectrometry Visualization J. Proteome Res. (IF 4.4) Pub Date : 2024-04-29 Justin C. Sing, Joshua Charkow, Mohammed AlHigaylan, Ira Horecka, Leon Xu, Hannes L. Röst
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Benefit of In Silico Predicted Spectral Libraries in Data-Independent Acquisition Data Analysis Workflows J. Proteome Res. (IF 4.4) Pub Date : 2024-04-26 An Staes, Teresa Mendes Maia, Sara Dufour, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Kris Gevaert, Francis Impens, Simon Devos
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An Efficient, Amine-Specific, and Cost-Effective Method for TMT 6/11-plex Labeling Improves the Proteome Coverage, Quantitative Accuracy and Precision J. Proteome Res. (IF 4.4) Pub Date : 2024-04-25 Yan Cai, Chenchen Chang, Qin Yang, Rijing Liao
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Pan-Cancer Proteomics Analysis Reveals Wiskott–Aldrich Syndrome Protein as a Potential Regulator of Programmed Death-Ligand 1 J. Proteome Res. (IF 4.4) Pub Date : 2024-04-25 Liling Hu, Danya Liu, Dandan Zheng, Jiangli Lu, Xiaoyi Yuan, Yuying Li, Fujin Shi, Xinyu Shi, Qing-Yu He, Qiuli Li, Chris Zhiyi Zhang
The programmed death-ligand 1 (PD-L1) is a key mediator of immunosuppression in the tumor microenvironment. The expression of PD-L1 in cancer cells is useful for the clinical determination of an immune checkpoint blockade (ICB). However, the regulatory mechanism of the PD-L1 abundance remains incompletely understood. Here, we integrated the proteomics of 52 patients with solid tumors and examined immune
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Dynamics of Single-Cell Protein Covariation during Epithelial–Mesenchymal Transition J. Proteome Res. (IF 4.4) Pub Date : 2024-04-25 Saad Khan, Rachel Conover, Anand R. Asthagiri, Nikolai Slavov
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Analysis of Tandem Mass Spectrometry Data with CONGA: Combining Open and Narrow Searches with Group-Wise Analysis J. Proteome Res. (IF 4.4) Pub Date : 2024-04-23 Jack Freestone, William S. Noble, Uri Keich
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N-Terminomic Identification of Intracellular MMP-2 Substrates in Cardiac Tissue J. Proteome Res. (IF 4.4) Pub Date : 2024-04-22 Bridgette Hartley, Wesam Bassiouni, Andrej Roczkowsky, Richard Fahlman, Richard Schulz, Olivier Julien
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Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn (Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis J. Proteome Res. (IF 4.4) Pub Date : 2024-04-22 Rosimeire Barboza Bispo, Antônio Teixeira do Amaral Junior, Vitor Batista Pinto, Talles de Oliveira Santos, Valter Jário de Lima, Bruna Rohem Simão, Anne Fischer, Michael J. Naldrett, Sophie Alvarez
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Identification and Evaluation of Blood-Based Biomarkers for Abdominal Aortic Aneurysm J. Proteome Res. (IF 4.4) Pub Date : 2024-04-22 Ben Li, Hamzah Khan, Farah Shaikh, Abdelrahman Zamzam, Rawand Abdin, Mohammad Qadura
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Spatial Proteomics Reveals Alcohol-Induced Damages to the Crypts and Villi of the Mouse Small Intestine J. Proteome Res. (IF 4.4) Pub Date : 2024-04-24 Patil Shivprasad Suresh, Xinguo Sun, Zhanxiang Zhou, Qibin Zhang
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Isoglutaminyl Cyclase Overexpression Enhances KYSE30 Cancer Cell Proliferation and Migration via the MAPK Signaling Pathway J. Proteome Res. (IF 4.4) Pub Date : 2024-04-24 Xiaojie Chen, Xi Yu, Yangqing Cui, Lang Du, Qingqing Zhou, Wei Xiong, Chenyang Li, Chenshu Xu, Haiqiang Wu
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Establishing Personalized Blood Protein Reference Ranges Using Noninvasive Microsampling and Targeted Proteomics: Implications for Antidoping Strategies J. Proteome Res. (IF 4.4) Pub Date : 2024-04-24 Vincent R. Richard, Georgia Mitsa, Azad Eshghi, Daria Chaplygina, Yassene Mohammed, David R. Goodlett, Rene P. Zahedi, Mario Thevis, Christoph H. Borchers
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Proteogenomic Gene Structure Validation in the Pineapple Genome J. Proteome Res. (IF 4.4) Pub Date : 2024-04-23 Norazrin Ariffin, David Wells Newman, Michael G. Nelson, Ronan O’cualain, Simon J. Hubbard
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Integrated Exploration of Epigenetic Dysregulation Reveals a Stemness/EMT Subtype and MMP12 Linked to the Progression and Prognosis in Hepatocellular Carcinoma J. Proteome Res. (IF 4.4) Pub Date : 2024-04-23 Anning Zuo, Jinyu Li, Siyuan Weng, Hui Xu, Yuyuan Zhang, Libo Wang, Zhe Xing, Peng Luo, Quan Cheng, Jing Li, Xinwei Han, Zaoqu Liu
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Neuropeptidomics of the American Lobster Homarus americanus J. Proteome Res. (IF 4.4) Pub Date : 2024-04-22 Gaoyuan Lu, Vu Ngoc Huong Tran, Wenxin Wu, Min Ma, Lingjun Li
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Identification of TFG- and Autophagy-Regulated Proteins and Glycerophospholipids in B Cells J. Proteome Res. (IF 4.4) Pub Date : 2024-04-22 Tobit D. Steinmetz, Jana Thomas, Lena Reimann, Ann-Kathrin Himmelreich, Sebastian R. Schulz, Florian Golombek, Kathrin Castiglione, Hans-Martin Jäck, Susanne Brodesser, Bettina Warscheid, Dirk Mielenz
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Role of the Putative Histidine Kinase BP1092 in Bordetella pertussis Virulence Regulation and Intracellular Survival J. Proteome Res. (IF 4.4) Pub Date : 2024-04-22 Martina Debandi, Mariela Carrica, Christian Hentschker, Carlos Baroli, Uwe Völker, Maria Eugenia Rodriguez, Kristin Surmann, Yanina Lamberti
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Pirin Promotes the Progression of Non-Small-Cell Lung Cancer by Increasing ODC1 to Suppress Autophagy J. Proteome Res. (IF 4.4) Pub Date : 2024-04-22 Yan-Ping Li, Zi-Jia Huang, Quan-Kuo He, Yi-Xiang Li, Xiang-Pei Zhao, Zhong-Qi Ma, Mei-Jing Qin, Ai-Wen Chen, Qiu Wei, Yang Wang, Chun-Hua Lu
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How Much Storage Precision Can Be Lost: Guidance for Near-Lossless Compression of Untargeted Metabolomics Mass Spectrometry Data J. Proteome Res. (IF 4.4) Pub Date : 2024-04-19 Junjie Tong, Miaoshan Lu, Ruimin Wang, Shaowei An, Jinyin Wang, Tong Wang, Cong Xie, Changbin Yu
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Multiomics Analysis Revealed Colorectal Cancer Pathogenesis J. Proteome Res. (IF 4.4) Pub Date : 2024-04-18 Yong-Jiang Xu, Yuan He, Cong Chen, Jiachen Shi, Mengxue He, Yanjun Liu, Yu Zhang, Yuanfa Liu, Yi Zhang
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In-Depth Proteome Coverage of In Vitro-Cultured Treponema pallidum and Quantitative Comparison Analyses with In Vivo-Grown Treponemes J. Proteome Res. (IF 4.4) Pub Date : 2024-04-18 Simon Houston, Alloysius Gomez, Andrew Geppert, Mara C. Goodyear, Caroline E. Cameron
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Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone J. Proteome Res. (IF 4.4) Pub Date : 2024-04-18 Annika Topitsch, Tim Halstenbach, René Rothweiler, Tobias Fretwurst, Katja Nelson, Oliver Schilling
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AlphaFun: Structural-Alignment-Based Proteome Annotation Reveals why the Functionally Unknown Proteins (uPE1) Are So Understudied J. Proteome Res. (IF 4.4) Pub Date : 2024-04-16 Hengxin Pan, Zhenqi Wu, Wanting Liu, Gong Zhang
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Molecular-Level Dysregulation of Insulin Pathways and Inflammatory Processes in Peripheral Blood Mononuclear Cells by Circadian Misalignment J. Proteome Res. (IF 4.4) Pub Date : 2024-04-15 Jason E. McDermott, Jon M. Jacobs, Nathaniel J. Merrill, Hugh D. Mitchell, Osama A. Arshad, Ryan McClure, Justin Teeguarden, Rajendra P. Gajula, Kenneth I. Porter, Brieann C. Satterfield, Kirsie R. Lundholm, Debra J. Skene, Shobhan Gaddameedhi, Hans P. A. Van Dongen
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Platelet-Rich Plasma in Young and Elderly Humans Exhibits a Different Proteomic Profile J. Proteome Res. (IF 4.4) Pub Date : 2024-04-15 Zhitong Jiang, Can Huang, Erliang Guo, Xiangbin Zhu, Na Li, Yu Huang, Peihe Wang, Hui Shan, Yuxin Yin, Hong Wang, Lei Huang, Zhen Han, Kunfu Ouyang, Lu Sun
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Bone Proteomics Method Optimization for Forensic Investigations J. Proteome Res. (IF 4.4) Pub Date : 2024-04-15 Luke Gent, Maria Elena Chiappetta, Stuart Hesketh, Pawel Palmowski, Andrew Porter, Andrea Bonicelli, Edward C. Schwalbe, Noemi Procopio
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Analysis of Vascular Smooth Muscle Cells from Thoracic Aortic Aneurysms Reveals DNA Damage and Cell Cycle Arrest as Hallmarks in Bicuspid Aortic Valve Patients J. Proteome Res. (IF 4.4) Pub Date : 2024-04-09 Ariadna Martin-Blazquez, Marta Martin-Lorenzo, Aranzazu Santiago-Hernandez, Angeles Heredero, Alicia Donado, Juan A Lopez, Miriam Anfaiha-Sanchez, Rocio Ruiz-Jimenez, Vanesa Esteban, Jesus Vazquez, Gonzalo Aldamiz-Echevarria, Gloria Alvarez-Llamas
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Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization J. Proteome Res. (IF 4.4) Pub Date : 2024-04-11 Ran Zhang, Lan Huang, Xiaohan Zhang, Yuanling Yu, Te Liang, Hongye Wang, Xiaomei Zhang, Di Hu, Bingwei Wang, Youchun Wang, Junyi Jiang, Xiaobo Yu
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An XIC-Centric Strategy for Improved Identification and Quantification in Proteomic Data Analyses J. Proteome Res. (IF 4.4) Pub Date : 2024-04-10 Guanghui Wang, Zheng Zhang, Yi Liu, Meghan C. Burke, Sergey L. Sheetlin, Stephen E. Stein
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Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing J. Proteome Res. (IF 4.4) Pub Date : 2024-04-09 Steven R. Shuken, Qing Yu, Steven P. Gygi
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Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine J. Proteome Res. (IF 4.4) Pub Date : 2024-04-05 Annie Ha, Amanda Khoo, Vladimir Ignatchenko, Shahbaz Khan, Matthew Waas, Danny Vesprini, Stanley K. Liu, Julius O. Nyalwidhe, Oliver John Semmes, Paul C. Boutros, Thomas Kislinger
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Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute J. Proteome Res. (IF 4.4) Pub Date : 2024-04-04 Md. Yasir Arafat, Kanika Narula, Mohit Kumar, Niranjan Chakraborty, Subhra Chakraborty
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Wheat-Based Glues in Conservation and Cultural Heritage: (Dis)solving the Proteome of Flour and Starch Pastes and Their Adhering Properties J. Proteome Res. (IF 4.4) Pub Date : 2024-04-04 Rocio Prisby, Alessandra Luchini, Lance A. Liotta, Caroline Solazzo
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Identification of the Most Immunoreactive Antigens of Candida auris to IgGs from Systemic Infections in Mice J. Proteome Res. (IF 4.4) Pub Date : 2024-04-04 Maialen Areitio, Aitziber Antoran, Oier Rodriguez-Erenaga, Leire Aparicio-Fernandez, Leire Martin-Souto, Idoia Buldain, Beñat Zaldibar, Alba Ruiz-Gaitan, Javier Pemán, Aitor Rementeria, Andoni Ramirez-Garcia
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Reinforcing the Evidence of Mitochondrial Dysfunction in Long COVID Patients Using a Multiplatform Mass Spectrometry-Based Metabolomics Approach J. Proteome Res. (IF 4.4) Pub Date : 2024-04-02 Sara Martínez, Oihane E. Albóniga, María Rosa López-Huertas, Ana Gradillas, Coral Barbas
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Differential Contributions of Interferon Classes to Host Inflammatory Responses and Restricting Virus Progeny Production J. Proteome Res. (IF 4.4) Pub Date : 2024-04-02 Krystal K. Lum, Tavis J. Reed, Jinhang Yang, Ileana M. Cristea
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Proteomics Defines Plasma Biomarkers for the Early Diagnosis of Biliary Atresia J. Proteome Res. (IF 4.4) Pub Date : 2024-04-03 Ming Fu, Zhipeng Guo, Yan Chen, Jonathan R. Lamb, Suirui Zhong, Huimin Xia, Zhe Wen, Ruizhong Zhang
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Identification and Functional Analysis of Lysine 2-Hydroxyisobutyrylation in Cyanobacteria J. Proteome Res. (IF 4.4) Pub Date : 2024-04-02 Qiaoya Li, Jian Lin, Haiyan Ma, Li Yuan, Xin Liu, Jie Xiong, Wei Miao, Mingkun Yang, Feng Ge
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I’m Walking into Spiderwebs: Making Sense of Protein–Protein Interaction Data J. Proteome Res. (IF 4.4) Pub Date : 2024-03-31 Chase L. S. Skawinski, Priya S. Shah
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Comparative Proteomics Elucidates the Potential Mechanism of Sperm Capacitation of Chinese Mitten Crabs (Eriocheir sinensis) J. Proteome Res. (IF 4.4) Pub Date : 2024-04-01 Xiaodong Cui, Xueqian Cai, Fenghao Zhang, Weiwei Zhang, Huan Liu, Shumei Mu, Shuai Guo, Haifu Wan, Han Zhang, Zhaohui Zhang, Xianjiang Kang
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Use of Nonhuman Sera as a Highly Cost-Effective Internal Standard for Quantitation of Multiple Human Proteins Using Species-Specific Tryptic Peptides: Applicability in Clinical LC-MS Analyses J. Proteome Res. (IF 4.4) Pub Date : 2024-03-27 Geraldine Williams, Lewis Couchman, David R. Taylor, Jatinderpal K. Sandhu, Oliver C. Slingsby, Leong L. Ng, Cajetan F. Moniz, Donald J. L. Jones, Colleen B. Maxwell