RSS:Journal of Proteome Research

Journal of Proteome Research

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[ASAP] Proteomic Profiling Reveals Candidate Proteins and Pathways Associated with Chemo-Radio-Sensitivity and Relapse in Rhabdomyosarcoma

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00453

— Zhiyuan Zhou, Ying Ye, Wenbin Guan, Chuanying Zhu, and Lu Wen 2026-01-15 18:25:04

[ASAP] Better Inputs, Better Learning: A Peptide Embedding Tutorial for Proteomic Mass Spectrometry

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00563

— Luke Squires, Jose Humberto Giraldez Chavez, Alfred Nilsson, Lukas Käll, and Samuel H Payne 2026-01-13 18:22:39

[ASAP] A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00775

— Carolina Rojas Ramírez, Fengchao Yu, Daniel A. Polasky, and Alexey I. Nesvizhskii 2026-01-13 14:38:31

[ASAP] On the Feasibility of Clinical Studies with Cross-Linking Mass Spectrometry

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00803

— Sung-Gun Park, Ethan L. Ostrom, Sophia Liu, David J. Marcinek, and James E. Bruce 2026-01-13 20:18:12

[ASAP] Quantitative Proteomics Reveals Significant Downregulation of Glutathione Metabolism in Sepsis-Induced Liver Injury

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00912

— Qi Cheng, Beiyuan Zhang, Haozhen Ren, Jingzi Zhang, Yuqing Gong, Yingchen Wang, Lei Fang, and Wenkui Yu 2026-01-12 15:41:52

[ASAP] Quantitative Tissue Proteomics Reveals Protein Signatures Associated with SARS-CoV-2 Variant Infection in Hamsters

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00851

— Justin J. Frere, Boris Bonaventure, Haylen T. Rosberger, Andrew P. Kurland, David Sachs, Aum R. Patel, Amit Garg, Ma Gonzalez, Benjamin R. tenOever, Jean K. Lim, and Jeffrey R. Johnson 2026-01-10 14:59:17

[ASAP] FGA Serves as a Potential Diagnostic Marker and Therapeutic Target for Elderly Acute Kidney Injury

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00826

— Hong Yu, Jiacen Dai, Shuping Deng, Lingwen Xu, Qihui Kuang, Xiao Wei, Yuan Yuan, Fang Dong, Xiong Wang, and Pengcheng Luo 2026-01-09 20:32:45

[ASAP] Proteomics Using Draft Genomes: A Case Study in Spotted Hyena

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00873

— David L. Tabb, Aidan Swartz, Roxanne L. Higgitt, Liam Bell, Victor Guryev, and Michele A. Miller 2026-01-09 20:00:00

[ASAP] Improving the Annotation for Spatial Proteomics: A Computational Approach to Enhance Molecular Characterization of Thyroid Nodules

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00432

— Vasco Coelho, Nicole Monza, Natalia S. Porto, Giulia Capitoli, Vincenzo L’Imperio, Daniele M. Papetti, and Vanna Denti 2026-01-08 09:05:07

[ASAP] Untargeted Serum Metabolomics Reveals Differential Signatures in Gallstone-Associated and Gallstone-Free Gallbladder Cancer Variants

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00403

— Cinmoyee Baruah, Amit Rai, Anupam Sarma, Gayatri Gogoi, Uttam Konwar, Utpal Dutta, Subhash Khanna, Sheelendra P. Singh, and Pankaj Barah 2026-01-06 16:44:56

[ASAP] Influence of Bead Chemistry and Protein-to-Bead Ratio on the Efficiency of Solid-Phase Proteolysis

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00630

— Salem Al Siblani, Jean Armengaud, and Clément Lozano 2026-01-06 17:20:50

[ASAP] Vibe Coding Omics Data Analysis Applications

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00984

— Jesse G. Meyer 2026-01-06 12:20:57

[ASAP] The 2025 Report on the Human Proteome from the HUPO Human Proteome Project

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00759

— Eric W. Deutsch, Cecilia Lindskog, Bogdan Budnik, Claudia Ctortecka, Tiannan Guo, Charles Pineau, Gong Zhang, Marie Andken, Clarissa Zheng, Zhi Sun, Jonathan M. Mudge, Sandra Orchard, Christopher M. Overall, Nicolle H. Packer, Susan T. Weintraub, Michael H. A. Roehrl, Edouard Nice, Jennifer E. Van Eyk, Uwe Völker, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, and Gilbert S. Omenn 2026-01-05 17:54:06

[ASAP] High-Risk Host Cell Protein Profiling with Sub-ppm Sensitivity by iRT-Assisted Targeted Mass Spectrometry

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00680

— Qi Wang, Ting Dong, Muchen Li, Xueliang Wang, Min Xu, Yiqing Cui, He Zhu, Tianli Zhang, Xingli Gao, Lin Zhu, Lili Wang, Le Yu, Yongsheng Xiao, and Jun Tian 2026-01-02 20:00:00

[ASAP] Cyp7a1 and Cyp8b1 Downregulation Characterizes Concanavalin-A-Induced Acute Liver Injury: Insights from Multiomics Analysis

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00646

— Xinlei Liu, Rui Liu, Meng Zhang, Di Ma, Yingming Tian, and Yancheng Wang 2025-12-31 11:09:44

[ASAP] Seasonal Changes in the Seminal Plasma Proteome of the Crab-Eating Fox (Cerdocyon thous)

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00694

— Jaqueline Candido Carvalho, Marcos Gomides Carvalho, Viviane M. Codognoto, Laiza Sartori Camargo, Ramanathan Kasimanickam, John Kastelic, Fabiana Ferreira de Souza, and João Carlos Pinheiro Ferreira 2025-12-31 12:55:39

[ASAP] Phosphopeptidome Profiling of Human Plasma for Hepatocellular Carcinoma Biomarker Discovery

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c01004

— Shafaq Saleem, Muhammad Salman Sajid, Rency S. Varghese, Zaki A. Sherif, Alexander Kroemer, and Habtom W. Ressom 2025-12-31 18:44:06

[ASAP] Improvements to Casanovo, a Deep Learning De Novo Peptide Sequencer

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00706

— Gwenneth Straub, Varun Ananth, William E. Fondrie, Chris Hsu, Daniela Klaproth-Andrade, Marina Pominova, Michael Riffle, Justin Sanders, Bo Wen, Lingwen Xu, Melih Yilmaz, Michael J. MacCoss, Sewoong Oh, Wout Bittremieux, and William Stafford Noble 2025-12-30 20:47:33

[ASAP] Integrated Quantitative Proteomic Analysis of Biomarkers Derived from Fetal Membranes and Plasma Exosomes in Preterm Birth: A Pilot Study

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00724

— Jia Mai, Rong Zhou, HongJian Xie, YingYing Li, Lan Mei, Ling Yang, and XiaoJuan Liu 2025-12-30 14:59:16

[ASAP] Machine Learning-Based Multi-Omics Integration for Identification of Hepatocellular Carcinoma Biomarkers in an Egyptian Cohort

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00741

— Rency S. Varghese, Xinran Zhang, Muhammad S. Sajid, Dina H. Ziada, and Habtom W. Ressom 2025-12-30 15:12:54

[ASAP] Proteomics Insight into the Pathogenic Evolution of Chronic Hepatitis B across Distinct Clinical Stages

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00750

— Junhua Xie, Jun Lai, Yanzhe Zhang, Ye Liu, and Zhixiang Yan 2025-12-30 18:30:21

[ASAP] 1H NMR-Based Quantitative Lipoprotein Measurement Cross-Validation with Enzymatic Methods Applied to the OMNI-Heart Dietary Intervention Study

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00859

— Andong Zhu, Reika Masuda, Philipp Nitschke, Gengjie Jia, Jianbin Yan, Elaine Holmes, Jeremy K. Nicholson, Julien Wist, Andres Bernal, and Ruey Leng Loo 2025-12-29 16:26:32

[ASAP] Global Analysis of the Acetylome in Cisplatin-Induced Renal Fibrosis in C57BL/6 Mice

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00906

— Huilan Yang, Zhiyi Zhang, Min Chen, Jie Kong, Tao Ding, Xiaoyue Tang, Qiaochu Wang, Chunmei Shi, Lirong Liu, Jiangfeng Liu, and Juntao Yang 2025-12-29 13:10:46

[ASAP] Correlation of Plasma and Liver Tissue Proteomics for Plasma Biomarkers in Metabolic Dysfunction-Associated Steatotic Liver Disease

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00749

— Achuthan Sourianarayanane, Ju-Seog Lee, Honsoul Kim, and Brett S Phinney 2025-12-27 15:00:36

[ASAP] Protein Language Models: Applications and Perspectives

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00506

— Mickael Leclercq and Arnaud Droit 2025-12-26 16:55:54

[ASAP] Proteomic Profiling of Plasma Extracellular Vesicles Combined with Multivariate Modeling Identified Potential Biomarkers for Distinguishing Benign Pulmonary Nodules from Early-Stage Lung Adenocarcinoma

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00610

— Shujun Liu, Yating Ma, Bo Sun, Mei Yang, Mindi Zhao, and Chuanbao Li 2025-12-26 16:56:48

[ASAP] Metabolic Signature of a Healthy Lifestyle and the Risk of MASLD and Other Chronic Liver Diseases: An Observational and Mendelian Randomization Study

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00677

— Zhuoshuai Liang, Huizhen Jin, Wenhui Gao, Hongrui Zhang, Xinmeng Hu, Ruofei Li, Xiaoyang Li, Yi Cheng, Lingfei Guo, and Yawen Liu 2025-12-26 09:35:50

[ASAP] Early Detection of Infectious Diseases: A Review of Recent Advances in Pathogen Identification, Molecular Tools, and Metabolomics-Driven Biomarker Discovery

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c01014

— Patrica-Ivy Agorsor and Michael O. Eze 2025-12-26 16:56:27

[ASAP] Identification and Validation of Novel Biomarkers for Unstable Angina Using Olink Proteomics

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00831

— Ting Cao, Wenli Li, Jungang Pang, Shaohua Tan, and Jun Liu 2025-12-24 17:18:30

[ASAP] Penicillin–Streptomycin Treatment Rewires Core Metabolic and Ribosomal Programs in HepG2 Cells

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00934

— Cameron S. Movassaghi and Jesse G. Meyer 2025-12-24 13:40:28

[ASAP] Proteome-Wide Multipoint Internal Calibration Curves for Evaluating Peptide-Level Linearity in Relative Quantitative Proteomics

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00179

— Cristina Chiva, Zahra Elhamraoui, Julia Morales-Sanfrutos, Olga Pastor, and Eduard Sabidó 2025-12-23 12:46:17

[ASAP] Toward Proteomic-Based Prediction of Ex Vivo Platinum Sensitivity in Ovarian Cancer Ascitic Cellular Aggregates: A Pilot Study

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00771

— Jack Scanlan, Parul Mittal, Noor A. Lokman, Martin K. Oehler, Peter Hoffmann, and Manuela Klingler-Hoffmann 2025-12-23 17:27:53

[ASAP] TAG-PL: A Universal Proximity Labeling Platform for Mapping Mitochondrial Proteomes and Organelle Interactions under Stress

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00855

— Enming Miao, Xuyang Yue, Zhixiong Tao, Hongqiang Qin, and Mingliang Ye 2025-12-23 12:27:23

[ASAP] Temporal Profiling of Peroxynitrite-Mediated Protein Nitration and Phosphorylation Using Proteomics Analysis

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00417

— Yating Yao, Shuang Wang, Jingyi Li, Xiaohua Wang, and Jinghua Yang 2025-12-22 16:58:20

[ASAP] Redox Stoichiometry at the Single-Residue Level Using Mass Spectrometry Reveals Dynamic Methionine Sulfoxide Speciation in Actin and Calmodulin during Brain Aging

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00715

— Jiwoo Hwang, Madeleine F. Clore, Filipa Blasco Tavares Pereira Lopes, Marzieh Ayati, Daniela Schlatzer, Xin Qi, Rihua Wang, Mehmet Koyuturk, and Mark R. Chance 2025-12-22 20:00:00

[ASAP] A Covalent Protein Painting Assay Differentiates Amyloid-β Polymorphs in Alzheimer Disease

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00735

— Tom Casimir Bamberger, Jolene K. Diedrich, Titus Jung, Jeffrey B. Lane, Jan-Hannes Schaefer, Gabriel C. Lander, Douglas Galasko, and John R. Yates III 2025-12-22 19:10:44

[ASAP] Physiological Consequences of Overexpression of a Twin-Arginine Translocase in Bacillus subtilis Revealed by 14N/15N Labeling

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00787

— Margarita Bernal-Cabas, Minia Antelo-Varela, Bimal Prajapati, Tobias Schilling, Marina López-Álvarez, Stefano Grasso, Sandra Maaβ, Andreas Otto, Girbe Buist, Dörte Becher, and Jan Maarten van Dijl 2025-12-22 09:31:06

[ASAP] Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00872

— Leander Roeland van der Hoeven, Maico Lechner, Cristina Hernandez-Rollan, Tanveer Singh Batth, and Jesper V. Olsen 2025-12-22 16:14:33

[ASAP] Proximity Labeling Reveals RNA-Binding Proteins Associating with the Human Mitochondrial Import Receptor TOMM20

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00905

— Saira Akram, Katharina I. Zittlau, Karan Sharma, Julia C. Fitzgerald, Nisha Rafiq, Boris Maček, and Ralf-Peter Jansen 2025-12-22 14:33:43

[ASAP] Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC–MS Plasma Proteomics

Journal of Proteome Research

DOI: 10.1021/acs.jproteome.5c00420

— Erkka Järvinen, Xiaonan Liu, Markku Varjosalo, and Salla Keskitalo 2025-12-21 14:50:35