Journal of proteome research

Keyphrases

Publications

volume 23, number 8, 2024

Madeline Isom, Eden P Go, Heather Desaire
Enabling Lipidomic Biomarker Studies for Protected Populations by Combining Noninvasive Fingerprint Sampling with MS Analysis and Machine Learning. Journal of proteome research 23 (8) (2024)
Hui-Su Kim, Yong-In Kim, Je-Yeol Cho
ARID3C Acts as a Regulator of Monocyte-to-Macrophage Differentiation Interacting with NPM1. Journal of proteome research 23 (8) (2024)
Boomathi Pandi, Stella Brenman, Alexander Black, Dominic C M Ng, Edward Lau, Maggie P Y Lam
Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart. Journal of proteome research 23 (8) (2024)
Ryan M Riley, Gian Luca Negri, S-W Grace Cheng, Sandra Elizabeth Spencer, Ryan D Morin, Gregg B Morin
Mass Spectrometry Acquisition and Fractionation Recommendations for TMT11 and TMT16 Labeled Samples. Journal of proteome research 23 (8) (2024)
Rachel L Lombardi, John S Ramsey, Jaclyn E Mahoney, Michael J MacCoss, Michelle L Heck, Carolyn M Slupsky
Longitudinal Transcriptomic, Proteomic, and Metabolomic Response of Citrus sinensis to Diaphorina citri Inoculation of Candidatus Liberibacter asiaticus. Journal of proteome research 23 (8) (2024)
Mudassir Shah, Lei Guo, Xiangnan Xu, Lingli Deng, Keyi Lu, Ji-Yang Dong, Chao Zhao, Jingjing Xu
eLIMS: Ensemble Learning-Based Spatial Segmentation of Mass Spectrometry Imaging to Explore Metabolic Heterogeneity. Journal of proteome research 23 (8) (2024)
Deepali Rathore, Matthew J Marino, Jiraphorn Issara-Amphorn, Sung Hwan Yoon, Nathan P Manes, Aleksandra Nita-Lazar
Lipopolysaccharide Regulates the Macrophage RNA-Binding Proteome. Journal of proteome research 23 (8) (2024)
Gerhard Hagn, Samuel M Meier-Menches, Günter Plessl-Walder, Gaurav Mitra, Thomas Mohr, Karin Preindl, Andreas Schlatter, Doreen Schmidl, Christopher Gerner, Gerhard Garhöfer, Andrea Bileck
Plasma Instead of Serum Avoids Critical Confounding of Clinical Metabolomics Studies by Platelets. Journal of proteome research 23 (8) (2024)
Linda Berg Luecke, Roneldine Mesidor, Jack Littrell, Morgan Carpenter, Melinda Wojtkiewicz, Rebekah L Gundry
Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N -Glycocapture Data. Journal of proteome research 23 (8) (2024)
Yuqing Zhang, Hui Zhao, Jinhui Zhao, Wangjie Lv, Xueni Jia, Xin Lu, Xinjie Zhao, Guo-Wang Xu
Quantified Metabolomics and Lipidomics Profiles Reveal Serum Metabolic Alterations and Distinguished Metabolites of Seven Chronic Metabolic Diseases. Journal of proteome research 23 (8) (2024)
Zohreh Sharifi, Shu Yue Luo, John Maringa Githaka, Arashdeep Saini, Nicolas Touret, Ing Swie Goping, Olivier Julien
Comparing the BAD Protein Interactomes in 2D and 3D Cell Culture Using Proximity Labeling. Journal of proteome research 23 (8) (2024)
Elizabeth F Bayne, Kevin M Buck, Anna G Towler, Yanlong Zhu, Melissa R Pergande, Tianhua Zhou, Scott Price, Kalina J Rossler, Vanessa Morales-Tirado, Sarah Lloyd, Fei Wang, Yupeng He, Yu Tian, Ying Ge
High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. Journal of proteome research 23 (8) (2024)
Weifen Sun, Ao Huang, Shubo Wen, Ruicong Yang, Xiling Liu
Temporal Assessment of Protein Stability in Dried Blood Spots. Journal of proteome research 23 (8) (2024)
Christoph Bueschl, Gabriel Riquelme, Nicolás Zabalegui, Maximilian A Rey, María Eugenia Monge
Tidy-Direct-to-MS: An Open-Source Data-Processing Pipeline for Direct Mass Spectrometry-Based Metabolomics Experiments. Journal of proteome research 23 (8) (2024)
Daniel Radford-Smith, Tang T Ng, Abi G Yates, Isobel Dunstan, Timothy D W Claridge, Daniel C Anthony, Fay Probert
Ex-Vivo 13 C NMR Spectroscopy of Rodent Brain: TNF Restricts Neuronal Utilization of Astrocyte-Derived Metabolites. Journal of proteome research 23 (8) (2024)
Krystal K Lum, Tavis J Reed, Jinhang Yang, Ileana M Cristea
Differential Contributions of Interferon Classes to Host Inflammatory Responses and Restricting Virus Progeny Production. Journal of proteome research 23 (8) (2024)
Chase L S Skawinski, Priya S Shah
I'm Walking into Spiderwebs: Making Sense of Protein-Protein Interaction Data. Journal of proteome research 23 (8) (2024)
Rupanshee Srivastava, Nidhi Singh, Tripti Kanda, Sadhana Yadav, Shivam Yadav, Neelam Atri
Cyanobacterial Proteomics: Diversity and Dynamics. Journal of proteome research 23 (8) (2024)
Rosimeire Barboza Bispo, Antônio Teixeira do Amaral, Vitor Batista Pinto, Talles de Oliveira Santos, Valter Jário de Lima, Bruna Rohem Simão, Anne Fischer, Michael J Naldrett, Sophie Alvarez
Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn ( Zea mays L. var. everta ): Insights from Proteomic and Metabolite Analysis. Journal of proteome research 23 (8) (2024)
Ariana E Shannon, Claire E Boos, Brian C Searle, Amanda B Hummon
Gas-Phase Fractionation Data-Independent Acquisition Analysis of 3D Cocultured Spheroid Tumor Model Reveals Altered Translational Processes and Signaling Using Proteomics. Journal of proteome research 23 (8) (2024)
David J Degnan, Logan A Lewis, Lisa M Bramer, Lee Ann McCue, James J Pesavento, Mowei Zhou, Aivett Bilbao
IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data. Journal of proteome research 23 (8) (2024)
Ming-Ming Zhang, Bing Yuan, Ya-Ting Wang, Feng-Li Zhang, Chen-Guang Liu, Xin-Qing Zhao
Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. Journal of proteome research 23 (8) (2024)
Lauren Fields, Nhu Q Vu, Tina C Dang, Hsu-Ching Yen, Min Ma, Wenxin Wu, Mitchell Gray, Lingjun Li
EndoGenius: Optimized Neuropeptide Identification from Mass Spectrometry Datasets. Journal of proteome research 23 (8) (2024)
Friederike Gutmann, Raphaela Fritsche-Guenther, Daniela B Dias, Jennifer A Kirwan
Comparing the Extraction Performance in Mouse Plasma of Different Biphasic Methods for Polar and Nonpolar Compounds. Journal of proteome research 23 (8) (2024)
Fenglong Jiao, Clinton Yu, Andrew Wheat, Lijun Chen, Tung-Shing Mamie Lih, Hui Zhang, Lan Huang
DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples. Journal of proteome research 23 (8) (2024)
Yun-Chung Hsiao, Yifei Yang, Chih-Wei Liu, Jingya Peng, Jiahao Feng, Haoduo Zhao, Taylor Teitelbaum, Kun Lu
Multiomics to Characterize the Molecular Events Underlying Impaired Glucose Tolerance in FXR-Knockout Mice. Journal of proteome research 23 (8) (2024)
Hanna G Budayeva, Taylur P Ma, Shuai Wang, Meena Choi, Christopher M Rose
Increasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data Acquisition. Journal of proteome research 23 (8) (2024)
Sara Bonini, Dominic Winter
Two-Step Enrichment Facilitates Background Reduction for Proteomic Analysis of Lysosomes. Journal of proteome research 23 (8) (2024)
Xi Yan, Xinglai Zhang, Haiying Li, Yongdong Zou, Wei Lu, Man Zhan, Zhiyuan Liang, Hongbin Zhuang, Xiaoqian Ran, Guanwei Ma, Xixiao Lin, Hongbo Yang, Yuhan Huang, Hanghang Wang, Haorong Wu
Application of Proteomics and Machine Learning Methods to Study the Pathogenesis of Diabetic Nephropathy and Screen Urinary Biomarkers. Journal of proteome research 23 (8) (2024)
Lindsey D Ulmer, Daniele Canzani, Christopher N Woods, Natalie L Stone, Maria K Janowska, Rachel E Klevit, Matthew F Bush
High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid. Journal of proteome research 23 (8) (2024)
Douwe Schulte, Joost Snijder
A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics. Journal of proteome research 23 (8) (2024)
Shenyu Zhang, Zhengyu Ma
trans -Interacting Plasma Membrane Proteins and Binding Partner Identification. Journal of proteome research 23 (8) (2024)
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
Endogenous Protein-Protein Interaction Network of the NPC Cholesterol Transporter 1 in the Cerebral Cortex. Journal of proteome research 23 (8) (2024)
Jessica L Nickerson, Liam V Sheridan, Alan A Doucette
Impact of Surfactants on Cumulative Trypsin Activity in Bottom-Up Proteome Analysis. Journal of proteome research 23 (8) (2024)
Sara Martínez, Oihane E Albóniga, María Rosa López-Huertas, Ana Gradillas, Coral Barbas
Reinforcing the Evidence of Mitochondrial Dysfunction in Long COVID Patients Using a Multiplatform Mass Spectrometry-Based Metabolomics Approach. Journal of proteome research 23 (8) (2024)
Md Yasir Arafat, Kanika Narula, Mohit Kumar, Niranjan Chakraborty, Subhra Chakraborty
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. Journal of proteome research 23 (8) (2024)
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
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. Journal of proteome research 23 (8) (2024)
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 Álvarez-Llamas
Analysis of Vascular Smooth Muscle Cells from Thoracic Aortic Aneurysms Reveals DNA Damage and Cell Cycle Arrest as Hallmarks in Bicuspid Aortic Valve Patients. Journal of proteome research 23 (8) (2024)
Louise M Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer, Ralf Gabriels
MS 2 Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0. Journal of proteome research 23 (8) (2024)
Kamila Říhová, Petr Lapčík, Barbora Veselá, Lucia Knopfová, David Potěšil, Jana Pokludová, Jan Šmarda, Eva Matalová, Pavla Bouchalova, Petr Beneš
Caspase-9 Is a Positive Regulator of Osteoblastic Cell Migration Identified by diaPASEF Proteomics. Journal of proteome research 23 (8) (2024)
Vanya Bhushan, Aleksandra Nita-Lazar
Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. Journal of proteome research 23 (8) (2024)
Kongxin Gu, Haruka Kumabe, Takumi Yamamoto, Naoto Tashiro, Takeshi Masuda, Shingo Ito, Sumio Ohtsuki
Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition. Journal of proteome research 23 (8) (2024)
Gwang Bin Lee, Wan Nur Atiqah Binti Mazli, Ling Hao
Multiomics Evaluation of Human iPSCs and iPSC-Derived Neurons. Journal of proteome research 23 (8) (2024)
Feroza K Choudhury, Viji Premkumar, Jana Zecha, Jonathan Boyd, Andrew S Gaynor, Zengli Guo, Tom Martin, Raffaello Cimbro, Erik L Allman, Sonja Hess
Multiomics Characterization of a Less Invasive Microfluidic-Based Cell Sorting Technique. Journal of proteome research 23 (8) (2024)
Fernanda Monedeiro, Barbara Ehall, Katrin Tiffner, Anita Eberl, Eva Svehlikova, Barbara Prietl, Verena Pfeifer, Julia Senekowitsch, Anu Remm, Ana Rebane, Christoph Magnes, Thomas Pieber, Frank Sinner, Thomas Birngruber
Characterization of Inflammatory Mediators and Metabolome in Interstitial Fluid Collected with Dermal Open Flow Microperfusion before and at the End of Dupilumab Treatment in Atopic Dermatitis. Journal of proteome research 23 (8) (2024)
Maik Damm, Mert Karış, Daniel Petras, Ayse Nalbantsoy, Bayram Göçmen, Roderich D Süssmuth
Venomics and Peptidomics of Palearctic Vipers: A Clade-Wide Analysis of Seven Taxa of the Genera Vipera , Montivipera , Macrovipera , and Daboia across Türkiye. Journal of proteome research 23 (8) (2024)
Liya Popova, Rachel A Carr, Valerie J Carabetta
Recent Contributions of Proteomics to Our Understanding of Reversible N ε -Lysine Acylation in Bacteria. Journal of proteome research 23 (8) (2024)
Kevin D Culver, Patric W Sadecki, Jessica K Jackson, Zoe A Brown, Megan E Hnilica, Jingyun Wu, Lindsey Neil Shaw, Andrew J Wommack, Leslie M Hicks
Identification and Characterization of CC-AMP1-like and CC-AMP2-like Peptides in Capsicum spp. Journal of proteome research 23 (8) (2024)
Louise Ulrich Kurt, Milan Avila Clasen, Ísis Venturi Biembengut, Max Ruwolt, Fan Liu, Fabio César Gozzo, Diogo Borges Lima, Paulo Costa Carvalho
RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control. Journal of proteome research 23 (8) (2024)
Melanie T Odenkirk, Xueyun Zheng, Jennifer E Kyle, Kelly G Stratton, Carrie D Nicora, Kent J Bloodsworth, Catriona A Mclean, Colin L Masters, Matthew E Monroe, James D Doecke, Richard D Smith, Kristin E Burnum-Johnson, Blaine R Roberts, Erin S Baker
Deciphering ApoE Genotype-Driven Proteomic and Lipidomic Alterations in Alzheimer's Disease Across Distinct Brain Regions. Journal of proteome research 23 (8) (2024)