From canonical to unique: extension of a lipophilicity scale of amino acids to non-standard residues by Antonio Viayna, Paulina Matamoros, David Blázquez-Ruano, William J. Zamora

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Phosphatidylinositol promoted the proliferation and invasion of pituitary adenoma cells by regulating POU1F1 expression by Tongjiang Xu, Xiaodong Zhai, RuiWei Wang, Xiaoben Wu, ZhiZhen Zhou, MiaoMiao Shang, Chongcheng Wang, Tengfei Qi, Wei Yang

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Characteristics and multi-omics analysis of spontaneous spondyloarthritis in non-human primates: Case report by Lei Cai, Qing Lv, Ronghua Ma, Wei Liu, Yalun Guan, Zhongqiang Huang, Qingyu Liu, Yunfeng Li, Shuhua Liu, Ge Li, Yu Zhang

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Pulse protein quality and derived bioactive peptides by Matthew G. Nosworthy, Matthew G. Nosworthy, Bianyun Yu, L. Irina Zaharia, Gerardo Medina, Nii Patterson

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Structural characterization of stem cell factors Oct4, Sox2, Nanog and Esrrb disordered domains, and a method to detect phospho-dependent binding partners by Bouguechtouli, Chafiaa, Ghouil, Rania, Alik, Ania, Dingli, Florent, Loew, Damarys, Theillet, Francois-Xavier

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Revealing novel protein interaction partners of glyphosate in Escherichia coli by Alix Sarah Aldehoff, Dominique Türkowsky, Patrick Lohmann, Masun Nabhan Homsi, Ulrike Rolle–Kampczyk, Elke Ueberham, Jörg Lehmann, Martin von Bergen, Nico Jehmlich, Sven–Bastiaan Haange

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Human milk whey proteins: Constituents, influencing factors, detection methods, and comparative analysis with other sources by Xing Li, Xiaomei Zhang, Minghui Zhang, Xiaojia Liu, Ziyue Gao, Junying Zhao, Weicang Qiao, Lijun Chen

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Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours by Surbhi Mishra, Mysore Vishakantegowda Tejesvi, Jenni Hekkala, Jenni Turunen, Niyati Kandikanti, Anna Kaisanlahti, Marko Suokas, Sirpa Leppä, Pia Vihinen, Hanne Kuitunen, Kaisa Sunela, Jussi Koivunen, Arja Jukkola, Ilja Kalashnikov, Päivi Auvinen, Okko-Sakari Kääriäinen, T. Peñate Medina, O. Peñate Medina, Juha Saarnio, Sanna Meriläinen, Tero Rautio, Raila Aro, Reetta Häivälä, Juho Suojanen, Mikael Laine, Pande Putu Erawijattari, Leo Lahti, Peeter Karihtala, Terhi S. Ruuska, Justus Reunanen

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The emergence of cell-based protein arrays to test for polyspecific off-target binding of antibody therapeutics by Diana M. Norden, Carmen T. Navia, Jonathan T. Sullivan, Benjamin J. Doranz

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The grapevine ABC transporter B family member 15 is a trans-resveratrol transporter out of grapevine cells by Ascensión Martínez-Márquez, Ascensión Martínez-Márquez, Viviana Martins, Susana Sellés-Marchart, Susana Sellés-Marchart, Hernâni Gerós, Purificación Corchete, Roque Bru-Martínez, Roque Bru-Martínez, Roque Bru-Martínez

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Plasma prolactin axis shift from placental to pituitary origin in late prepartum mice by Taku James Sairenji, Shinnosuke Masuda, Yuya Higuchi, Mitsue Miyazaki, Hiroyuki Yajima, Oh Kwan Ee, Yuki Fujiwara, Takuya Araki, Noriaki Shimokawa, Noriyuki Koibuchi

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AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation by Matteo Manfredi, Gabriele Vazzana, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

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DRomics, a workflow to exploit dose-response omics data in ecotoxicology by Delignette-Muller, Marie Laure, Siberchicot, Aurélie, Larras, Floriane, Billoir, Elise

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Radio-protective effects of ultra-fine bubble hydrogen water and serum protein responses in whole-body radiation-exposed mice by Masaru Yamaguchi, Khin Thandar Htun, Youta Tatara, Yoshiaki Sato, Masato Hosoda, Suchart Kothan, Chikashi Kamimura, Osamu Inanami, Ikuo Kashiwakura

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Podophyllotoxin mediates hepatic toxicity via the C5a/C5aR/ROS/NLRP3 and cGMP/PKG/mTOR axis in rats based on toxicological evidence chain (TEC) concept by phosphoproteomic analysis by Chuanxin Liu, Xiaobin Huang, Jiao Kong, Xuejiao Li, Yuming Wang, Fangfang Zhang, Jiajia Duan

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MiR-18a-LncRNA NONRATG-022419 pairs targeted PRG-1 regulates diabetic induced cognitive impairment by regulating NGF\BDNF-Trkb signaling pathway by Qiong Xiang, Hu Lin, Jia-Sheng Tao, Chuan-Jun Fu, Li-Ni Liu, Jing Deng, Xian-Hui Li

“…Proteome Science…”
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Secretory mitophagy: an extracellular vesicle-mediated adaptive mechanism for cancer cell survival under oxidative stress by Purva V. Gade, Angela Victoria Rojas Rivera, Layla Hasanzadah, Sofie Strompf, Thomas Raymond Philipson, Matthew Gadziala, Atharva Tyagi, Arnav Bandam, Rithvik Gabbireddy, Fatah Kashanchi, Amanda Haymond, Lance A. Liotta, Marissa A. Howard

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iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control by Huanhuan Gao, Yi Zhu, Dongxue Wang, Zongxiang Nie, He Wang, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He, Tiannan Guo

“…Abstract Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. …”
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Characterization of Bozitinib as a potential therapeutic agent for MET-amplified gastric cancer by Hang Lin, Lingzhi Qu, Hudie Wei, Ming Guo, Xiaojuan Chen, Qianmeng Lin, Huajun Zhang, Shuyan Dai, Yongheng Chen

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A computational tool to infer enzyme activity using post-translational modification profiling data by Dehui Kong, Aijun Zhang, Ling Li, Zuo-Fei Yuan, Yingxue Fu, Long Wu, Ashutosh Mishra, Anthony A. High, Junmin Peng, Xusheng Wang

“…Despite their crucial roles, measuring enzyme activities is typically indirect and performed on a smaller scale, unlike protein abundance measured by high-throughput proteomics. Moreover, it is challenging to derive the activity of enzymes from proteome-wide post-translational modification (PTM) profiling data. …”
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