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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PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways by Julian Müller, Florian P. Bayer, Mathias Wilhelm, Maximilian G. Schuh, Bernhard Kuster, Matthew The

“…Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform that offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams. …”
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Gas-phase fractionation DDA promotes in-depth DIA phosphoproteome analysis by Zhiwei Tu, Yabin Li, Shuhui Ji, Shanshan Wang, Rui Zhou, Gertjan Kramer, Yu Cui, Fei Xie

“…Data-independent acquisition (DIA) is a promising method for quantitative proteomics. Library-based DIA database searching against project-specific data-dependent acquisition (DDA) spectral libraries is the gold standard. …”
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Post-Translational Modifications of Proteins Orchestrate All Hallmarks of Cancer by Pathea Shawnae Bruno, Aneeta Arshad, Maria-Raluca Gogu, Natalie Waterman, Rylie Flack, Kimberly Dunn, Costel C. Darie, Anca-Narcisa Neagu

“…Aberrant PTMs can be considered as enabling characteristics of cancer as long as they orchestrate all malignant modifications and variability in the proteome of cancer cells, cancer-associated cells, and tumor microenvironment (TME). …”
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Comparative analysis of anticoagulant influence on PMI estimation based on porcine blood metabolomics profile measured using GC-MS by Patrycja Mojsak, Paulina Samczuk, Paulina Samczuk, Paulina Klimaszewska, Michal Burdukiewicz, Michal Burdukiewicz, Jaroslaw Chilimoniuk, Krystyna Grzesiak, Krystyna Grzesiak, Karolina Pietrowska, Justyna Ciborowska, Anna Niemcunowicz-Janica, Adam Kretowski, Adam Kretowski, Michal Ciborowski, Michal Ciborowski, Michal Szeremeta

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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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Multi-omics analysis of hexaploid triticale that show molecular responses to salt stress during seed germination by Dongxia Wang, Jiedong Li, Shiming Li, Jiongjie Fu, Baolong Liu, Baolong Liu, Baolong Liu, Dong Cao, Dong Cao, Dong Cao

“…After integrating GWAS-target genes with transcriptomics and proteomics approaches that the candidate gene late embryogenesis abundant protein 14 (LEA14) was up-regulated at the transcriptomic and proteomic levels. …”
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The PHD transcription factor Cti6 is involved in the fungal colonization and aflatoxin B1 biological synthesis of Aspergillus flavus by Zhang Mengjuan, Lin Guanglan, Pan Xiaohua, Song Weitao, Tan Can, Chen Xuan, Yang Yanling, Zhuang Zhenhong

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Gene Identification and Characterization of Correlations for DEPs_DEGs Same Trend Responding to Salinity Adaptation in Scylla paramamosain by Huan Wang, Hongling Wei, Lei Tang, Junkai Lu, Changkao Mu, Chunlin Wang

“…In our previous study, we had analyzed the mechanism of adapting sudden drop in salinity from the level of transcriptomics and proteomics, respectively. This study performed a correlation analysis of RNA sequencing transcriptomics and iTRAQ proteomics in order to investigate the adaptation mechanisms to sudden salinity drop from 23‰ to 3‰. …”
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Polypeptide Expression in Prostate Hyperplasia and Prostate Adenocarcinoma by Ayodele Alaiya, Uwe Roblick, Lars Egevad, Adelaide Carlsson, Bo Franzén, Daniela Volz, Sören Huwendiek, Stig Linder, Gert Auer

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Clastogenic Effects of Glyphosate in Bone Marrow Cells of Swiss Albino Mice by Sahdeo Prasad, Smita Srivastava, Madhulika Singh, Yogeshwer Shukla

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Paracetamol metabolism by endothelial cells – Potential mechanism underlying intravenous paracetamol-induced hypotension by Johs Dannesboe, Joakim A. Bastrup, Kathrine Holm Nielsen, Pelle Munck, Morten B. Thomsen, Clare L. Hawkins, Thomas A. Jepps

“…Proteomic analyses of mesenteric arteries from rats administered intravenous APAP are consistent with a key role of the vascular wall in APAP metabolism, with similar proteomic pathway changes identified in HCAECs. …”
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Periodontal Indices as Predictors of Cognitive Decline: Insights from the PerioMind Colombia Cohort by Catalina Arévalo-Caro, Diego López, Jose Antonio Sánchez Milán, Cristina Lorca, María Mulet, Humberto Arboleda, Sergio Losada Amaya, Aida Serra, Xavier Gallart-Palau

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Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL by Lavinia Arseni, Gianluca Sigismondo, Haniyeh Yazdanparast, Johanne U. Hermansen, Norman Mack, Sibylle Ohl, Verena Kalter, Murat Iskar, Mathias Kalxdorf, Dennis Friedel, Mandy Rettel, Yashna Paul, Ingo Ringshausen, Eric Eldering, Julie Dubois, Arnon P. Kater, Marc Zapatka, Philipp M. Roessner, Eugen Tausch, Stephan Stilgenbauer, Sascha Dietrich, Mikhail M. Savitski, Sigrid S. Skånland, Jeroen Krijgsveld, Peter Lichter, Martina Seiffert

“…A comparative analysis of exome, transcriptome and proteome of sorted leukemic murine cells during treatment and after relapse suggests alterations in the proteasome activity as a driver of ibrutinib resistance. …”
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Techniques for Molecular Imaging Probe Design by Fred Reynolds, Kimberly A. Kelly

“…With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. …”
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An integrated approach using proximity labelling and chemical crosslinking to probe in situ host-virus protein–protein interactions by Jiaqi Li, Zhewang Lin

“…In this perspective, we discuss the integration of two latest proteomic techniques, based on in situ proximity labelling and chemical crosslinking methods, to uncover host-virus protein–protein interactions in living cells.…”
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Multiplexed Dilute-and-Shoot Liquid Chromatography–Multiple-Reaction Monitoring Mass Spectrometry Clinical Assay for Metanephrines and Catecholamines in Human Urine by Deema O. Qasrawi, Adriano M. C. Pimenta, Evgeniy V. Petrotchenko, Shaun Eintracht, Christoph H. Borchers

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Effect of potato glycoside alkaloids on mitochondria energy metabolism of Fusarium solani, the root rot pathogen of Lycium barbarum by Ruiyun Li, Bin Wang, Wei Chen, Chongqing Zhang, Nan Li, Yupeng Wang, Yuke Yan, Yuyan Sun, Jing He, Jing He

“…The results from both parallel reaction monitoring (PRM) and real-time RT-qPCR were consistent with the overall trends observed in TMT proteomics, thereby confirming the validity of the TMT proteomics analysis. …”
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Association of Inflammatory and Oxidative Stress Markers with Metabolic Syndrome in Asian Indians in India by Veena S. Rao, Radhika K. Nagaraj, Sridhara Hebbagodi, Natesha B. Kadarinarasimhiah, Vijay V. Kakkar

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Determination of Dabigatran Concentration in Human Plasma and Breast Milk by F. Sidgwick, A. Porter, P. Ayuk, F. Kamali, A. Truemann

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