Journal of Proteome Research
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#1Jingfu Zhao (TTU: Texas Tech University)H-Index: 7
#2Ehwang Song (TTU: Texas Tech University)H-Index: 15
Last. Yehia Mechref (TTU: Texas Tech University)H-Index: 67
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The mature HIV-1 envelope (Env) glycoprotein is composed of gp120, the exterior subunit, and gp41, the transmembrane subunit assembled as trimer by noncovalent interaction. There is a great body of literature to prove that gp120 binds to CD4 first, then to the coreceptor. Binding experiments and functional assays have demonstrated that CD4 binding induces conformational changes in gp120 that enable or enhance its interaction with a coreceptor. Previous studies provided different glycomic maps fo...
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#1Polina Kudriavtseva (HSE: National Research University – Higher School of Economics)
#2Matvey Kashkinov (HSE: National Research University – Higher School of Economics)
Last. Attila Kertesz-Farkas (HSE: National Research University – Higher School of Economics)
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Spectrum annotation is a challenging task due to the presence of unexpected peptide fragmentation ions as well as the inaccuracy of the detectors of the spectrometers. We present a deep convolutional neural network, called Slider, which learns an optimal feature extraction in its kernels for scoring mass spectrometry (MS)/MS spectra to increase the number of spectrum annotations with high confidence. Experimental results using publicly available data sets show that Slider can annotate slightly m...
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#1Adak Karamafrooz (UMN: University of Minnesota)H-Index: 2
Last. Laurie L. Parker (UMN: University of Minnesota)H-Index: 16
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The DNAJB1-PRKACA fusion is the signature genetic event of fibrolamellar hepatocellular carcinoma (FL-HCC), a rare but lethal liver cancer that primarily affects adolescents and young adults. A deletion fuses the first exon of the HSP40 gene (DNAJB1), with exons 2-10 of protein kinase A (PRKACA), producing the chimeric kinase DNAJB1-PKAca (J-PKAca). The HSP40 portion's scaffolding/chaperone function has been implicated in redirecting substrate recognition to upregulate oncogenic pathways, but th...
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#1Shuting Yu (Shanxi University)H-Index: 2
#2Jian-Xin Fan (Shanxi University)H-Index: 1
Last. Zhenyu Li (Shanxi University)H-Index: 25
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With the increasing knowledge about the important roles of gut microbiota on the biological system, a systematic strategy to profile the fecal metabolome is urgently needed. Thus, an unbiased, efficient, and reproducible fecal metabolite extraction protocol needs to be established; however, the effect of biphasic extraction methods for the fecal samples remains unclear. In this study, five different methods were assessed in the extraction of polar and non-polar metabolites for the liquid chromat...
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Last. D. Votion (University of Liège)H-Index: 12
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Atypical myopathy (AM) is a severe rhabdomyolysis syndrome that occurs in grazing horses. Despite the presence of toxins in their blood, all horses from the same pasture are not prone to display clinical signs of AM. The objective of this study was to compare the blood metabolomic profiles of horses with AM clinical signs with those of healthy co-grazing (Co-G) horses. To do so, plasma samples from 5 AM horses and 11 Co-G horses were investigated using untargeted metabolomics. Metabolomic data w...
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#1Bocheng Yin (UVA: University of Virginia)H-Index: 6
#2Laura Rose Caggiano (UVA: University of Virginia)H-Index: 1
Last. Sarah E. Ewald (UVA: University of Virginia)H-Index: 11
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Tissue microenvironment properties like blood flow, extracellular matrix, or proximity to immune-infiltrate are important regulators of cell biology. However, methods to study regional protein expression in the native tissue environment are limited. To address this need, we developed a novel approach to visualize, purify, and measure proteins in situ using automated spatially targeted optical microproteomics (AutoSTOMP). Here, we report custom codes to specify regions of heterogeneity in a tissu...
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#1Marica Grossegesse (RKI: Robert Koch Institute)H-Index: 3
#2Paula Leupold (RKI: Robert Koch Institute)
Last. Andreas Nitsche (RKI: Robert Koch Institute)H-Index: 47
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Mass spectrometry-based proteomics is applied in SARS-CoV-2 research and is, moreover, being discussed as a novel method for SARS-CoV-2 diagnostics. However, the safe inactivation of coronaviruses by proteomics lysis buffers has not been systematically analyzed yet. Hence, for safety reasons a heating step prior to sample preparation is often performed. This step could be omitted once the safe inactivation with the typical buffers is proven. Here we test five different proteomics lysis buffers-4...
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#1Raiha Tahir (JHUSOM: Johns Hopkins University School of Medicine)H-Index: 4
#2Anil K. MadugunduH-Index: 15
Last. Akhilesh PandeyH-Index: 109
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Nonreceptor tyrosine kinases (NRTKs) represent an important class of signaling molecules driving diverse cellular pathways. Aberrant expression and hyperphosphorylation of TNK2, an NRTK, have been implicated in multiple cancers. However, the exact proteins and cellular events that mediate phenotypic changes downstream of TNK2 are unclear. Biological systems that employ proximity-dependent biotinylation methods, such as BioID, are being increasingly used to map protein-protein interactions, as th...
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#1Jianmei Tao (HUST: Huazhong University of Science and Technology)
#2Shuailong Jia (HUST: Huazhong University of Science and Technology)H-Index: 7
Last. Zhifeng Du (HUST: Huazhong University of Science and Technology)H-Index: 11
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Cisplatin is widely used for the treatment of various solid tumors. It is mainly administered by intravenous injection, and a substantial amount of the drug will bind to plasma proteins, a feature that is closely related to its pharmacokinetics, activity, toxicity, and side effects. However, due to the unique properties of platinum complexes and the complexity of the blood proteome, existing methods cannot systematically identify the binding proteome of cisplatin in blood. In this study, high-ab...
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#1Amanda E. StarrH-Index: 18
#2Shelley A. DeekeH-Index: 10
Last. Daniel FigeysH-Index: 63
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Inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis, are chronic diseases of the gastrointestinal tract, with an unknown etiology, that affect over 6.8 million people worldwide. To characterize disease pathogenesis, proteomic and bioinformatic analyses were performed on colon biopsies collected during diagnostic endoscopy from 119 treatment-naive pediatric patients, including from 78 IBD patients and 41 non-IBD patients who served as controls. Due to the pre...
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