Bartkowiak, Kai Mossahebi Mohammadi, Parinaz Gärtner, Sebastian Kwiatkowski, Marcel Andreas, Antje Geffken, Maria Peine, Sven Verpoort, Karl Scholz, Ursula Deutsch, Thomas M
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Published in
Journal of proteome research
In cancer metastasis, single circulating tumor cells (CTCs) in the blood and disseminated tumor cells (DTCs) in the bone marrow mediate cancer metastasis. Because suitable biomarker proteins are lacking, CTCs and DTCs with mesenchymal attributes are difficult to isolate from the bulk of normal blood cells. To establish a procedure allowing the isol...
Molendijk, Jeffrey Yip, Rui Parker, Benjamin L
Published in
Journal of proteome research
We have developed the underrepresented post-translational modification (PTM) database (urPTMdb), a PTM gene set database to accelerate the discovery of enriched protein modifications in experimental data. urPTMdb provides curated lists of proteins reported to be substrates of underrepresented modifications. Their enrichment in proteomics datasets c...
Hempel, Benjamin-Florian Damm, Maik Petras, Daniel Kazandjian, Taline D Szentiks, Claudia A Fritsch, Guido Nebrich, Grit Casewell, Nicholas R Klein, Oliver Süssmuth, Roderich D
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Published in
Journal of proteome research
Among venomous animals, toxic secretions have evolved as biochemical weapons associated with various highly specialized delivery systems on many occasions. Despite extensive research, there is still limited knowledge of the functional biology of most animal toxins, including their venom production and storage, as well as the morphological structure...
Kalpongnukul, Nuttiya Bootsri, Rungnapa Wongkongkathep, Piriya Kaewsapsak, Pornchai Ariyachet, Chaiyaboot Pisitkun, Trairak Chantaravisoot, Naphat
Published in
Journal of proteome research
Glioblastoma (GBM) is a devastating primary brain cancer with a poor prognosis. GBM is associated with an abnormal mechanistic target of rapamycin (mTOR) signaling pathway, consisting of two distinct kinase complexes: mTORC1 and mTORC2. The complexes play critical roles in cell proliferation, survival, migration, metabolism, and DNA damage response...
Chen, Hauh-Jyun Candy Chen, Chau-Yi Fang, Ya-Hsuan Hung, Kai-Wei Wu, Deng-Chyang
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Journal of proteome research
Malondialdehyde (MDA) is the most abundant α,β-unsaturated aldehyde generated from endogenous peroxidation of polyunsaturated fatty acids and is present in cigarette smoke. Post-translational modifications of blood hemoglobin can serve as biomarkers for exposure to chemicals. In this study, two types of MDA-induced modifications, the N-propenal and...
Wei, Pinghui He, Meiqin Han, Guoge
Published in
Journal of proteome research
Age-related macular degeneration is a metabolic compromise disorder whose main pathological feature is choroidal neovascularization (CNV) formation. Using untargeted metabolomics analysis, we determined to assess the metabolomic alterations in a CNV rat model to provide an insight into its pathogenesis. In the CNV model, there were 24 significantly...
He, Tianen Liu, Youqi Zhou, Yan Li, Lu Wang, He Chen, Shanjun Gao, Jinlong Jiang, Wenhao Yu, Yi Ge, Weigang
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Published in
Journal of proteome research
Isobaric labeling-based proteomics is widely applied in deep proteome quantification. Among the platforms for isobaric labeled proteomic data analysis, the commercial software Proteome Discoverer (PD) is widely used, incorporating the search engine CHIMERYS, while FragPipe (FP) is relatively new, free for noncommercial purposes, and integrates the ...
Phlairaharn, Teeradon Grégoire, Samuel Woltereck, Lukas R Petrosius, Valdemaras Furtwängler, Benjamin Searle, Brian C Schoof, Erwin M
Published in
Journal of proteome research
In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyze...
Liu, Chuang Sun, Dawei Chen, Yuhui Wang, Can Li, Jinglin Lin, Jiwen
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Journal of proteome research
The radula is a unique foraging organ to Mollusca, which is important for their evolution and taxonomic classification. Many radulae are mineralized with metals. Although the remarkable mechanical properties of mineralized radulae are well-studied, the formation of mineralization from nonmineralized radulae is poorly understood. Taking advantage of...
Di Cesare, Francesca Tenori, Leonardo Luchinat, Claudio Saccenti, Edoardo
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Journal of proteome research
This study investigated the associations between the levels of 27 plasma metabolites, 114 lipoprotein parameters, determined using nuclear magnetic resonance spectroscopy, and the ABO blood groups and the Rhesus (Rh) blood system in a cohort of n = 840 Italian healthy blood donors of both sexes. We observed good multivariate discrimination between ...
