كتاب
Automating Assignment, Quantitation, and Biological Annotation of Redox Proteomics Datasets with ProteoSushi
| العنوان: | Automating Assignment, Quantitation, and Biological Annotation of Redox Proteomics Datasets with ProteoSushi |
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| المؤلفون: | van der Post, Sjoerd, 1981, Seymour, Robert W., Mooradian, Arshag D., Held, Jason M. |
| المساهمون: | Göteborgs universitet, Sahlgrenska akademin, Institutionen för biomedicin, avdelningen för medicinsk kemi och cellbiologi, Gothenburg University, Sahlgrenska Academy, Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology |
| المصدر: | Methods in Molecular Biology. :61-84 |
| مصطلحات موضوعية: | Bioinformatik och systembiologi, Bioinformatics and Systems Biology, Bioinformatics, Cysteines, Posttranslational modifications, Protein inference, Proteomics, ProteoSushi, Reactive oxygen species, Redox, Systems biology |
| الوصف: | Redox proteomics plays an increasingly important role characterizing the cellular redox state and redox signaling networks. As these datasets grow larger and identify more redox regulated sites in proteins, they provide a systems-wide characterization of redox regulation across cellular organelles and regulatory networks. However, these large proteomic datasets require substantial data processing and analysis in order to fully interpret and comprehend the biological impact of oxidative posttranslational modifications. We therefore developed ProteoSushi, a software tool to biologically annotate and quantify redox proteomics and other modification-specific proteomics datasets. ProteoSushi can be applied to differentially alkylated samples to assay overall cysteine oxidation, chemically labeled samples such as those used to profile the cysteine sulfenome, or any oxidative posttranslational modification on any residue. Here we demonstrate how to use ProteoSushi to analyze a large, public cysteine redox proteomics dataset. ProteoSushi assigns each modified peptide to shared proteins and genes, sums or averages signal intensities for each modified site of interest, and annotates each modified site with the most up-to-date biological information available from UniProt. These biological annotations include known functional roles or modifications of the site, the protein domain(s) that the site resides in, the protein’s subcellular location and function, and more. |
| URL الوصول: | https://gup.ub.gu.se/publication/326284 |
| قاعدة البيانات: | SwePub |
| تدمد: | 10643745 19406029 |
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| DOI: | 10.1007/978-1-0716-1831-8_4 |