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xiSPEC: web-based visualization, analysis and sharing of proteomics data

Lars Kolbowski, Colin Combe, Juri Rappsilber
2018 Nucleic Acids Research  
We present xiSPEC, a standard compliant, nextgeneration web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data.  ...  Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML  ...  /), Lutz Fischer for creating the Java application backend service for the annotation of spectra data (https://github.com/Rappsilber-Laboratory/xiAnnotator) and Martin Graham for his help with JavaScript  ... 
doi:10.1093/nar/gky353 pmid:29741719 pmcid:PMC6030980 fatcat:fkycuzqpvbhpdp665qq3in67ty

xiNET: Cross-link Network Maps With Residue Resolution

Colin W. Combe, Lutz Fischer, Juri Rappsilber
2015 Molecular & Cellular Proteomics  
xiNET is a visualization tool for exploring cross-linking/ mass spectrometry results. The interactive maps of the cross-link network that it generates are a type of nodelink diagram.  ...  Molecular & Cellular Proteomics  ...  Acknowledgments-We thank Jimi-Carlo Bukowski-Wills for discussion regarding the web-implementation of the project, Tatsiana Auchynnikava for comments on the manuscript and all members of our laboratory  ... 
doi:10.1074/mcp.o114.042259 pmid:25648531 pmcid:PMC4390258 fatcat:a64p4mcdhjaijjh5psvqxw6nry

The landscape of tumor fusion neoantigens: a pan-cancer analysis

Zhiting Wei, Chi Zhou, Zhanbing Zhang, Ming Guan, Chao Zhang, Zhongmin Liu, Qi Liu
2019 iScience  
In the present study, we performed a comprehensive analysis of the landscape of tumor fusion neoantigens in cancer and proposed a score scheme to quantitatively assess their immunogenic potentials.  ...  Compared with SNV&indel-based neoantigens, fusion-based neoantigens are not well characterized.  ...  Peptide-spectrum matches were visualized by xiSPEC (Kolbowski, Combe and Rappsilber, 2018) , a web-based spectrum viewer.  ... 
doi:10.1016/j.isci.2019.10.028 pmid:31677477 pmcid:PMC6838548 fatcat:kd5v54hirncntg3ru4j5gh2vby