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xiSPEC: web-based visualization, analysis and sharing of proteomics data
2018
Nucleic Acids Research
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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
2015
Molecular & Cellular Proteomics
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
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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
2019
iScience
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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