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J Proteome Res. 2019 Feb 1;18(2):759-764. doi: 10.1021/acs.jproteome.8b00726. Epub 2018 Dec 19.

Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates.

Author information

1
Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States.
2
Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.

Abstract

Proxl is an open-source web application for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data and results. Proxl's core features include comparing data sets, structural analysis, customizable and interactive data visualizations, access to all underlying mass spectrometry data, and quality-control tools. All features of Proxl are designed to be independent of specific cross-linker chemistry or software analysis pipelines. Proxl's sharing tools allow users to share their data with the public or securely restrict access to trusted collaborators. Since being published in 2016, Proxl has continued to be expanded and improved through active development and collaboration with cross-linking researchers. Some of Proxl's new features include a centralized, public site for sharing data, greatly expanded quality-control tools and visualizations, support for stable isotope-labeled peptides, and general improvements that make Proxl easier to use, data easier to share and import, and data visualizations more customizable. Source code and more information are found at http://proxl-ms.org/ .

KEYWORDS:

bioinformatics; cross-linking; data visualization; database; proteomics; software; structure

PMID:
30525651
PMCID:
PMC6417915
[Available on 2020-02-01]
DOI:
10.1021/acs.jproteome.8b00726

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