+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

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

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

Journal of Proteome Research 18(2): 759-764

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/ .

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 065985660

Download citation: RISBibTeXText

PMID: 30525651

DOI: 10.1021/acs.jproteome.8b00726

Related references

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. Journal of Proteome Research 15(8): 2863-2870, 2016

Protein cross-linking tools for the construction of nanomaterials. Current Opinion in Biotechnology 39: 61-67, 2016

Mass Spectrometry-Based Tools to Characterize DNA-Protein Cross-Linking by Bis-Electrophiles. Basic and Clinical Pharmacology and Toxicology 121(Suppl. 3): 63-77, 2017

Intermolecular protein cross-linking during acrolein toxicity: efficacy of carbonyl scavengers as inhibitors of heat shock protein-90 cross-linking in A549 cells. Chemical Research in Toxicology 20(11): 1629-1637, 2007

Cross-linking reagents as tools for identifying components of the yeast mitochondrial protein import machinery. Methods in Cell Biology 34: 419-426, 1991

Cross-linking analysis of the two forms of protein I, a major outer membrane protein of Escherichia coli. Journal of Bacteriology 138(1): 254-256, 1979

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer. Journal of Proteome Research 15(9): 3441-3448, 2016

BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Research 32(Database Issue): D431-D433, 2004

The MOSART database: linking the SART CORS clinical database to the population-based Massachusetts PELL reproductive public health data system. Maternal and Child Health Journal 18(9): 2167-2178, 2014

Photochemical cross-linking of the Escherichia coli single-stranded DNA-binding protein to oligodeoxynucleotides. Identification of phenylalanine 60 as the site of cross-linking. Journal of Biological Chemistry 259(17): 10850-6, 1984

Protein Interactions Captured by Chemical Cross-linking: Simple Cross-linking Screen Using Sulfo-MBS. Csh Protocols 2007: Pdb.Prot4587, 2007

DNA-protein cross-linking: model systems for pyrimidine-aromatic amino acid cross-linking. Organic Letters 8(4): 681-683, 2006

Physicochemical properties and microstructures of soy protein isolate gels produced using combined cross-linking treatments of microbial transglutaminase and Maillard cross-linking. Food Research International 41(6): 0-605, 2008

Updates on corneal collagen cross-linking: Indications, techniques and clinical outcomes. Journal of Current Ophthalmology 29(4): 235-247, 2017

Protein Interactions Captured by Chemical Cross-linking: One-Step Cross-linking with Formaldehyde. Csh Protocols 2007: Pdb.Prot4634, 2007