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QARIP: A web server for quantitative proteomic analysis of regulated intramembrane proteolysis.
Nucleic Acids Res. 41, W459-W464 (2013)
Regulated intramembrane proteolysis (RIP) is a critical mechanism for intercellular communication and regulates the function of membrane proteins through sequential proteolysis. RIP typically starts with ectodomain shedding of membrane proteins by extracellular membrane-bound proteases followed by intramembrane proteolysis of the resulting membrane-tethered fragment. However, for the majority of RIP proteases the corresponding substrates and thus, their functions, remain unknown. Proteome-wide identification of RIP protease substrates is possible by mass spectrometry-based quantitative comparison of RIP substrates or their cleavage products between different biological states. However, this requires quantification of peptides from only the ectodomain or cytoplasmic domain. Current analysis software does not allow matching peptides to either domain. Here we present the QARIP (Quantitative Analysis of Regulated Intramembrane Proteolysis) web server which matches identified peptides to the protein transmembrane topology. QARIP allows determination of quantitative ratios separately for the topological domains (cytoplasmic, ectodomain) of a given protein and is thus a powerful tool for quality control, improvement of quantitative ratios and identification of novel substrates in proteomic RIP datasets. To our knowledge, the QARIP web server is the first tool directly addressing the phenomenon of RIP. The web server is available at http://webclu.bio.wzw.tum.de/qarip/. This website is free and open to all users and there is no login requirement.
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8.278
2.341
16
20
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Mass-spectrometry ; Peptide ; Identification ; Quantification ; Annotation ; Lessons
Language
english
Publication Year
2013
HGF-reported in Year
2013
ISSN (print) / ISBN
0305-1048
e-ISSN
1362-4962
Journal
Nucleic Acids Research
Quellenangaben
Volume: 41,
Issue: W1,
Pages: W459-W464
Publisher
Oxford University Press
Reviewing status
Peer reviewed
POF-Topic(s)
30505 - New Technologies for Biomedical Discoveries
Research field(s)
Enabling and Novel Technologies
PSP Element(s)
G-503700-001
PubMed ID
23729472
WOS ID
WOS:000323603200073
Erfassungsdatum
2013-09-20