RIP is a two step process, that involves the sequential cleavage of membrane proteins by ectodomain shedding and intramembrane proteolysis. This results in the release of protein fragments into the extracellular space and the cytosol, where they contribute to cell-cell communication and serve as putative biomarkers under pathophysiological conditions. RIP is mediated by over 30 different proteases and affects more than 1000 membrane proteins, but for the majority of substrates the responsible protease is unknown. In order to accurately monitor the RIP process on a membrane proteome wide scale, differential quantitation of RIP products within the chosen compartment is needed. For example, when comparing a lysate of a control cell line with a sheddase knockout cell line, peptide ratios for the intracellular domain of the protease substrate may remain the same, but the ratios of peptides mapping to the extracellular region will be dramatically different. The differential analysis therefore results in a more specific and sensitive quantitation, especially if using data that is oversampled, i.e. where the peptide sequence of most proteins is covered to a larger extent. QARIP features a simple and straightforward workflow in order to aid in the evaluation of RIP data, by automatically assigning detected peptides to extracellular, intracellular or transmembrane domains.
Reference: Ivankov D.N., Bogatyreva N.S., Hoenigschmid P., Dislich B., Hogl S., Kuhn P.H., Frishman D., Lichtenthaler S.F. QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis. Nucleic Acids Res. 2013. 41(W1):W459-W464.
QARIP server helps to look at experimental proteomics data and compare them with control conditions. In order to use QARIP it is nessessary to upload your data as a text tab-delimited file (up to 5 Mb). The uploaded file should contain the following fields:
- Protein identifier;
- Peptide sequence;
- Peptide abundance for the control conditions;
- Peptide abundance for the experiment.
The first line of uploaded file should contain the same header information as in the example. After successful uploading, QARIP gives your personal JobID for access to the data. It's nessessary to save it! Then the QARIP will make mapping your proteins to Uniprot, make topology prediction by Phobius, and make simple numerical analysis of peptide abundance in extracellular and intracellular protein parts. Data processing may take up to one hour for larger datasets. And finally, you can have the results using your personal JobID.
The data are kept confidential and are deleted after one week upon last access to the data.
- Protein identifier;
- Peptide sequence;
- Peptide abundance for the control conditions;
- Peptide abundance for the experiment.
The first line of uploaded file should contain the same header information as in the example. After successful uploading, QARIP gives your personal JobID for access to the data. It's nessessary to save it! Then the QARIP will make mapping your proteins to Uniprot, make topology prediction by Phobius, and make simple numerical analysis of peptide abundance in extracellular and intracellular protein parts. Data processing may take up to one hour for larger datasets. And finally, you can have the results using your personal JobID.
The data are kept confidential and are deleted after one week upon last access to the data.
There are two steps in working with the server: