PXD004218 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Direct in-gel profiling of protease specificity (DIPPS) |
Description | Determination of protease specificity is of crucial importance for understanding protease function. We have developed the first gel-based label-free proteomic approach (DIPPS) that enables quick and reliable determination of protease cleavage specificities under large variety of experimental conditions. The methodology is based on in-gel digestion of the gel-separated proteome with the studied protease, enrichment of cleaved peptides by gel extraction and subsequent mass spectrometry analysis combined with a length-limited unspecific database search. We applied the methodology to profile ten proteases ranging from highly specific (trypsin, endoproteinase GluC, caspase-7 and legumain) to broadly specific (matrix-metalloproteinase-3, thermolysin and cathepsins K, L, S and V). Using DIPPS, we were able to perform specificity profiling of thermolysin at its optimal temperature of 75C, which confirmed the applicability of the method to extreme experimental conditions. Moreover, DIPPS enabled the first global specificity profiling of legumain at pH as low as 4.0, which revealed a pH-dependent change in the specificity of this protease, further supporting its broad applicability. |
HostingRepository | PRIDE |
AnnounceDate | 2017-07-06 |
AnnouncementXML | Submission_2017-08-09_02:48:22.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Marko Fonovic |
SpeciesList | scientific name: Aeropyrum pernix; NCBI TaxID: 56636; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2016-05-24 08:28:04 | ID requested | |
1 | 2017-07-06 05:44:57 | announced | |
⏵ 2 | 2017-08-09 02:48:23 | announced | Updated publication reference for PubMed record(s): 28733325. |
Publication List
Vidmar R, Vizovi, š, ek M, Turk D, Turk B, Fonovi, ć M, Protease cleavage site fingerprinting by label-free in-gel degradomics reveals pH-dependent specificity switch of legumain. EMBO J, 36(16):2455-2465(2017) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: cathepsin, legumain, specificity profiling, degradomics, protease |
Contact List
prof. dr. Marko Fonovic |
contact affiliation | Department of Biochemistry and Molecular and Structural Bilogy, Jozef Stefan Institute, Ljubljana, Slovenia |
contact email | marko.fonovic@ijs.si |
lab head | |
Marko Fonovic |
contact affiliation | Jozef Stefan Institute |
contact email | marko.fonovic@ijs.si |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD004218
- Label: PRIDE project
- Name: Direct in-gel profiling of protease specificity (DIPPS)