PXD004218-1

PXD004218 is an original dataset announced via ProteomeXchange.

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 75C, 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_2017-07-06_05:44:56.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

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.

Dataset with its publication pending

curator keyword: Technical

submitter keyword: cathepsin, legumain, specificity profiling, degradomics, protease

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/07/PXD004218

PRIDE project URI

• PRIDE
  1. PXD004218
     1. Label: PRIDE project
     2. Name: Direct in-gel profiling of protease specificity (DIPPS)