PXD000503

PXD000503 is an original dataset announced via ProteomeXchange.

Title	Time-resolved substrate degradomics
Description	20110318_GluC: Cell culture supernatants from Balb/c 3T3 mouse fibroblasts that had been incubated with the endoproteinase GluC (Staphylococcus aureus protease V8) as test protease for 1, 2, 4, 8, and 16 hours or buffer alone (0, 12, and 16 hours controls) were subjected to 8plex-iTRAQ-TAILS analysis. Labeling scheme: 113: 0h control, 114: 1h, 115: 2h, 116: 4h, 117: 8h, 118: 12h control, 119: 16h, 121: 16h control. 20130214_MMP10: Cell culture supernatants from matrix metalloproteinase (MMP) 10 deficient murine embryonic fibroblasts that had been incubated with recombinant human MMP10 as test protease for 1, 2, 4, 8, and 16 hours or buffer alone (0 and 16 hours controls) were subjected to 8plex-iTRAQ-TAILS analysis. Labeling scheme: 113: 0h control, 114: 1h, 115: 2h, 116: 4h, 117: 8h, 118: 12h, 119: 16h, 121: 16h control.MS data analysis: Mascot Distiller (Matrix Science) was used to extract peak lists from raw files and for merging of corresponding CID/HCD spectra pairs. Peak lists (mgf) were searched by Mascot v2.3 search engine against a mouse UniProtKB database (release 2012_03; 54232 entries), to which reversed decoy sequences as well as sequences for common contaminants and either for GluC or for human MMP10, respectively, had been added and with following parameters: semi-Arg-C for enzyme specificity allowing up to 2 missed cleavages; carbamidomethyl(C), iTRAQ(K) as fixed modifications; acetyl (N-term), iTRAQ(N-term), oxidation(M), and deamidation(NQ) as variable modifications; parent mass error at 10 ppm, fragment mass error at 0.8 Da. For GluC experiments an additional search was performed using the same parameters but with semi-GluC as enzyme and allowing up to 5 missed cleavages. The Trans-Proteomic Pipeline (TPP v4.6, rev 1, Build 201212051643)46 was used to secondary validate Mascot search results and to compile a single peptide list from all peptide fractions obtained from both the pre-pullout and the pullout samples. First, data were processed by PeptideProphet setting the ‘minimum peptide length’ to 1, using ‘accurate mass binning’ and omitting the ‘NTT model’. Next, iProphet was employed for additional validation and for combining PeptideProphet results from multiple searches, and only peptides with an iProphet probability of >=0.9 (corresponding to false discovery rate (decoy) of <1%) were included in subsequent analyses. For relative quantification iTRAQ reporter ion intensities were extracted from mgf files using a modified version of i-Tracker47 with a mass tolerance of 0.1 Da and purity corrections supplied by the iTRAQ manufacturer and assigned to filtered peptides.
HostingRepository	PRIDE
AnnounceDate	2014-08-08
AnnouncementXML	Submission_2014-08-08_01:55:39.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ulrich auf dem Keller
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	deamidated residue; monohydroxylated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap; LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-09 01:49:11	ID requested
1	2013-12-13 03:01:20	announced
1	2013-12-13 03:06:05	announced
2	2014-07-25 01:41:04	announced	Updated project metadata.
⏵ 3	2014-08-08 01:55:40	announced	Updated project metadata.

Schlage P, Egli FE, Nanni P, Wang LW, Kizhakkedathu JN, Apte SS, auf dem Keller U, Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome. Mol Cell Proteomics, 13(2):580-93(2014) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: protease, TAILS, 8plex-iTRAQ, kinetics, MMP

Ulrich auf dem Keller
contact affiliation	Department of Biology
contact email	ulrich.aufdemkeller@biol.ethz.ch
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/2013/12/PXD000503

PRIDE project URI

• PRIDE
  1. PXD000503
     1. Label: PRIDE project
     2. Name: Time-resolved substrate degradomics