PXD007096

PXD007096 is an original dataset announced via ProteomeXchange.

Title	A Tandem Mass Tag (TMT) proteomic analysis during the early phase of experimental pancreatitis
Description	We performed in a rat pancreatitic model a quantitative shotgun proteomic profiling of the soluble and whole membrane fractions from the pancreas during the early phase of cerulein (Cer)-induced AP compared to controls. Three control and three pancreatitic samples from both the soluble and the whole membrane fractions were analysed in two independent TMT6plex experiments. After trypsin digestion and TMT labelling, the peptide mixtures were fractionated into 12 fractions by off-gel electrophoresis. ESI LTQ-OT MS was performed on a LTQ Orbitrap velos equipped with a NanoAcquity system from Waters. MS data were analysed for protein identifications using EasyProt (v2.3) and peak lists were generated into .mgf format with EasyProtConv (CID/HCD merging was used to improve peptide identification and quantification). Searches were conducted against UniProt Swiss-Prot database (UniProtKB release 2014_10 of Oct, 29, 2014), specifying Rattus norvegicus taxonomy. Only proteins with at least two unique peptide sequences and a false discovery rate (FDR) ≤ 1 % were selected for further quantification. Proteins were clustered based on shared peptides indistinguishable by MS. Quantification was conducted using Isobar R package (v.1.9.3.2). We identified 997 proteins, of which 353 were significantly differentially expressed (22, 256 or 55 in both, the soluble or the membrane fractions, respectively).
HostingRepository	PRIDE
AnnounceDate	2018-05-22
AnnouncementXML	Submission_2018-05-22_05:45:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Violeta García-Hernández
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-21 06:22:18	ID requested
⏵ 1	2018-05-22 05:45:51	announced

Garc, í, a-Hern, á, ndez V, S, á, nchez-Bernal C, Schvartz D, Calvo JJ, Sanchez JC, S, á, nchez-Yag, ü, e J, A tandem mass tag (TMT) proteomic analysis during the early phase of experimental pancreatitis reveals new insights in the disease pathogenesis. J Proteomics, 181():190-200(2018) [pubmed]

curator keyword: Biological

submitter keyword: Acute pancreatitis, cerulein, rat pancreas, subcellular fractions, TMT (Tandem Mass Tags)

Jesús Sánchez-Yagüe
contact affiliation	Department of Biochemistry and Molecular Biology, University of Salamanca (Salamanca, Spain). Instituto de Investigación Biomédica de Salamanca (IBSAL) (Salamanca, Spain).
contact email	sanyaj@usal.es
lab head
Violeta García-Hernández
contact affiliation	University of Salamanca. IBSAL.
contact email	violeta_gh@usal.es
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/2018/05/PXD007096

PRIDE project URI

• PRIDE
  1. PXD007096
     1. Label: PRIDE project
     2. Name: A Tandem Mass Tag (TMT) proteomic analysis during the early phase of experimental pancreatitis