A Tandem Mass Tag (TMT) proteomic analysis during the early phase of experimental pancreatitis

ABSTRACT: 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).

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Pancreas

DISEASE(S): Acute Pancreatitis

SUBMITTER: Violeta García-Hernández  

LAB HEAD: Jesús Sánchez-Yagüe

PROVIDER: PXD007096 | Pride | 2018-05-22

REPOSITORIES: Pride