Project PXD010691

PRIDE Assigned Tags:
Biological Dataset
Dataset Belongs to:
Liver (B/D-HPP)

Summary

Title

PLASMA PROTEOMIC ANALYSIS OF RARE BMI-DISCORDANT MONOZYGOTIC TWIN PAIRS

Description

The aim of the current study is to establish the effect of excess body wiehgt and liver fat on plasma proteomic profile without interference from genetic variation. Label-free proteomics (HDMSE) was performed on plasma samples of young healthy monozygotic twins who were discordant for BMI. the twins were further subdivided into groups of liver fat discordant and liver fat concordant to see the efefct fo liver fat on plasma proteomic signature.

Sample Processing Protocol

Plasma samples from twnety six twin pairs were collected and top 12 high-abundant plasma proteins were depleted by immunoaffinity spin columns. Equal amount of protein was dried and dissolved in 6M urea. The total proteins were reduced, alkylated and trypsin digested. Then peptides were cleaned with Pierce C18 (Thermofisher) according to manufacturer’s protocol, dried and dissolved to 0.1% formic acid in water. The tryptic peptide mixture, totalling 1.4 µg peptide, was analysed by Waters Synapt G2-Si, coupled to the nano-Acquity UPLC system.

Data Processing Protocol

The raw data were processed using Progenesis QI for Proteomics software (v2, Nonlinear Dynamics), and matched against the Uniprot FASTA sequences. Search parameters variations (from default settings) were: fixed at cysteine (carbamidomethyl) and variable in methionine (oxidation), trypsin cleavage with 2 missed cleavages. False discovery rate was set to 4%. Protein identification required 2 unique peptides, and the parsimony principle was used to group peptides into protein categories. All peptide Ids where the mass error was more than 10 ppm were deleted.

Contact

Sakari Joenväärä, Helsinki University
Risto Renkonen, Transplantation laboratory, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland ( lab head )

Submission Date

06/08/2018

Publication Date

01/02/2019

Instrument

Synapt MS

Software

Not available

Quantification

Not available

Experiment Type

HDMSE

Publication

    Sahebekhtiari N, Saraswat M, Joenväärä S, Jokinen R, Lovric A, Kaye S, Mardinoglu A, Rissanen A, Kaprio J, Renkonen R, Pietiläinen KH. Plasma Proteomics Analysis Reveals Dysregulation of Complement Proteins and Inflammation in Acquired Obesity - A Study on Rare Bmi-Discordant Monozygotic Twin Pairs. Proteomics Clin Appl. 2019:e1800173 PubMed: 30688043