Project PXD004366

PRIDE Assigned Tags:
Biological Dataset Biomedical Dataset

Summary

Title

N-glycoproteomics of induced pluripotent stem cells, embryonic stem cells, and parental cells

Description

We tried to understand the N-glycoproteom molecular differences between induced pluripotent stem cells and embryonic stem cells. This is important to improve the reprograming process and induced pluripotency in the context of post translational protein N-glycosylation

Sample Processing Protocol

Hydrazide chemistry has been used to enrich the N-glycopeptides.

Data Processing Protocol

We used MaxQuant tool for dataprocssesing. We used enzyme trypsin, two missed cleavages, peptide length of seven amino acids, false discovery rate (FDR) of 0.01, variable modifications of oxidation (M) and acetylation (protein N-terminal), and fixed modification of carbamidomethyl (C) as search parameters. In addition, we set the variable modification deamidation (NQ) for the N-glycopeptides identification.

Contact

Putty-Reddy Sudhir, GRC
Prof. Chung-Hsuan Chen, Distinguished Research Fellow & Director Genomics Research Center Academia Sinica Taipei 115, Taiwan ( lab head )

Submission Date

20/06/2016

Publication Date

23/12/2016

Tissue

Not available

Instrument

LTQ Orbitrap

Software

Not available

Modification

deamidated residue

Quantification

Label free

Experiment Type

Shotgun proteomics

Publication

    Sudhir PR, Kumari MP, Hsu WT, Chen CH, Kuo HC, Chen CH. Integrative omics connects N-glycoproteome-wide alterations with pathways and regulatory events in induced pluripotent stem cells. Sci Rep. 2016 Nov 3;6:36109 PubMed: 27808266