Proteomics

Dataset Information

0

Human stomach LC-MSMS China Human Proteome Project


ABSTRACT: With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptide characterization, where peptide backbones and N-glycan moieties are selectively fragmented at high and low NCEs, respectively. Initially, a dependent setting of a central value plus minus a variation is available to the users to set up NCEs, and the combination of 30±10% to give the energies 20%/30%/40% has been mostly adopted in the literature. With the recent availability of independent NCE setup, we found that the combination of 20%/30%/30% is better than 20%/30%/40%; in the analysis of complex intact N-glycopeptides enriched from gastric cancer tissues, total IDs with spectrum-level FDR≤1%, site-specific IDs with site-determining fragment ions and structure-specific IDs with structure-diagnostic fragment ions were increased by 42% (4,767->6,746), 57% (599->942), and 97% (1771->3495), respectively. This finding will benefit all the coming N-glycoproteomics studies using HCD as the dissociation method.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Stomach

DISEASE(S): Stomach Cancer

SUBMITTER: Yue Wang  

LAB HEAD: Zhixin Tian

PROVIDER: PXD016865 | Pride | 2020-05-11

REPOSITORIES: Pride

Dataset's files

Source:

Similar Datasets

2023-12-30 | PXD036101 | Pride
2023-07-04 | PXD036095 | Pride
2021-11-03 | PXD022896 | Pride
2020-02-21 | PXD013836 | Pride
2020-10-05 | PXD018506 | Pride
2024-01-26 | PXD039247 | Pride
2022-02-17 | PXD025886 | Pride
2022-10-14 | PXD032149 | Pride
2020-05-13 | PXD013340 | Pride
2022-04-04 | PXD030288 | Pride