Glyc A P

A Comprehensive Glyc osylation A nalysis P latform

Introduction

Cao Weiqian's team from the Biomedical Research Institute of Fudan University, in collaboration with Shanghai Omicsolution Co., Ltd. , published a research paper entitled 'GlycAP, a glycogenic analysis platform for site-specific N-glycation research' https://doi.org/10.1016/j.ijms.2022.116947 in the journal Int J Mass Spectrum. This article introduces a new N-glycoproteome analysis platform called GlycAP in detail. The platform is embedded with different analysis modules, including qualitative analysis, quantitative analysis, functional analysis and clinical analysis, which shortens the distance from the results of mass spectrum search to finding potential biomarkers in different glycopeptides.GlycAP provides users with a relatively complete process analysis platform for glycosylation proteome identification and analysis. It connects the conventional analysis together and directly connects with the search results of the glycopeptide software pGlyco3 and pGlycoQuant, which can simplify the steps used by users and improve the degree of automation of analysis. Even new researchers can conduct complete glycosylation analysis. GlycAP also supports the introduction of new analytical modules and processes, which greatly improves the flexibility of analysis.

Function

Spectrum Identification

Identify glycopeptides with the latest version of pGlyco software

Qualitative analysis

Show the micro-heterogeneity and other properties of your dataset

Quantitative Analysis

Quantify glycopeptides with pGlycoquant

Functional Analysis

Proteomics analysis with GO and KEGG

Clinical Analysis

Disease and prognosis prediction

Databases

Useful databases in glycomics

Relative Websites

Useful platforms in glycomics

Question & Answers

The Q&As about the GAP operation guide

Reference

[1] Kong, S., Gong, P., Zeng, WF. et al. pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level. Nat Commun 13, 7539 (2022). https://doi.org/10.1038/s41467-022-35172-x

[2] Zeng, W.F., Cao, W., et al., Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3. Nature Methods, 2021. 18(12): p. 1515-+

Version

Spectrum identification

For users who want to use our qualitative analysis module, we recommend pGlyco3.0 for spectrum identification. pGlyco3.0 is a free software which is designed for the identification and annotation of intact glycopeptides by using mass spectrometry.

pGlyco3.0: https://github.com/pFindStudio/pGlyco3

For users who want to use our quantitative analysis module, we recommend pGlyco3.0 for spectrum identification and pGlycoQuant for glycopeptide quantitation. pGlycoQuant is a free software which enables intact glycopeptide quantitation. It is compatible with search engines including pGlyco 2.0, pGlyco3, Byonic and MSFragger-Glyco.

pGlycoQuant: http://www.oglyp.org/pglycoquant

Cite us:

Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3. Wen-Feng Zeng, Wei-Qian Cao, Ming-Qi Liu, Si-Min He, Peng-Yuan Yang. Nature methods, 18, 1515–1523, 2021.
pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation. Wei-qian Cao, Si-yuan Kong, Wen-feng Zeng, Peng-yun Gong, Bi-yun Jiang, Xin-hang Hou, Yang Zhang, Huan-huan Zhao, Ming-qi Liu, Xi-hua Qiao, Meng-xi Wu, Guo-quan Yan, Chao Liu, Peng-yuan Yang. doi: https://doi.org/10.1101/2021.11.15.468561