Proteomics

Dataset Information

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Effecst of metformin on the human gut micorbiome

ABSTRACT: To test the effects of metformin on the human gut micorbiome, we fist collected human stool samples. We processed the samples in vitro culturing under anaerobic condition for 24 hours using the rapidAIM assay and either and cultured them with metformin, or DMSO as a control. We know that metformin can alter the human gut microbiome and were interested in better analyzing which functional proceses were altered.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Human Gut Metagenome

SUBMITTER: Caitlin Simopoulos  

LAB HEAD: Daniel Figeys

PROVIDER: PXD016427 | Pride | 2021-03-16

REPOSITORIES: Pride

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Dataset's files

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Leyuan_20190531_RapidAIM_mp_vs_mg_CTRL_1.raw Raw
Leyuan_20190531_RapidAIM_mp_vs_mg_CTRL_2.raw Raw
Leyuan_20190531_RapidAIM_mp_vs_mg_CTRL_3.raw Raw
Leyuan_20190531_RapidAIM_mp_vs_mg_CTRL_4.raw Raw
Leyuan_20190531_RapidAIM_mp_vs_mg_CTRL_5.raw Raw
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Publications

pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies.

Simopoulos Caitlin M A CMA   Ning Zhibin Z   Zhang Xu X   Li Leyuan L   Walker Krystal K   Lavallée-Adam Mathieu M   Figeys Daniel D  

Bioinformatics (Oxford, England) 20200801 14

<h4>Motivation</h4>Enzymatic digestion of proteins before mass spectrometry analysis is a key process in metaproteomic workflows. Canonical metaproteomic data processing pipelines typically involve matching spectra produced by the mass spectrometer to a theoretical spectra database, followed by matching the identified peptides back to parent-proteins. However, the nature of enzymatic digestion produces peptides that can be found in multiple proteins due to conservation or chance, presenting diff  ...[more]

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