Browse
Submit Data
Databases
API
Help

Dataset Information

318 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human Fecal Gut Microbiome proteomics

ABSTRACT: 5 human fecal gut samples, collected and prepared for standard MudPIT data collection from healthy volunteers, searched with the ComPIL database. x3 replicates each

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Human Metagenome

SUBMITTER: Greg Stupp

LAB HEAD: Dennis Wolan

PROVIDER: PXD003907 | Pride | 2016-08-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	071414_ComPIL.fasta.gz	Fasta.gz
	081715_H1_velos1_FTMS_MS2_hcd35_01.ms2	Other
	081715_H1_velos1_FTMS_MS2_hcd35_01.raw	Raw
	081715_H1_velos1_FTMS_MS2_hcd35_01.sqt	Other
	081715_H1_velos1_FTMS_MS2_hcd35_02.ms2	Other

Items per page:

1 - 5 of 713

Publications

A comprehensive and scalable database search system for metaproteomics.

Chatterjee Sandip S Stupp Gregory S GS Park Sung Kyu Robin SK Ducom Jean-Christophe JC Yates John R JR Su Andrew I AI Wolan Dennis W DW

BMC genomics 20160816 1

<h4>Background</h4>Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metapr ...[more]

PMID: 27528457

Similar Datasets

HEK293 searched with UniProt Human and ComPIL

Project description:HEK293 proteome searched with UniProt Human and ComPIL

2016-05-25 | PXD003896 | Pride

Morphine treatment induces distinct changes in the gut microbiome at day 3 post treatment

Project description:Opioids such as morphine have many beneficial properties as analgesics, however, opioids may induce multiple adverse gastrointestinal symptoms. We have recently demonstrated that morphine treatment results in significant disruption in gut barrier function leading to increased translocation of gut commensal bacteria. However, it is unclear how opioids modulate the gut homeostasis. By using a mouse model of morphine treatment, we studied effects of morphine treatment on gut microbiome. We characterized phylogenetic profiles of gut microbes, and found a significant shift in the gut microbiome and increase of pathogenic bacteria following morphine treatment when compared to placebo. In the present study, wild type mice (C57BL/6J) were implanted with placebo, morphine pellets subcutaneously. Fecal matter were taken for bacterial 16s rDNA sequencing analysis at day 3 post treatment. A scatter plot based on an unweighted UniFrac distance matrics obtained from the sequences at OTU level with 97% similarity showed a distinct clustering of the community composition between the morphine and placebo treated groups. By using the chao1 index to evaluate alpha diversity (that is diversity within a group) and using unweighted UniFrac distance to evaluate beta diversity (that is diversity between groups, comparing microbial community based on compositional structures), we found that morphine treatment results in a significant decrease in alpha diversity and shift in fecal microbiome at day 3 post treatment compared to placebo treatment. Taxonomical analysis showed that morphine treatment results in a significant increase of potential pathogenic bacteria. Our study shed light on effects of morphine on the gut microbiome, and its role in the gut homeostasis.

2018-04-16 | E-MTAB-5546 | biostudies-arrayexpress

Morphine treatment leads to temporal modulation of the gut microbiome

Project description:Opioid analgesics are frequently prescribed in the United States and worldwide. However, serious side effects such as addiction, immunosuppression and gastrointestinal symptoms limit long term use. In the current study using a chronic morphine-murine model a longitudinal approach was undertaken to investigate the role of morphine modulation of gut microbiome as a mechanism contributing to the negative consequences associated with opioids use. The results revealed a significant shift in the gut microbiome and metabolome within 24 hours following morphine treatment when compared to placebo. Morphine induced gut microbial dysbiosis exhibited distinct characteristic signatures profiles including significant increase in communities associated with pathogenic function, decrease in communities associated with stress tolerance. Collectively, these results reveal opioids-induced distinct alteration of gut microbiome, may contribute to opioids-induced pathogenesis. Therapeutics directed at these targets may prolong the efficacy long term opioid use with fewer side effects.

2018-04-16 | E-MTAB-5550 | biostudies-arrayexpress

EBIO does not induce cardiomyogenesis in human pluripotent stem cells but modulates cardiac subtype enrichment by lineage-selective survival

Project description:Human embryonic stem cell (HES3) aggregates were differentiated into cardiomyocytes using biphasic WNT pathway modulation (CHIR99021 and IWP2) in 20mL scale using agitated Erlenmeyer Flask. On day 6 of differentiation, cells were treated with 1mM 1-EBIO or solvent control (DMSO) for 10 days.

2017-01-04 | E-MTAB-5192 | biostudies-arrayexpress

Quantitative metaproteomics and activity-based probe enrichment on fecal samples from a mouse model of inflammatory bowel disease

Project description:Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across the two mouse cohorts, as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control; thereby, limiting genetic and environmental variables that influence microbiome composition.

2017-01-16 | PXD005667 | Pride

Spectral entropy as a measure of the metaproteome complexity

Project description:The diversity and complexity of the microbiome's genomic landscape are not always mirrored in its proteomic profile. Despite the anticipated proteomic diversity, observed complexities of microbiome sample are often lower than expected. Two main factors contribute to this discrepancy: limitations in mass spectrometry's detection sensitivity and bioinformatics challenges in metaproteomics identification. This study introduces a novel approach to evaluating sample complexity directly at the full mass spectrum (MS1) level rather than relying on peptide identifications. When analyzing under identical mass spectrometry conditions, microbiome samples displayed significantly higher complexity, as evidenced by the spectral entropy and peptide candidate entropy, compared to single-species samples. The research provides solid evidence for the complexity of microbiome in proteomics indicating the optimization potential of the bioinformatics workflow.

2024-05-27 | PXD050781 | Pride

Stool-derived 16s rRNA V4 sequencing from intestinal-epithelium-LSD1-cKO mice against WT controls (both at 2-month-old and P14 timepoints)

Project description:Villin-Cre+ Lsd1fl/fl (cKO) mice display an immature intestinal epithelium characterized by an incomplete differentiation of enterocytes and secretory lineages, reduced number of goblet cells and a complete loss of Paneth cells. This experiment aims to elucidate the differences in stool microbial composition derived from WT (Villin-Cre- Lsd1fl/fl) and cKO mice both in adult (2-month-old) and neonatal (14 days postpartum P14) stages. Different timepoints are crucial to understand the role of intestinal maturation in microbiome composition since said maturation is dependent on time-dependent external cues happening at P14-21 (weaning and transition from milk to solid foods).

2023-10-31 | E-MTAB-12489 | biostudies-arrayexpress

Extracellular vesicle fibrinogen induces encephalitogenic CD8+ T cells in a mouse model of multiple sclerosis

Project description:Extracellular vesicles isolated from murine and human patient blood plasma was subjected to proteomic analysis to determine the EV proteome in healthy, non-disease murine and human samples and during disease.

2019-09-27 | PXD013630 | Pride

Stool-derived 16s rRNA V4 sequencing from inducible intestinal-epithelium-LSD1-cKO mice (Villin-CreERT2+ Lsd1fl/fl (icKO)) against WT (Villin-CreERT2+ Lsd1fl/+ (icKO)) controls (before and 1-6 weeks after tamoxifen treatment)

Project description:Upon tamoxifen induced recombination, Villin-CreERT2+ Lsd1fl/fl (icKO) mice develop an immature intestinal epithelium characterized by an incomplete differentiation of enterocytes and secretory lineages, reduced number of goblet cells and a complete loss of Paneth cells. The main goal of this experiment was to test whether maturation of intestinal epithelium affects microbiota establishment and development. In addition, this loss of differentiated cell types after Lsd1 recombination is gradual and dependent on renewal times of each specific cell type (i.e. enterocytes take less than a week to be fully replenished while Paneth cells cycle around every 4 weeks). Hence by collecting stool from the same mouse at different time points after tamoxifen induced recombination a relationship between loss of particular cell types and changes in bacterial populations can be established. In addition, we wanted to test whether maturation of intestinal epithelium affects microbiota establishment and development

2023-10-31 | E-MTAB-12626 | biostudies-arrayexpress

Triflic acid-treatment enables LC-MS/MS analysis of insoluble bacterial biomass

Project description:Established bacterial proteome sample preparations, including sonication and bead beating, leave insoluble carbohydrate-rich cell envelope pellets with an abundance of vital proteins often overlooked or missed in LC-MS/MS analyses. Triflic acid selectively removes glycans and we demonstrate that in comparison to sonication alone, incubation of whole bacterial cells as well as post-sonication insoluble pellets yields membrane and cell envelope-associated proteins for LC-MS/MS detection. We provide a detailed side-by-side comparison of triflic acid and sonication preparations for Gram- (Pseudomonas aeruginosa), Gram+ (Bacillus subtilis), and a complex bacterial human distal gut microbiome sample. Further, human Jurkat cells that lack a peptidoglycan and are readily solubilized by established methods, reveal only subtle differences in measurable proteins by LC-MS/MS between sonication and triflic acid preparations. Critically, we show that our new triflic acid-based proteome preparation method is broadly applicable and greatly improves our ability to detect and quantitate bacterial cell envelope proteins.

2019-01-29 | PXD009004 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data