Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Streamlined TMT labeling workflow for proteomics and metaproteomics

ABSTRACT: This study established a streamlined TMT labeling workflow that is readily compatible with high throughput proteomics and metaproteomics sample preparation. The method was then evaluated using two different sample types, microbiome and intestinal Caco-2 cell line, with TMT11plex mix reagents.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive

ORGANISM(S): Homo Sapiens (human) Metagenome

TISSUE(S): Cell Culture

SUBMITTER: Xu Zhang

LAB HEAD: Xu Zhang

PROVIDER: PXD034791 | Pride | 2023-02-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis.

Creskey Marybeth M Li Leyuan L Ning Zhibin Z Fekete Emily Ef EE Mayne Janice J Walker Krystal K Ampaw Anna A Ben Robert R Zhang Xu X Figeys Daniel D

Proteomics 20230113 21-22

Multiplexed quantitative proteomics using tandem mass tag (TMT) is increasingly used in -omic study of complex samples. While TMT-based proteomics has the advantages of the higher quantitative accuracy, fewer missing values, and reduced instrument analysis time, it is limited by the additional reagent cost. In addition, current TMT labeling workflows involve repeated small volume pipetting of reagents in volatile solvents, which may increase the sample-to-sample variations and is not readily sui ...[more]

PMID: 36528842

Similar Datasets

Streamlined TMT labeling workflow for proteomics and metaproteomics

Project description:This study established a streamlined TMT labeling workflow that is readily compatible with high throughput proteomics and metaproteomics sample preparation. The method was then evaluated using two different sample types, microbiome and intestinal Caco-2 cell line, with TMT11plex mix reagents.

2023-02-07 | PXD034936 | Pride

Microbiota biobanking using ice recrystalization inhibitor

Project description:This study use different ice recrystalization inhibitors (IRIs) for better storing live microbiota. We evaluated whether the addition of IRIs can improve the cultivibility of microbiome and maintain their resposnes to prebiotic kestose. Frozen or fresh microbiota were cultured with or without kestose for 24 hours, and microbiota samples were collected for metaproteomics analysis.

2023-02-07 | PXD034979 | Pride

Effects of 5 drugs on the human gut microbiome.

Project description:We processed a human stool sample and cultured the processed microbiome in vitro under anaerobic condition for 48 hours using the rapidAIM assay. The microbiome was treated with either azathioprine, ciprofolxacin, diclofenac, nicatidine, paracetamol or control DMSO. Each drug was used at three different concentrations. We compared these results to those acquired using MS1-only data.

2022-07-29 | PXD024845 | Pride

Effect of Edurans secretome of human microbiome

Project description:A rapid ex vivo microbiome assay and metaproteomics approach was used for evaluating the impacts of E. durans derived secretome on a human gut microbiome cultured in vitro.

2024-01-31 | PXD040751 | Pride

Evaluate gut microbiome biobanking

Project description:A rapid ex vivo microbiome assay and metaproteomics approach was used for rapid evaluation of the cultivability of bio-banked live microbiota, which shows minimal detrimental influences of long-term freezing in deoxygenated glycerol buffer on the cultivability of fecal microbiota.

2022-02-16 | PXD028857 | Pride

Functional effects of sweeteners on ex vivo human gut microbiome

Project description:We systematically investigated the responses of five human gut microbiomes to 21 common sweeteners, using an approach combining high-throughput ex vivo microbiome culturing and metaproteomics to quantify functional changes in different taxa. Hierarchical clustering based on metaproteomic responses of individual microbiomes resulted in two clusters. The first cluster was composed of non-caloric artificial sweeteners (NAS) and two sugar alcohols with shorter carbon backbones (4-5 carbon atoms), and the second cluster was composed of sugar alcohols with longer carbon backbones. The metaproteomic functional responses of the second cluster were similar to the prebiotic fructooligosaccharides and kestose, indicating that these sugar alcohol-type sweeteners have potential prebiotic functions.

2022-06-23 | PXD030458 | Pride

Effects of BAFASAL on human microbiome

Project description:This project aims to examinw the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

2022-02-17 | PXD027172 | Pride

Specific Gut Microbial Enzymes Drive Colitis Promotion by Triclosan

Project description:Triclosan (TCS), an antimicrobial agent in thousands of consumer products, is a risk factor for colitis and colitis-associated colorectal cancer. While the intestinal toxicities of TCS require the presence of gut microbiota, the molecular mechanisms involved have not been defined. Here we show that intestinal commensal microbes mediate metabolic activation of TCS in the colon and drive its gut toxicology. Using a range of in vitro, ex vivo, and in vivo approaches, we identify specific microbial β-glucuronidase (GUS) enzymes involved and pinpoint molecular motifs required to metabolically activate TCS in the gut. Finally, we show that targeted inhibition of bacterial GUS enzymes abolishes the colitis-promoting effects of TCS, supporting the essential roles of specific microbial proteins in TCS toxicity. Our results define a mechanism by which intestinal microbes cause the gut toxicity of environmental chemicals and suggest a therapeutic approach to alleviate colitis and associated diseases.

2021-11-04 | PXD025887 | Pride

Deciphering Differential Gut Bacterial Drug Metabolism with Activity-Based Protein Profiling

Project description:Gut bacterial β-glucuronidases (GUS) promote the toxic side effects of therapeutics by reactivating drugs from their inactive glucuronide conjugates. It is increasingly clear that the interindividual variability of bacterial GUS-producing species in the gut microbiota contributes to differential drug responses. Indeed, the anticancer drug irinotecan exhibits variable clinical toxicity outcomes that have been linked to interindividual differences in the composition of the gut microbiota. However, identification of the specific GUS enzymes responsible for drug metabolism in the context of the complexity of the human fecal microbiota has not been achieved. Here we pinpoint the specific bacterial GUS enzymes that reactivate SN-38, the active metabolite of irinotecan, from complex human fecal microbiota samples with activity-based protein profiling (ABPP). We identify and quantify gut bacterial GUS enzymes from human feces with ABPP-enabled proteomics and then integrate this information with ex vivo kinetics to reveal the specific GUS enzymes responsible for the reactivation of SN-38. The same ABPP approach also reveals the molecular basis for differential gut bacterial GUS inhibition between human fecal samples. Taken together, this work provides an unprecedented pipeline to identify the specific bacterial GUS enzymes responsible for drug-induced GI toxicity from the complexity of human feces, which may serve as highly precise biomarkers of clinical outcomes for irinotecan and other therapeutics.

2019-12-03 | PXD014864 | Pride

Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics

Project description:A differential lysis approach was developed with different strength of lysis buffers (urea and/or sodium dodecyl sulfate) and applied on human stool samples to separate different microbial species to increase the depth of metaproteomic measurements. We showed that the lysates dominating by proteins from Gram-positive (G+) or negative bacteria (G-) can be achieved by differential lysis

2023-03-27 | PXD016787 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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