Dataset Information

Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics

ABSTRACT: Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human) Human Gut Metagenome

TISSUE(S): Feces

SUBMITTER: Alessandro Tanca

LAB HEAD: Sergio Uzzau

PROVIDER: PXD049294 | Pride | 2024-05-31

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	HT-methods_plates_120samples.pdResult	Other
	HT-methods_plates_120samples_MasterProteins.xlsx	Xlsx
	HT-methods_plates_120samples_PSMs.xlsx	Xlsx
	HT-methods_plates_120samples_PeptideGroups.xlsx	Xlsx
	LT-methods_tubes_28samples.pdResult	Other

Items per page:

1 - 5 of 157

Publications

Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics.

Tanca Alessandro A Deledda Maria Antonietta MA De Diego Laura L Abbondio Marcello M Uzzau Sergio S

mSystems 20240627 7

The application of fecal metaproteomics to large-scale studies of the gut microbiota requires high-throughput analysis and standardized experimental protocols. Although high-throughput protein cleanup and digestion methods are increasingly used in shotgun proteomics, no studies have yet critically compared such protocols using human fecal samples. In this study, human fecal protein extracts were processed using several different protocols based on three main approaches: filter-aided sample prepa ...[more]

PMID: 38934547

Similar Datasets

Project description:Treatment failures of antibiotic therapy are of major concern and can be caused by a misalignment of the antibiotic susceptibility determined in vitro with the behaviour of the pathogen in the patient. The aim of this study was to investigate the transcriptomic response of the uropathogenic strain E. coli CFT073 to antibiotic treatment in blood stream infection (BSI) models in order to understand and avoid antibiotic therapy failures in urosepsis treatments. Blood stream infection models were established by growing E. coli CFT073 in pooled human serum with and without ciprofloxacin and compared to Iso-sensitest medium. The antibiotic challenge was introduced at mid-logarithmic phase of growth of the organism to depict a clinical scenario . Global gene expression profiling of these conditions was examined using commercial DNA microarrays. The organismâs metabolic genes appeared to be regulated differently in each medium, this indicated that the bacterial growth regulation were different between the models. Bacterial growth in human serum mainly involved regulations of amino acid synthesis/utilisation such as glycine, arginine, thiamine, regulations of fimbrial proteins and bacteriophage genes. When comparing the responses to antibiotic challenge, bacteria grown in the respective medium displayed specific responses to the antibiotic challenge which were not seen in the other media. The common functions of genes that responded to the ciprofloxacin challenge were SOS response, DNA repair, DNA replication, fimbrial genes and bacteriophage initiation. A subset of the bacteriophage genes showed similar responses between the three models. From genes that were differentially regulated, responses observed in the serum model appeared to have the highest fold changes. In this study we established new models to investigate blood stream infections. They have been used to identify previously unknown differences in the molecular response to antibiotic treatment by the uropathogenic E. coli CFT073 depending on the media. These unique responses will help to unravel the complexity of bloodstream infection and can help to improve the antibiotic therapy that is used. A 20 array study using total RNA recovered from bacteria from bacteria that were either grown in human serum or Iso-Sensitest (IST) broth, with and without ciprofloxacin challenge. Arrays were performed in 5 biological replicates from each condition.Upon QC checks, certain biological repeats were excluded due to poor hybridisation results.