Project description:The data set consist of three different sources. 1) All files with ecoli_* derive from a pure culture of Escherichia coli K-12 (MG1655). 2) All files with SIHUMI_standard_* derive from a mixed culture of 8 bacteria (SIHUMIx) Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Clostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655) and Lactobacillus plantarum (DSMZ 20174). A standard proteomic protocol was used for purification. 3) All files with SIHUMI_small_* derive from the same bacteria culture as second source in contrast a variety of different proteomic protocols were used to enhance enrichment of small (<100 AS) Proteins. The goal of the project was to design a workflow to quickly prioritize novel protein candidates. The workflow was designed to be robust in a meta-omics context and facilitate the integration of transcriptomic and other information on a genomic level. The MS-data from the first source was used to test the workflow under well controlled conditions, namely in pure culture and near complete annotation. The workflow was used with data from the second source to see if good results can be produced in a mixed culture. To enhance the chances of finding novel proteins we incorporated the data from the third source.

2021-09-09 | PXD023243 | Pride

Bacteroides thetaiotaomicron strain:DSMZ 2079

Project description:Bacteroides thetaiotaomicron strain:DSMZ 2079 Genome sequencing and assembly

| PRJNA543750 | ENA

Pleurotus sapidus strain:DSMZ 8266

Project description:Pleurotus sapidus strain:DSMZ 8266 Genome sequencing and assembly

| PRJNA854300 | ENA

Lactiplantibacillus plantarum strain:DSMZ 20174

Project description:Lactiplantibacillus plantarum strain:DSMZ 20174 Genome sequencing and assembly

| PRJNA531377 | ENA

Bifidobacterium saguini strain:DSMZ 23967

Project description:Bifidobacterium saguini strain:DSMZ 23967 Genome sequencing and assembly

| PRJNA688882 | ENA

Rhodoferax antarcticus strain:DSMZ 24876

Project description:Rhodoferax antarcticus strain:DSMZ 24876 Genome sequencing and assembly

| PRJNA356916 | ENA

Blautia producta strain:DSMZ 2950

Project description:Blautia producta strain:DSMZ 2950 Genome sequencing and assembly

| PRJNA531376 | ENA

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