PXD013979

PXD013979 is an original dataset announced via ProteomeXchange.

Title	Rapid and culture free identification of Francisella in hare carcasses by high-resolution mass spectrometry
Description	Zoonotic pathogens that can be transmitted via food to humans have a high potential for large-scale emergencies, comprising severe effects on public health, critical infrastructures, and the economy. In this context, the development of laboratory methods to rapidly detect zoonotic bacteria in the food supply chain, including high-resolution mass spectrometry are needed. In this work, an optimized sample preparation method for liquid chromatography-mass spectrometry (LC-MS) based proteome profiling was established for Francisella isolates and a cluster analysis, as well as a phylogenetic tree, was calculated to shed light on evolutionary relationships. Furthermore, this method was applied to tissues of infected hare carcasses from Germany. Even though the non-informative data outnumbered by a manifold the information of the zoonotic pathogen in the resulting proteome profiles, the standardized evaluation of MS data within an established automated analysis pipeline identified F. tularensis and thus is in principle an applicable method to monitor food supply chains.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:08:06.277.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Natalie Witt
SpeciesList	scientific name: Francisella hispaniensis; NCBI TaxID: 622488; scientific name: Francisella tularensis subsp. mediasiatica; NCBI TaxID: 135248; scientific name: Francisella philomiragia; NCBI TaxID: 28110; scientific name: Francisella tularensis subsp. holarctica; NCBI TaxID: 119857; scientific name: Francisella tularensis subsp. tularensis; NCBI TaxID: 119856; scientific name: Francisella tularensis subsp. novicida; NCBI TaxID: 264; scientific name: Lepus europaeus; NCBI TaxID: 9983;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-23 03:09:32	ID requested
1	2020-06-30 04:29:01	announced
⏵ 2	2024-10-22 05:08:06	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biomedical

submitter keyword: proteome profiling, detection of pathogens, high-resolution mass spectrometry, phylogenetic analysis,Francisella tularensis

David Meierhofer
contact affiliation	Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility
contact email	Meierhof@molgen.mpg.de
lab head
Natalie Witt
contact affiliation	Max Planck Institute for Molecular Genetics
contact email	witt_n@molgen.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD013979

PRIDE project URI

• PRIDE
  1. PXD013979
     1. Label: PRIDE project
     2. Name: Rapid and culture free identification of Francisella in hare carcasses by high-resolution mass spectrometry