PXD010279-2

PXD010279 is an original dataset announced via ProteomeXchange.

Title	A metabolic labeling strategy for relative protein quantification in Clostridioides difficile
Description	Clostridioides difficile (formerly Clostridium difficile) is a Gram-positive, spore-forming pathogen which cases drug-induced Clostridioides difficile-associated diseases in hospitals worldwide. A detailed analysis of the proteome may provide new targets for drug development or therapy strategies to combat this pathogen. So far, quantitative proteome analyses could only be carried out by label-free or chemical labeling methods. However, the application of metabolic labeling would allow for accurate quantification of significant differences, even in the case of very small changes. Additionally, it would be possible to perform bias free studies of the membrane or surface proteome which require elaborated preparations and are therefore prone to higher standard deviations during the quantification. Up to now, the implementation of metabolic labeling strategies of C. difficile was hampered by the very specific metabolic requirements of this anaerobic pathogen. To solve this problem, media were evaluated and the cultivation procedure with 15N labeled media for the C. difficile 630Δerm strain was optimized to gain a high incorporation rate. In the following proof-of-principle experiment, the cytosolic sub-proteomes of C. difficile cells of three different cultivation media and two growth phases were analyzed resulting in reproducible data which are shown in detail.
HostingRepository	PRIDE
AnnounceDate	2018-10-25
AnnouncementXML	Submission_2018-11-21_08:13:46.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anke Trautwein-Schult
SpeciesList	scientific name: Peptoclostridium difficile (strain 630) (Clostridium difficile); NCBI TaxID: 272563;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-02 01:42:50	ID requested
1	2018-10-25 02:44:41	announced
⏵ 2	2018-11-21 08:13:47	announced	Updated publication reference for PubMed record(s): 30386308.
3	2024-10-22 04:46:42	announced	2024-10-22: Updated project metadata.

Trautwein-Schult A, Maa, ß S, Plate K, Otto A, Becher D, . Front Microbiol, 9():2371(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: Clostridioides difficile, metabolic labeling, relative protein quantification, proteomics, mass spectrometry

Prof. Dr. Dörte Becher
contact affiliation	Department of Microbial Proteomics, Institute for Microbiology, University of Greifswald, Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Anke Trautwein-Schult
contact affiliation	University of Greifswald
contact email	anke.trautwein-schult@uni-greifswald.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/2018/10/PXD010279

PRIDE project URI

• PRIDE
  1. PXD010279
     1. Label: PRIDE project
     2. Name: A metabolic labeling strategy for relative protein quantification in Clostridioides difficile