PXD008242

PXD008242 is an original dataset announced via ProteomeXchange.

Title	‘One-pot’ sample processing method for proteome-wide analysis of microbial cells and spores
Description	Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles. The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead-beating in 6M urea under reductive conditions. The heterogeneous mixture was then double-digested with LysC and trypsin. Next, the peptide mixture was pre-fractionated with Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) followed by reverse phase LC-FT-MS analysis of the fractions. ‘One-pot’ method is a simple, robust method that yields identification of >1000 proteins with high confidence, across all spore layers from Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile. This method can be employed for proteome-wide analysis of non-spore-forming as well as spore-forming pathogens. Analysis of spore protein profile will help to understand the sporulation and germination processes and to distinguish immunogenic protein markers.
HostingRepository	PRIDE
AnnounceDate	2018-07-05
AnnouncementXML	Submission_2018-07-05_10:23:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bhagyashree Swarge
SpeciesList	scientific name: Bacillus subtilis PY79; NCBI TaxID: 1415167; scientific name: Bacillus cereus (strain ATCC 14579 / DSM 31); NCBI TaxID: 226900; scientific name: Peptoclostridium difficile (strain 630) (Clostridium difficile); NCBI TaxID: 272563;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	apex ultra

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-20 05:39:02	ID requested
⏵ 1	2018-07-05 10:23:03	announced

Swarge BN, Roseboom W, Zheng L, Abhyankar WR, Brul S, de Koster CG, de Koning LJ, "One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores. Proteomics Clin Appl, 12(5):e1700169(2018) [pubmed]

curator keyword: Technical, Biomedical

submitter keyword: Mass spectrometry, One-pot method, Proteomics, Spores, ZIC-HILIC

Prof. Dr. Chris G. De Koster
contact affiliation	Department of Mass Spectrometry of Bio-Macromolecules, Swammerdam Institue for Life Sciences, University of Amsterdam, The Netherlands.
contact email	C.G.deKoster@uva.nl
lab head
Bhagyashree Swarge
contact affiliation	University of Amsterdam
contact email	b.n.swarge@uva.nl
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/2018/07/PXD008242

PRIDE project URI

• PRIDE
  1. PXD008242
     1. Label: PRIDE project
     2. Name: ‘One-pot’ sample processing method for proteome-wide analysis of microbial cells and spores