PXD003667

PXD003667 is an original dataset announced via ProteomeXchange.

Title	Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH-LC/MS/MS analysis of planktonic and sessile cells
Description	Early and mature biofilm formation in the extremely halophilic euryarchaeon Halobacterium salinarum strain R1 was characterized by SWATH-LC/MS/MS. Using a simple surfactant-assisted protein solubilization protocol and one-dimensional ultrahigh performance nanoflow chromatography on the front end, 63.2% and 58.6% of the predicted Hbt. salinarum R1 proteome could be detected and quantified, respectively. Analysis of biophysical protein properties, functional analysis and pathway mapping indicate that we achieved a comprehensive characterization of the proteome. 60.8% of quantified proteins (or 34.5% of the predicted proteome) exhibited significant abundance changes between planktonic and biofilm states, demonstrating that haloarchaeal biofilm formation represents a profound “lifestyle change” on the molecular level. Taken together our results and analysis constitute the first comprehensive study to track the molecular changes from planktonic cells to initial and mature archaeal biofilms on the proteome level. Proteins exemplifying different protein expression level profiles were selected, and their corresponding gene transcripts targeted by qRT-PCR to test the feasibility of establishing rapid PCR-based assays for archaeal biofilm formation.
HostingRepository	PRIDE
AnnounceDate	2016-09-28
AnnouncementXML	Submission_2016-09-28_06:32:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christof Lenz
SpeciesList	scientific name: Halobacterium salinarum; NCBI TaxID: 2242;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-19 07:06:30	ID requested
⏵ 1	2016-09-28 06:32:17	announced

Losensky G, Jung K, Urlaub H, Pfeifer F, Fr, ö, ls S, Lenz C, Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH-LC/MS/MS analysis of planktonic and sessile cells. Proteomics, 17(7):(2017) [pubmed]

curator keyword: Biological

submitter keyword: SWATH, label-free, quantitation, Archaea, Biofilm

Christof Lenz
contact affiliation	Max Planck Institute for Biophysical Chemistry Bioanalytical Mass Spectrometry Am Fassberg 11 D-37077 Göttingen Germany
contact email	christof.lenz@mpibpc.mpg.de
lab head
Christof Lenz
contact affiliation	Max Planck Institute for Biophysical Chemistry
contact email	christof.lenz@mpibpc.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/2016/09/PXD003667

PRIDE project URI

• PRIDE
  1. PXD003667
     1. Label: PRIDE project
     2. Name: Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH-LC/MS/MS analysis of planktonic and sessile cells