PXD009004

PXD009004 is an original dataset announced via ProteomeXchange.

Title	Triflic acid-treatment enables LC-MS/MS analysis of insoluble bacterial biomass
Description	Established bacterial proteome sample preparations, including sonication and bead beating, leave insoluble carbohydrate-rich cell envelope pellets with an abundance of vital proteins often overlooked or missed in LC-MS/MS analyses. Triflic acid selectively removes glycans and we demonstrate that in comparison to sonication alone, incubation of whole bacterial cells as well as post-sonication insoluble pellets yields membrane and cell envelope-associated proteins for LC-MS/MS detection. We provide a detailed side-by-side comparison of triflic acid and sonication preparations for Gram- (Pseudomonas aeruginosa), Gram+ (Bacillus subtilis), and a complex bacterial human distal gut microbiome sample. Further, human Jurkat cells that lack a peptidoglycan and are readily solubilized by established methods, reveal only subtle differences in measurable proteins by LC-MS/MS between sonication and triflic acid preparations. Critically, we show that our new triflic acid-based proteome preparation method is broadly applicable and greatly improves our ability to detect and quantitate bacterial cell envelope proteins.
HostingRepository	PRIDE
AnnounceDate	2019-01-29
AnnouncementXML	Submission_2019-01-29_00:15:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ana Wang
SpeciesList	scientific name: Bacillus subtilis; NCBI TaxID: 1423; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Pseudomonas aeruginosa PAO1; NCBI TaxID: 208964;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-21 05:47:49	ID requested
⏵ 1	2019-01-29 00:15:44	announced

Wang AY, Thuy-Boun PS, Stupp GS, Su AI, Wolan DW, Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass. J Proteome Res, 17(9):2978-2986(2018) [pubmed]

curator keyword: Technical

submitter keyword: LC-MS/MS, bacteria, microbiome, triflic acid

Dennis Wolan
contact affiliation	Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA.
contact email	wolan@scripps.edu
lab head
Ana Wang
contact affiliation	TSRI
contact email	anawang@scripps.edu
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/2019/01/PXD009004

PRIDE project URI

• PRIDE
  1. PXD009004
     1. Label: PRIDE project
     2. Name: Triflic acid-treatment enables LC-MS/MS analysis of insoluble bacterial biomass