PXD001646

PXD001646 is an original dataset announced via ProteomeXchange.

Title	E. coli source tracking
Description	We report a novel, peptide identification-free shotgun proteomics workflow as a bacterial fingerprinting method. This method uses a similarity-clustering algorithm to segregate the mass spectra that are presumably derived from individual peptide speciess and merge them into discrete units of consensus spectra that comprise the proteomic fingerprints of the bacterial isolates being investigated. The novel method was compared to a traditional peptide identification-based shotgun proteomics workflow and a commonly used PCR-DNA fingerprinting technique for performance benchmarking in differentiating 73 isolates of E. coli by their animal sources (human, cow, dog, and pig). The fingerprints generated using by the novel method were richer in information, more discriminative in separating the E. coli isolates by animal sources, and more accurate in classifying query isolates to the correct animal sources . Our data suggest that, by taking a snapshot of the system-wide expression of bacterial cells and circumventing peptide identification, the novel method generated fingerprints that not only reflected the adaptation of E. coli to different animal hosts more precisely than PCR-DNA fingerprinting but also constituted a fuller representation of the bacterial cells' proteomes than traditional shotgun proteomics.
HostingRepository	PRIDE
AnnounceDate	2015-10-05
AnnouncementXML	Submission_2015-10-05_05:59:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wenguang Shao
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-05 01:29:45	ID requested
⏵ 1	2015-10-05 05:59:07	announced

Shao W, Zhang M, Lam H, Lau SC, A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation. Sci Rep, 5():14337(2015) [pubmed]

curator keyword: Biological, Technical

submitter keyword: 73 E. coli strains from different animal hosts(cow

pig

dog and human)

environmental samples

LTQ

Henry Lam
contact affiliation	Hong Kong University of Science and Technology
contact email	kehlam@ust.hk
lab head
Wenguang Shao
contact affiliation	Hong Kong Uni. of Sci.& Tech.
contact email	shaowenguang@gmail.com
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/2015/10/PXD001646

PRIDE project URI

• PRIDE
  1. PXD001646
     1. Label: PRIDE project
     2. Name: E. coli source tracking