PXD005283

PXD005283 is an original dataset announced via ProteomeXchange.

Title	A novel protein extraction method for proteomics of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae)
Description	Fungal proteomics is a developing field that requires renewed interest and attention from the scientific community in many aspects. One of the most compelling objectives of fungal biology is to find out how fungal pathogens colonize a host, in order to find new ways of impeding this colonization, and proteomics is an important and useful tool to this end. However, fungi are also taxonomically interesting and are important biochemical model organisms for the study of many cellular processes, such as cytoskeletal regulation. Additionally, fungi are sources of secondary metabolites, many of which serve as medications for humans. Nevertheless, much work remains in developing systems-biology approaches to understanding fungal gene expression and secondary metabolism. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive, complex, protein extraction methodologies. In this work, an application of a modified Folch extraction to protein extraction was used to perform de novo peptide sequencing of the proteome from the plant and human pathogen Lasiodiplodia theobromae, which greatly streamlined and simplified the analysis process. Using a metaproteomics bioinformatics approach, many novel proteins for L. theobromae were identified and targeted for further biochemical characterization and annotation efforts.
HostingRepository	PRIDE
AnnounceDate	2017-04-05
AnnouncementXML	Submission_2017-11-13_00:21:49.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005283
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Carla Uranga
SpeciesList	scientific name: Lasiodiplodia theobromae; NCBI TaxID: 45133;
ModificationList	Ammonia-loss; Glu->pyro-Glu; Oxidation; Acetyl; Carbamidomethyl; Gln->pyro-Glu
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-07 02:48:36	ID requested
1	2017-04-05 05:39:10	announced
⏵ 2	2017-11-13 00:21:50	announced	Updated publication reference for PubMed record(s): 28580409, 26926564.

Uranga CC, Ghassemian M, Hern, á, ndez-Mart, í, nez R, (Botryosphaeriaceae). Data Brief, 13():124-128(2017) [pubmed]

Uranga CC, Beld J, Mrse A, C, ó, rdova-Guerrero I, Burkart MD, Hern, á, ndez-Mart, í, nez R, Fatty acid esters produced by Lasiodiplodia theobromae function as growth regulators in tobacco seedlings. Biochem Biophys Res Commun, 472(2):339-45(2016) [pubmed]

curator keyword: Biological

submitter keyword: Trunk-disease fungi, LC-nanoESI-MS, proteomics, de novo peptide sequencing, gene ontology

Majid Ghassemian, PhD
contact affiliation	University of California, San Diego Proteomics Mass Spectrometry Depertment
contact email	mghassemian@ucsd.edu
lab head
Carla Uranga
contact affiliation	UCSD/CICESE
contact email	urangacarla@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/2017/04/PXD005283

PRIDE project URI

• PRIDE
  1. PXD005283
     1. Label: PRIDE project
     2. Name: A novel protein extraction method for proteomics of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae)