PXD004338

PXD004338 is an original dataset announced via ProteomeXchange.

Title	Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani
Description	The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-based identification based on related Leishmania species (L. infantum, L. major and L. braziliensis) whose genomes have been sequenced. Recently, the genome of L. donovani was fully sequenced and the data became publicly available. We took advantage of the availability of its genomic sequence to carry out a more accurate proteogenomic analysis of L. donovani proteome using our previously generated dataset. This resulted in identification of 17,504 unique peptides upon database-dependent search against the annotated proteins in L. donovani. These peptides were assigned to 3999 unique proteins in L. donovani. 2296 proteins were identified in both the life stages of L. donovani, while 613 and 1090 proteins were identified only from amastigote and promastigote stages, respectively. The proteomic data was also searched against six-frame translated L. donovani genome, which led to 255 genome search-specific peptides (GSSPs) resulting in identification of 20 novel genes and correction of 40 existing gene models in L. donovani.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_02:49:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Leishmania donovani; NCBI TaxID: 5661;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-15 09:52:03	ID requested
1	2016-12-20 16:43:38	announced
⏵ 2	2017-10-24 02:49:05	announced	Updated project metadata.

Nirujogi RS, Pawar H, Renuse S, Kumar P, Chavan S, Sathe G, Sharma J, Khobragade S, Pande J, Modak B, Prasad TS, Harsha HC, Patole MS, Pandey A, Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. J Proteomics, 97():48-61(2014) [pubmed]

curator keyword: Biological

submitter keyword: Leishmania donovani, protoemics and proteogenomics

Akhilesh Pandey
contact affiliation	733 N. Broadway Room 527, Miller Research Building Baltimore MD 21205 USA
contact email	pandey@jhmi.edu
lab head
Akhilesh Pandey
contact affiliation	Johns Hopkins University
contact email	pandey@jhmi.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/2016/12/PXD004338

PRIDE project URI

• PRIDE
  1. PXD004338
     1. Label: PRIDE project
     2. Name: Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani