PXD002465

PXD002465 is an original dataset announced via ProteomeXchange.

Title	A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major
Description	Leishmania major is a kinetoplastid protozoan parasite which causes the debilitating infectious disease cutaneous leishmaniasis (CL). This disease results in scars and disfiguration of the infected individuals. The L. major genome was the first leishmanial genome to be sequenced in 2005 and this study resulted in the identification of 8,300 protein coding genes. This landmark study paved the way for further sequencing of other leishmanial parasites (L. infantum, L. braziliensis and L. donovani). A recent study provided the glimpse of the global transcriptome of L. major promastigotes. This study identified 1,884 uniquely expressed non-coding RNAs (ncRNA) in L. major. Additionally, we had previously mapped the global proteome of L. major promastigote using a proteogenomic approach which resulted in identification of 3,613 proteins in L. major promastigotes which covered 43% of its proteome. In the present study, we have carried out extensive analysis of the 1,884 novel ncRNAs using a proteogenomic approach to identify their protein coding potential. Our analysis resulted in identification of 10 novel protein coding genes based on peptide data and additional hundreds of proteins coding genes based on homology searches of previously classified ncRNA genes. We have analyzed each of these novel protein coding genes and in the process have improved the genome annotation of L. major on the basis of mass spectrometry derived peptide data and also based on homology.
HostingRepository	PRIDE
AnnounceDate	2019-02-12
AnnouncementXML	Submission_2019-02-12_07:53:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Leishmania major; NCBI TaxID: 5664;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-02 00:41:14	ID requested
1	2016-05-11 07:20:01	announced
⏵ 2	2019-02-12 07:53:51	announced	Updated publication reference for PubMed record(s): 27988178.

Pawar H, Pai K, Patole MS, A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major. Acta Trop, 167():21-25(2017) [pubmed]

curator keyword: Biological

submitter keyword: Cutaneous leishmaniasis, proteomics, gene annotations, non-coding RNA, protozoan parasite

Akhilesh Pandey
contact affiliation	McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 USA
contact email	pandey@jhmi.edu
lab head
Akhilesh Pandey
contact affiliation	Johns Hopkins University
contact email	pandey@jhmi.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002465
     1. Label: PRIDE project
     2. Name: A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major