PXD001071

PXD001071 is an original dataset announced via ProteomeXchange.

Title	Proteogenomics of Candida tropicalis – an opportunistic pathogen
Description	Candida tropicalis is an opportunistic pathogen which causes candidiasis in immune-compromised individuals. It is one of the members of the non-albicans group of Candida that are known to be azole resistant and is frequently seen in individuals being treated for cancers, HIV-infection and bone-marrow transplant. Although the genome of C. tropicalis was sequenced in the year 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out in-depth proteomic profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry and mapped ~44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2,740 proteins in the cell lysate of this yeast, we also analysed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons and corrected 49 computationally predicted gene models. To our knowledge, this is the first high-throughput proteomic study to refine the genome annotation of C. tropicalis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:11:56.465.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Keshava Prasad T. S.
SpeciesList	scientific name: Candida tropicalis (Yeast); NCBI TaxID: 5482;
ModificationList	L-methionine (S)-sulfoxide; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-06-18 01:51:45	ID requested
1	2017-05-08 02:52:30	announced
⏵ 2	2024-10-22 04:12:04	announced	2024-10-22: Updated project metadata.

Datta KK, Patil AH, Patel K, Dey G, Madugundu AK, Renuse S, Kaviyil JE, Sekhar R, Arunima A, Daswani B, Kaur I, Mohanty J, Sinha R, Jaiswal S, Sivapriya S, Sonnathi Y, Chattoo BB, Gowda H, Ravikumar R, Prasad TS, Proteogenomics of Candida tropicalis--An Opportunistic Pathogen with Importance for Global Health. OMICS, 20(4):239-47(2016) [pubmed]

10.1089/omi.2015.0197;

curator keyword: Biological, Biomedical

submitter keyword: genome annotation,shotgun proteomics

T. S. Keshava Prasad
contact affiliation	Institute of Bioinformatics, Discoverer Building, 7th Floor, International Tech Park, Whitefield, Bangalore - 560 066, Karnataka, India.
contact email	keshav@ibioinformatics.org
lab head
Keshava Prasad T. S.
contact affiliation	Institute of Bioinformatics, Bangalore, Karnataka, India.
contact email	keshav@ibioinformatics.org
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/2017/05/PXD001071

PRIDE project URI

• PRIDE
  1. PXD001071
     1. Label: PRIDE project
     2. Name: Proteogenomics of Candida tropicalis – an opportunistic pathogen