PXD012958-1

PXD012958 is an original dataset announced via ProteomeXchange.

Title	Proteomics pipeline for identifying variant proteins in Plasmodium falciparum parasites isolated from children presenting with malaria
Description	Plasmodium falciparum variant antigens named erythrocyte membrane protein 1 (PfEMP1) are important targets for developing a protective immunity to malaria caused by P. falciparum. One of the major challenges in P. falciparum proteomics studies is identifying PfEMP1s at the protein level due to antigenic variation. To identify these PfEMP1s using shotgun proteomics, we developed a pipeline that searches high resolution mass spectrometry spectra against a custom protein sequence database. An algorithm, LAX, was developed as part of the pipeline that matches sequences to the most similar PfEMP1 and calculates a weight value used for PfEMP1 protein inference. The pipeline was first validated in the analysis of a laboratory strain with a known PfEMP1, then it was implemented on the analysis of parasite isolates from malaria-infected pregnant women and finally on the analysis of parasite isolates from malaria infected children where there was an increase of PfEMP1s identified in 28 out of 31 isolates.
HostingRepository	PRIDE
AnnounceDate	2019-09-27
AnnouncementXML	Submission_2019-09-27_09:45:40.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Patricia Gonzales Hurtado
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-05 02:02:25	ID requested
⏵ 1	2019-09-27 09:45:42	announced

Gonzales Hurtado PA, Morrison R, Ribeiro JMC, Magale H, Attaher O, Diarra BS, Mahamar A, Barry A, Dicko A, Duffy PE, Fried M, Parasites Isolated from Children Presenting with Malaria. J Proteome Res, 18(11):3831-3839(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Variant antigens, Plasmodium Falciparum, PfEMP1, Proteogenomics

Michal Fried
contact affiliation	Laboratory of Malaria Vaccinology and Immunology, NIAID, NIH
contact email	michal.fried@nih.gov
lab head
Patricia Gonzales Hurtado
contact affiliation	NIAID
contact email	gonzalesp@nih.gov
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/2019/09/PXD012958

PRIDE project URI

• PRIDE
  1. PXD012958
     1. Label: PRIDE project
     2. Name: Proteomics pipeline for identifying variant proteins in Plasmodium falciparum parasites isolated from children presenting with malaria