PXD012958 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-03-05 02:02:25 | ID requested | |
⏵ 1 | 2019-09-27 09:45:42 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biomedical |
submitter keyword: Variant antigens, Plasmodium Falciparum, PfEMP1, Proteogenomics |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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[ - ]
- PRIDE
- PXD012958
- Label: PRIDE project
- Name: Proteomics pipeline for identifying variant proteins in Plasmodium falciparum parasites isolated from children presenting with malaria