Computational protocol: Proteomic analysis of exported chaperone/co-chaperone complexes of P. falciparum reveals an array of complex protein-protein interactions

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Protocol publication

[…] A full-scan survey MS experiment (m/z range from 375 to 1600; automatic gain control target, 1,000,000 ions; resolution at 400 m/z, 60,000; maximum ion accumulation time, 50 ms) was performed using the Orbitrap mass spectrometer, and the ten most intense ions were fragmented by collision-induced dissociation (CID). Raw data were converted to mgf files by Proteome Discoverer 1, and then identified using pFind 2.1 software to search in the human Uniprot_TrEMBL database (release on April 2012, human, 65,493 entries) and PlasmoDB database (release on October 2013, Plasmodium falciparum 3D7), respectively. Modifications were set as follows: static modification of carbamidomethyl (Cys), dynamic modification of deamination (Asn), oxidation (Met), and acetylation (Lys). Trypsin was selected as the enzyme, and two missed cleavages were allowed. The mass tolerance was set to 20 ppm for the precursor ions and 0.5 Da for the fragment ions. A false discovery rate (FDR) of 1% was estimated and applied to all data sets at the total peptide level. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium ( via the PRIDE partner repository with the dataset identifier PXD003789. […]

Pipeline specifications

Software tools Proteome Discoverer, pFind
Databases ProteomeXchange PlasmoDB
Application MS-based untargeted proteomics
Organisms Toxoplasma gondii, Homo sapiens, Plasmodium falciparum
Diseases Infection, Malaria