Project ID: IPD3121

Project Title: Proteomic characterization of the Plasmodium falciparum PCNA2 interactome

Principal Investigator: Suman Kumar Dhar

PI Affiliation: 1. Special Centre for Molecular Medicine, Jawaharlal Nehru University 2. TERI School Of Advanced Studies

Submitting Author: Stephy A. Varghese

Description: This project investigates the PCNA2 interactome in *Plasmodium falciparum* using LC-MS/MS. Samples were analysed using a Thermo Scientific Orbitrap Velos Pro mass spectrometer with data-dependent acquisition (DDA) and collision-induced dissociation (CID). Protein identification was performed using Proteome Discoverer 1.4 with SEQUEST HT against a *P. falciparum* protein database downloaded from PlasmoDB. Trypsin was used as the protease, with precursor and fragment ion mass tolerances of 20 ppm and 0.6 Da, respectively. Percolator was used for post-search validation.

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Meta Data

Sample Preparation: Anti-PCNA2 antibody was first immobilised on Protein A/G beads and covalently crosslinked using dimethyl pimelimidate (DMP). The antibody-coupled beads were then incubated with Plasmodium falciparum parasite lysate. The captured proteins were subsequently eluted from the beads.

Peptide Separation: The eluted proteins were digested with trypsin, and the resulting peptides were separated by liquid chromatography and analysed by tandem mass spectrometry (LC-MS/MS) using a Thermo Scientific Orbitrap Velos Pro mass spectrometer. Data were acquired using data-dependent acquisition (DDA) with collision-induced dissociation (CID).

Protein Characterization: MS/MS data were analysed using Thermo Scientific Proteome Discoverer 1.4 with SEQUEST HT as the search engine. Spectra were searched against Plasmodium falciparum 3D7 protein databases obtained from PlasmoDB, using trypsin as the protease. Percolator was used for post-search validation.

Experiment Type: Bottom-up

PubMed-ID:

Species: Plasmodium falciparum 3D7-36329

Tissue: Blood (bto:0000089)

Cell Type: Eukaryotic cell (cl:0000255)

Disease:

Instrument Details: LTQ Orbitrap Velos Pro (MS:1003096)

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