Computational protocol: The Chikungunya Virus Capsid Protein Contains Linear B Cell Epitopes in the N- and C-Terminal Regions that are Dependent on an Intact C-Terminus for Antibody Recognition

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Protocol publication

[…] Tandem mass spectra were processed using Proteome Discoverer (version 1.4, Thermo Fisher Scientific, San José, CA, USA) and submitted to Mascot (version 2.5.1, Matrix Science, London, UK). Fixed modification: carbamidomethyl-cysteine; variable modifications: deamidation (asparagine, glutamine) and oxidation (methionine). Enzyme: trypsin, 2 missed cleavages; MS tolerance 20 ppm; MSMS tolerance 0.6 Da using a database downloaded from UniprotKB on the 21 July 2014 consisting of the reference proteome for Aedes aegypti (UP000008820), chikungunya virus (strain 37997) (UP000008450), reference proteome chikungunya virus (strain S27-African prototype) with the sequence of the capsid protein added as a separate entry. Scaffold (4.4.1.1, Proteome Software, Portland, OR, USA, 2014) was used to validate Mascot protein identifications []. Scaffold probabilistically validates these peptide identifications using PeptideProphet []. A cut-off of 99% +2, +3 and 5 ppm error was used to validate the peptides. […]

Pipeline specifications

Software tools Proteome Discoverer, PeptideProphet
Application MS-based untargeted proteomics
Organisms Chikungunya virus, Homo sapiens
Diseases Protein Deficiency, Chikungunya Fever