Computational protocol: Defining the HLA class I‐associated viral antigen repertoire from HIV‐1‐infected human cells

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Protocol publication

[…] Raw data were converted to MASCOT generic files using msconvert or ProteinPilot 4.5 . Sequence interpretation of MS/MS spectra were performed using a database containing all annotated human SwissProt entries including translations of all six reading frames of the sequenced HIV‐1 IIIB genome in addition to translations of all known assigned HIV‐1 protein coding regions (GenBank KJ925006) or a database containing all annotated human SwissProt entries (02/2013, 20 253 entries) and all HIV‐1 entries in NCBI (02/2013, 446 954 entries) with PEAKS 7 and MASCOT 2.4 , . The probability score threshold was defined by decoy database searches implemented in the regarding search engines at a general false discovery rate of 5%. […]

Pipeline specifications

Software tools ProteoWizard, ProteinPilot
Application MS-based untargeted proteomics
Organisms Human immunodeficiency virus 1, Homo sapiens
Diseases Infection, HIV Infections