Computational protocol: Rab GTPase Prenylation Hierarchy and Its Potential Role in Choroideremia Disease

Similar protocols

Protocol publication

[…] Tandem mass spectra were processed using Proteome Discoverer (version 1.3, Thermo Fisher Scientific) and submitted to Mascot (version 2.2.06, Matrix Science). Variable modifications: carbamidomethyl-cysteine, deamidation (asparagine, glutamine); oxidation (methionine). Enzyme: trypsin, 2 missed cleavages, MS tolerance 20ppm, MSMS tolerance 0.8 Da. Scaffold (Proteome Software, Portland, Oregon, USA) [] was used to validate Mascot protein identifications.  Scaffold probabilistically validates these peptide identifications using PeptideProphet (3) and derives corresponding protein probabilities using ProteinProphet (2). The raw spectral counts and their normalization are summarized in the Tables S2 andS3 respectively. […]

Pipeline specifications

Software tools Proteome Discoverer, PeptideProphet, ProteinProphet
Application MS-based untargeted proteomics
Diseases Retinitis, Choroideremia, Genetic Diseases, Inborn