Computational protocol: The TBC1D15 Oncoprotein Controls Stem Cell Self-Renewal through Destabilization of the Numb-p53 Complex

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Protocol publication

[…] A database of semitryptic peptides, generated from the NCBI mouse database, was imported into Sorcerer 2 (SageN Research). The MS/MS spectra obtained from MudPIT were automatically extracted and searched against the database using Sorcerer SEQUEST. For the search, 57 Da was added to all cysteines to account for carboxyamidomethylation. An additional 42 Da was permitted on N-terminal residues to account for potential acetylation, and 16 Da was permitted on methionines to account for potential oxidation. The results from the SEQUEST searches were automatically filtered, organized, and displayed by PeptideProphet and ProteinProphet (Institute for Systems Biology). ProteinProphet computed a probability score from 0 to 1 for each protein, based on peptides assigned to MS/MS spectra and analyzed by.PeptideProphet. To minimize false positive identification, the thresholds for adjusted probability score for each peptide and for protein identification were set at g = 0.85. The false positive rate using these criteria was below 1%, based on decoy database analysis. […]

Pipeline specifications

Software tools Comet, PeptideProphet, ProteinProphet
Application MS-based untargeted proteomics
Organisms Homo sapiens
Diseases Neoplasms