Computational protocol: 11-Ketotestosterone and 11-Ketodihydrotestosterone in Castration Resistant Prostate Cancer: Potent Androgens Which Can No Longer Be Ignored

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Protocol publication

[…] Liquid chromatography was performed using a Thermo Scientific Ultimate 3000 RSLC equipped with a C18 trap column and a C18 analytical column. Samples were analysed using a Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer equipped with a Nanospray Flex ionization source. The raw files generated were imported into Proteome Discoverer v1.4 (Thermo Scientific) and processed using the Mascot and SequestHT algorithms. Peptide validation was performed using the percolator node set to search against a decoy database with a strict false discovery rate (FDR) of 1%. Additional analyses were performed using the X! Tandem Sledgehammer algorithm. Output files from the three algorithms were combined and analysed using Scaffold (Proteomesoftware). […]

Pipeline specifications

Software tools Proteome Discoverer, X! Tandem
Application MS-based untargeted proteomics
Organisms Homo sapiens
Diseases Prostatic Neoplasms
Chemicals Androgens, Androstenedione, Dehydroepiandrosterone, Dihydrotestosterone, Steroids