CPTAC human kidney tissue proteomics – data generation, quality control and quantification

The abundance of human kidney tissue proteins were obtained from the CPTAC pre-processed protein-level assembly¹³⁶ and downloaded from the proteomic data commons (data accessed May 2022, https://pdc.cancer.gov/pdc/study/PDC000127). The details of the biochemical analyses are reported in full in the original publication¹³⁶. In brief, we made use of the NAT samples (taken from regions of the kidney adjacent to renal clear cell tumours) and reviewed by a board-certified pathologist (to confirm the histological status)¹³⁶. Each kidney tissue sample was homogenised, lysed, digested and trypsinised. Samples were then multiplexed using tandem mass tag (TMT) and fractionated by basic reversed-phase liquid chromatography (bRPLC)¹³⁶. Peptides were then separated by ultra-high-performance liquid chromatography (UHPLC) and analysed using the Thermo Fusion Lumos mass spectrometer¹³⁶. The protein-level assembly of spectra and peptides into estimates of protein abundance was performed by a software workflow using the Philosopher pipeline¹⁷² including spectral search by MSFragger¹⁷³ and refinement by PeptideProphet¹⁷⁴. Peptide spectral match data for each sample were then normalised by log₂-transformed reference intensities determined for each TMT channel. A total of 83 NAT samples had raw protein-level abundance data; 72 of these had genotype information from whole genome sequencing available and 65 of these also had poly-A RNA-sequencing data. All samples used in this analysis were collected from patients of European ancestry. A total of 7291 proteins were quantifiable in all 72 samples and 7036 of these from 65 samples were available with measurable expression of their source gene in the RNA-sequencing data.