The recent combination of pressure cycling technology (PCT) and sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS, allows complex proteomic mass spectrometry data to be generated from small tissue biopsies (1-2mg) in less than 12 hours. ProCan aims to analyse 70,000 different cancer tissues over 7 years, utilising PCT-SWATH methodology. Optimisation of sample preparation steps is crucial for the success of this large scale, industrial analysis. The conventional sample preparation method utilises urea for protein denaturing and solubilisation. Urea is a well-used lysis buffer in shotgun proteomics but has a number of drawbacks. Concentrations of >1M have a detrimental effect on trypsin activity; it can introduce unwanted carbamylation of N-termini and lysine residues, when used at elevated temperatures, along with traditional 14-16 hour incubations; and it is used in high 6-8M concentrations, which requires desalting prior to MS injection. Sodium dodecylsulfate (SDS) is a detergent well known for protein solubilisation, but difficult to remove downstream, incompatible with LC-MS/MS analysis, and high concentrations are also known to effect trypsin activity. Sodium deoxycholate (SDC), on the other hand, can be easily removed with a simple acid precipitation step, and can be used at higher concentrations without affecting trypsin digestion. Using rat kidney biopsy punches the PCT protocol was optimised using various buffer components, and conditions. A combination of SDC and N-propanol instead of urea resulted in comparable numbers of protein IDs to that of the standard urea protocol. It produced a shorter, more efficient sample preparation method and resulted in the elimination of sample clean-up via solid phase extraction (SPE) prior to MS injection, thus improving sample throughput.