ProCan Laboratory

ProCan Laboratory encompasses sample management and processing.

Sample Management

The Pathology group is responsible for sample reception and storage processes, tumour sectioning, and preparation for proteomic processing and analysis. On arrival of samples, they attend to sample reception and logging into the ProCan Laboratory Information Management System (LIMS). Before samples are processed by the Proteomics teams, all studies require careful design to ensure that we will have all of the information necessary to correct for any potential batch effects. The Cancer Data Science team work with the other teams on batch design and sample randomisation to ensure the highest scientific rigour and that the data will be readily interpretable.

The Pathology team are caretakers of the physical samples, carefully labelling and storing them until scheduling determines that ProCan’s Cancer Proteomic team will soon be ready for them. Samples may be prepared onsite at ProCan or in collaborator laboratories. In general, it involves collection of a thin (ten micron) section of each sample into a small tube ready for the Proteomics team. A matched section from each sample is placed on a slide and stained for digital scanning and pathology review. This step allows visualisation of tissue composition and comparison of the histopathological features of each sample with proteomic profiles. This is important because, during cell lysis, the first step of the Proteomic Mass Spec workflow, the tissue structure is totally destroyed.

Sample Processing
Tissue samples are processed using physical disruption, heat, pressure, enzymatic digestion, and treatment with chemicals. This lyses cells, disrupting cell membranes and breaking up the bonds that give proteins their structure. Reduction removes the last of the chemical bonds that give proteins their structure, and alkylation caps the end of these bonds so they don’t re-form. Digestion of samples using a protease cuts the protein chains at specific points to release peptides. The peptide mixtures are cleaned up on cation exchange columns to remove other substances, prior to liquid chromatography (LC) and analysis on a mass spectrometer.

The Proteomics team maintains a facility of high-performance equipment, featuring barocyclers and six Mass Spectrometers. They schedule and run sample cohorts in batches. The Mass Spectrometers analyse peptides on the basis of their mass to charge (m/z) ratio after ionisation, and their fragmentation pattern. They can simultaneously measure tens of thousands of peptides, representing thousands of proteins, in a single sample. The end result of the process is that a tissue is "converted" to a raw data file which is a permanent digital record of the peptides it contained. The proteomics team tracks each step of this process in a Laboratory Information Management System (LIMS).