Each year, over 950 children and adolescents (0-19 year olds) in Australia – and 163,000 children worldwide – are diagnosed with cancer (1). The most common types of childhood cancers affect a range of tissues such as blood, lymph, bone marrow, nervous tissues, muscles, kidney, liver and bone. ProCan (The ACRF Centre for the Proteome of Human Cancer) is an industrial-scale proteomics facility at the Children's Medical Research Institute (CMRI). ProCan researchers have a major technological edge by combining pressure cycling technology with SWATH mass spectrometry (PCT-SWATH-MS) (2) that will be adopted to discover, verify and validate specific protein-based markers for many different types of cancers (from children to adults). To meet this goal, a major challenge is the generation of quantitatively accurate and highly reproducible data matrices of proteins with minimal missing values across cohorts of patients, whilst simultaneously accounting for variabilities among samples collected from different tissue origin.
Developing a SWATH-MS based profile of different normal tissues will provide an important reference to guide interpretation of cancer proteomic data. Specifically, it will assist in understanding aspects of tumour differentiation, and tissue origin in the case of metastatic disease. The study is designed to complement this aim by generating a rat tissue proteome using quantitative proteomics. In order to construct an organ specific quantitative proteome, PCT-SWATH-MS was applied to create specific spectral reference libraries of samples collected from seven different rat organs (Brain, Liver, Muscle, Spleen, Lung, Kidney and Testis). These results will be adopted for constructing a comprehensive proteomic profile for human tumour biopsies based on their site of origin.
1. 0-19 years incidence data. Australian Institute of Health and Welfare (AIHW) Australian Cancer Incidence and Mortality (ACIM) Books 2017
2. Guo T et al (2015) Nature Med 21: 407 – 15.