NSW Clinical Mass Spec Forum: Revolutionising Precision Oncology With Proteomics

Meeting Format: In-person & online

Location: Room CB04.05.430, Building 4 University of Technology, Sydney

Online link: https://zoom.uts.edu.au/j/89363453890

Meeting Chair: Dr. Mark Taylor, Mass Spectrometry Lead – NSW Health Pathology

5:30 – 6:00 pm Arrival and refreshments

6:00 – 6:35 pm Professor Phil Robinson – ProCan® - Adding Proteomics to Genomics for Precision Oncology

6:35 – 7:00 pm Mr. Dylan Xavier – Enabling Clinical Proteomics: Fast, Reproducible Tissue Processing with the Heat and Beat Workflow

7:00 – 7:30 pm Dr. Erin Sykes – TargetQuant – ADC panel: The journey of a thousand miles begins with a single…. Peptide

7:30 – 8:30 pm Refreshments and Networking

Professor Phil Robinson, PhD

ProCan® – Adding Proteomics to Genomics for Precision Oncology

ProCan® is an ambitious Australian-led initiative aiming to transform cancer diagnosis and treatment by integrating large-scale proteomics into clinical care. Established in 2016, ProCan has built the world’s largest pan-cancer proteome database, analysing over 32,000 tumour samples from more than 100 cancer types using advanced mass spectrometry. This resource captures comprehensive protein profiles, enabling unprecedented insights into tumour biology and supporting the discovery of clinically relevant biomarkers. ProCan’s achievements include the development of robust, high-throughput workflows and the creation of a globally standardised platform for proteomic data generation. The ultimate goal is to translate these discoveries into the clinic. This will be achieved through biomarker discovery and the development of targeted assays, such as the TargetQuant™ platform, initially for research and clinical trials, and ultimately for routine clinical use. These efforts are expected to accelerate precision oncology by enabling more accurate patient stratification and personalised therapy selection.

Bio

Professor Phillip J Robinson (ORCID: 0002-7878-0313) is a leading Australian proteomics researcher, cell biologist and pharmacologist based at the Children’s Medical Research Institute in Sydney. He has a PhD from the University of Sydney, and appointments at the Universities of Sydney and of Southern Denmark. He co-founded ProCan®, the world’s largest cancer proteome-mapping initiative, generating comprehensive proteomic profiles to advance precision oncology. His pioneering work in proteomics has driven the development of high-throughput technologies for cancer research and clinical translation. Professor Robinson’s research also encompasses drug discovery and development, particularly in designing modulators of endocytosis for therapeutic applications. With over 260 publications and numerous patents, he is recognised internationally for innovations that bridge fundamental science and translational medicine.

Mr. Dylan Xavier, MSc

Enabling Clinical Proteomics: Fast, Reproducible Tissue Processing with the Heat and Beat Workflow

Clinical proteomics requires rapid, reproducible workflows that are consistent and handle diverse sample types. Traditional solid tumour processing is hindered by variability from tissue preservation, inefficient protein extraction, and lengthy protocols. We developed "Heat and Beat" (HnB), a streamlined one-pot method combining lysis, reduction, alkylation, and digestion in a single step after 7-minute heat treatment. Using beadbeating and pressure cycling technology, HnB reduces processing time to 38 minutes while maintaining high reproducibility across the most common preservation formats (fresh frozen, OCT-embedded, and FFPE). This method delivers the high consistency and reproducibility that provides the foundation for both ongoing discovery and robust biomarker validation, accelerating the translation of proteomics into clinical practice.

Bio

Dylan Xavier brings nearly two decades of mass spectrometry and proteomics expertise to the challenge of translating proteomics into clinical practice. As ProCan's lead scientist in technology and innovation, he has developed high-throughput sample preparation workflows that have processed over 30,000 tumour samples, enabling the advancement of proteomic technologies to real-world applications in personalized cancer care. His technical expertise spans sample preparation, method development, discovery and targeted proteomics, and assay development. Dylan has actively collaborated with students, research partners, industry, and government organisations across various projects over two decades to advance the translation of proteomic research towards real world outcomes.

Dr. Erin Sykes , PhD

TargetQuant – ADC panel: The journey of a thousand miles begins with a single…. Peptide

Antibody-drug conjugates (ADCs) are a class of anti-cancer drugs undergoing intensive development. They consist of a cytotoxic drug attached via a chemical linker to an antibody recognising a protein expressed by cancer cells, thereby delivering the drug directly into the cancer cell. For appropriate ADC selection, it is critically important for the treating clinician to know whether the relevant protein target is expressed by the patient’s tumour. The TargetQuant™ assay panel enables simultaneous, precise quantification of 16 ADC target proteins in tumour specimens for which there are corresponding clinical trials available in Australia. This presentation will show the development of the ProCan TargetQuant™ assay panel and our results to date. The potential utility of the assays can be seen through the accurate quantitation of HER2 which demonstrated strong concordance with established diagnostic methods, such as in situ hybridisation, and improved accuracy over conventional immunohistochemistry. This panel has recently been implemented as a research only tool for commercial services such as candidate selection for clinical trials, while our long term-goal is for it to ultimately serve as a companion diagnostic test.

Bio

Erin is a molecular cancer biologist, who has spent the last 10 years in the field of proteomics, utilising mass spectrometry to identify cancer biomarkers and understand molecular pathways that contribute to cancer progression. Erin's work at ProCan focuses on translating the tens of thousands of cancer proteomes acquired in ProCan’s discovery projects into clinically applicable targeted proteomic assays using selected reaction monitoring (SRM). With these highly selective and robust assays, ProCan hopes to change the way in which patients are diagnosed and treated, selecting the most effective therapy for the individual. Prior to her role at ProCan, Erin's research in the field of proteomics involved melanoma biomarker discovery for patient stratification, understanding the contribution of the unfolded protein response to cancer progression, the role of the PTM AMPylation in melanoma biology and the development of synthetic antibodies for immunotherapy targeting leukaemias.