Poster Presentation AUS-oMicS 2025

The Monash Proteomics & Metabolomics Platform: An Integrated Multi-Omics Resource for Advanced Biomarker Discovery     (121192)

Joel R Steele 1 , Han Lee 1 , Erwin Tanuwidjaya 1 2 , Haijian Zhang 1 , Hossein Vaipour Kahrood 1 , Scott Blundell 1 , Iresha Hanchapola 1 , Komagal Sivaraman 1 , Anjani Mital 1 , Dylan H Multari 1 , Chris Xu 1 , Samantha J Emery-Corbin 1 , Christopher K Barlow 1 , Katherine J Jeppy 1 , Tasha Lumbantobing 1 , David L Steer 1 , Ghizal Siddiqui 3 , Dovile Anderson 3 , Joshua Morrow 3 , Jessica Ji 3 , Terry Lim 2 , Isaac Woodhouse 2 , Gabriel Goncalves 2 , Nivedhitha Selvakumar 2 , Cheng Huang 1 , Darren J Creek 3 , Pouya Faridi 2 , Ralf B Schittenhelm 1
  1. High-Precision Biomarker Discovery Platform, Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, MPMP, Clayton, VIC, Australia
  2. MPMP: Clinical Proteomics Node (CPN), School of Clinical Sciences, Monash University, CPN, Clayton, Victoria, Australia
  3. MPMP: Drug Target Identification Platform (DTIP), Monash Institute of Pharmaceutical Sciences, Monash University, MIPS, Parkville, Victoria, Australia

The Monash Proteomics & Metabolomics Platform(MPMP) provides comprehensive proteomic, metabolomic, and lipidomic support for researchers and clinicians through collaborative and fee-for-service engagements. We enable high-throughput molecular analyses of diverse sample types, from biofluids and tissues to single cells, using state-of-the-art instrumentation and robust data-integration pipelines. Recent expansions include Seer™ nanoparticle enrichment for ultra-deep proteome coverage, short-chain fatty acid profiling, RNA-MS, and next-gen MS (Astral + Stellar).

Objective

Present MPMP’s multi-omics services, illustrating how integrated proteomic, metabolomic, lipidomic, and immunopeptidomic analyses, coupled with end-to-end expertise to enable comprehensive biomarker discovery and mechanistic insights.

Methods

Samples are processed using either standardised pipelines or novel approaches for specific research questions. Established workflows include:

Molecule Identification & Quantification: DDA, DIA, TMT, and SIL-based quantitation.

Advanced Sample Prep & Enrichment: Seer™ enhanced analysis of biofluids, automated enrichments, XL-MS, drug target ID, LIP-MS, PTMs.

Specialised workflows: Metaproteomics, immunopeptidomics, single-cell proteomics (Cellenion), RNA mass-spectrometry, and hydrogen-deuterium exchange (Trajan).

Targeted & High-Sensitivity Methods: Over 15 MS including Astrals paired with Stellar workflows for sensitive-high throughput and robust measurements.

Data Processing & Integration: Our in-house Monash Analyst Suites facilitates label-free and label-based quantification, PTM analyses (Phospho-Analyst), emerging NPX-Analyst (Olink) modules and multi-omics data integration via Pathway-Analyst.

Results

Representative projects using these platforms reveal enhanced detection of low-abundance proteins, refined coverage of metaproteomic samples, and detailed molecular insights from single-cell analyses and immunopeptidomes. Integration of proteomic, metabolomic, and lipidomic data has elucidated complex biological pathways, while targeted cytokines, short-chain fatty acid and RNA MS pipelines provide additional resolution for functional studies.

Conclusion

MPMP’s integrated multi-omics capabilities, spanning standard proteomic workflows to novel RNA mass spectrometry, short-chain fatty acid analysis, and advanced data integration, offer a robust environment for biomarker discovery and hypothesis-driven research. Ongoing development of our Analyst Suite underscores our drive to enhance data interpretation and knowledge generation.