The number of methods employed to access biochemical information of life is continuously increasing with the pace of technological development. Outside the realms of transcriptomics and genomics, mass spectrometry is applied to proteins, lipids and small molecules. Highly specialised workflows are required to characterise these components robustly, and core facilities maintain the machinery and staffing for use by the wider research community.
Our mission at the Monash Proteomics & Metabolomics Platform is to provide the best possible proteomic (metabolomic and lipidomic) support for researchers, clinicians and the broader community by specialising in collaborative, fee-for-service and commercial engagements. As such, we offer standardised pipelines for the analysis of diverse sample types, from general analysis to the implementation of novel approaches and applications. Our major workflows include basic identification, label-free quantification (DDA & DIA), automated bead-based enrichment, label-based quantification (TMT SILAC), crosslinking, meta-proteomics, limited proteolysis (LIP-MS), thermal proteome profiling (TPP), post-translational modification analysis (including phosphorylation) and targeted methods for those crucial experiments where sensitivity and specificity are needed. Other methods we also employ are single-cell proteomics (Cellenion), hydrogen Deuterium Exchange (HDX) (Trajan), and targetted Proximity ligation assays (Olink). We offer complete end-to-end services as our standard: consultation, experimental design assistance, sample processing, MS acquisition and bioinformatic data analysis; we also provide in-house developed tools for further knowledge generation from complex proteomic outputs from experiments, further supporting researchers in their pursuit of developing new knowledge. This is a part of our ongoing development of the Monash Analyst-Suite, which includes the ability to qualitatively analyse experimental data alongside label-free quantitative analysis from total proteome experiments LFQ / TMT / DIA-Analyst, PTM analyses (Phospho-Analyst) and future tools of NPX-Analyst (Olink), data integration (Pathway-Analyst) and Single Cell Proteomics (SCP-Analyst). Here, we share information on our pipelines and the depth of analysis achievable, exemplified by representative projects analysed within our Platform.