The complexity of the proteome is vast but remains eclipsed by the number of methods used to access its crucial biological information. Practitioners within leading labs in the world focus heavily on specialised workflows that are further refined to specific biological contexts. Core facilities aim to offer methods that are routinely applied to these researchers' needs.
Our mission at the Monash Proteomics & Metabolomics Facility is to provide the best possible proteomic (metabolomic and lipidomic) support for researchers, clinicians and the broader community by specialising in both collaborative and fee-for-service engagements. To that end, we offer standardised pipelines for the analysis of diverse sample types, from general analysis and advice 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, crosslinking, meta-proteomics, post-translational modification analysis (including phosphorylation) and targeted methods for those crucial experiments where sensitivity and specificity are needed. Not only do we offer sample processing, MS acquisition and bioinformatic data analysis, but we also provide in-house developed tools for the study of the 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 Analyst-Suite, which includes the ability to qualitatively analyse experimental data alongside label-free quantitative analysis from MaxQuant/Fragpipe (LFQ-Analyst), phosphoproteomic data (Phospho-Analyst) with future programs of TMT-Analyst and DIA-Analyst. Here we share information on our pipelines and the depth of analysis achievable, exemplified by representative projects analysed within our facility