Proteomics: The science of protein analysis

What is proteomics?

Proteomics is the study of proteins and typically captures a comprehensive, quantitative image of protein expression in a sample matrix as well as its changes under the influence of biological perturbations.

By developing and implementing cutting-edge mass spectrometry-based proteomics and peptidomics methods, we aim to provide solutions and accelerate research in the food science space - from agriculture through to human health and nutrition.

Our facility

Our new Tuhiraki-based facility provides the ability to process a wide variety of protein and peptide samples from start to finish. We can facilitate aspects of experimental design and sample preparation through to analysis by state-of-the-art mass spectrometers and data interpretation.

We utilise four different tools in our research:


A. TimsTOF Pro2	B. Impact HD	C. MALDI-TOF/TOF (Ultraflex III)	D. Impact II
Our newest quadrupole - time-of-flight mass spectrometer, which enables 4D-proteomics and peptidomics through ion mobility. This instrument is used for in-depth proteome, peptidome or multi-omics applications and characterisation of protein modifications such as phosphorylation and glycosylation. It is equipped with a nanoElute 2 high-performance nanoflow liquid chromatography system.	This electrospray ionisation quadrupole - time-of-flight mass spectrometer provides high-resolution MS/MS data and is mainly used to identify and quantify peptides from proteomics or peptidomics experiments.  It is equipped with an UltiMate™ 3000 RSLCnano system.	This matrix-assisted laser desorption/ionization/time-of-flight applies an alternative way of ionization and is great for samples that just need a quick check, a fingerprint to detect if samples can be separated based on a profile or for bacterial identifications via BioTyper applications. MALDI is appropriate to analyse biomolecules like peptides or small proteins.	This electrospray ionisation quadrupole - time-of-flight mass spectrometer is our current workhorse at the facility that provides high resolution MS / MS data to obtain highly accurate qualitative and quantitative proteomics and peptidomics data. It is equipped with a nanoElute high-performance nanoflow liquid chromatography system.

Our capabilities

The Proteomics team have wide ranging expertise and capability within proteomic research.

Proteome Profiling

In proteome profiling, proteins are extracted from a large number of samples with different conditions (e.g. treated vs. non-treated).

A comparison is made between the abundance levels of all proteins identified across these samples to obtain a better understanding of what is happening to a biological system at a molecular level.

Protein Identification and PTM Characterisation

By linking acquired mass spectra with protein databases, we can identify the proteins present in samples and discover the post-translational modifications (PTMs) the proteins carry.

Peptidomics and bioactive peptides

Peptidomics focusses on characterising the small endogenous peptides in samples rather than the larger proteins. The peptides are isolated from samples by ultrafiltration using molecular weight cut-off filters.

Based on the identified peptide sequences, predictions can be made via our in-house database to see if these samples contain bioactive or taste-related peptides.

Redox Proteomics

Using our scoring system, we can compare the extent of protein modifications from redox reactions between different samples.

The redox scoring system is based on an oxidative cascade and delivers insight through the changes in consequences of the redox treatments at the molecular level.

Digestomics

Digestomic experiments put food through simulated gastro-intestinal digestion to analyse what proteins and peptides are being released during the different stages of digestion.

This allows us to track how proteins are broken down into their smaller building blocks and can be used to explore beneficial characteristics of foods.