AgResearch provides cutting-edge mass spectrometry-based protein analysis.

Our proteomics facility is leading research that identifies, characterises and quantifies proteins and peptides in samples spanning the food value chain.

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 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. Ion Trap (Amazon Speed ETD)

B. High-resolution Q-TOF (Impact HD) C. MALDI-TOF/TOF (Ultraflex III)

D. High-resolution Q-TOF (Impact II)

This ion trap instrument is able to perform LC-MS/MS analysis in both CID and ETD fragmentation mode. This makes this instrument a versatile tool when studying protein modifications. It is equipped with a nanoAdvance HPLC.

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 HPLC.

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 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 an Ultimate 3000 HPLC. 

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.


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. 


Below are a series of downloadable resources for our proteomics service.

Get in touch with our team

Contact us

Send an email to one of our team or check out our facilities located across Aotearoa New Zealand.

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