Welcome to the MacCoss Lab

Our Research Focus

The focus of our research is in the development of mass spectrometry and stable isotope-based approaches to improve our understanding of biology on a molecular, cellular, and whole organism level.

Current research areas include:

• New Mass Spectrometry Technologies: We are working on new methods to improve the sensitivity, speed, precision, accuracy, and dynamic range of quantitative measurements.
• Improved Sample Preparation: New biochemical sample preparation methods for the analysis of protein mixtures. We have been working on methods to reduce the cost and improve the robustness of historically challenging sample types.
• Experimental Design and Quality Control: We are very interested in quantitative experimental design. We develop novel methods to assess system suitability and data quality.
• Stable Isotope Methods: Developing stable isotope methods for studying protein metabolism and analyte quantity
• Spatial and Tissue Heterogeneity: We are developing methods for the multiplex analysis of proteins in individual cells, spatial regions, or functional subunits of complex tissue samples.
• Computational Tools: Development of computational tools for automated conversion of mass spectrometry data into biologically meaningful results

Highlighted Publications

• A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods, July 2025
• Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome - Nature Communications, July 2025
• Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods, July 2025
• Performance of novel tau antibodies across multiple modalities for Alzheimer’s disease assessment - Alzheimer’s & Dementia, July 2025
• Tissue-specific metabolomic signatures for a doublesex model of reduced sexual dimorphism - Royal Society Open Science, July 2025

Quantitative Proteomics Services

The MacCoss lab offers a number of mass spectrometry based proteomics services. These range from biofluid proteomics, targeted assay development, etc… For information about these services see here. Email at services[at]maccosslab[dot]org for mroe information

Nunn Lab

We share lab space and resources with Brook Nunn’s lab here in the Department of Genome Sciences. The focus in the Nunn lab is to use mass spectrometry-based proteomics as a tool to understand a variety of environmental questions- from proteins preserved in sediments of the deep sea to the adaptation of bacteria cells to subzero temperatures.

Support Our Research

The MacCoss lab has developed technologies and software tools that improve protein characterization in health and disease. If you’ve benefited from our tools and would like to see their continued development, consider making a tax-deductible donation.