On this episode of Translating Proteomics, Parag, Andreas, and special guest Don Kirkpatrick answer questions submitted by the Translating Proteomics community. They cover:

• Needs in plasma proteomics
• How proteomics impacts drug development – with special guest Don Kirkpatrick, Ph.D.!
• How lifestyle impacts the proteome
• How the Nautilus Proteome Analysis Platform is impacting tau and Alzheimer’s disease research

References

Shome et al., 2022 - Serum autoantibodyome reveals that healthy individuals share common autoantibodies

https://www.sciencedirect.com/science/article/pii/S2211124722006489

LaBaer Lab paper investigating autoantibody levels in plasma and their relationship to health.

Sylman et al., 2018 - A Temporal Examination of Platelet Counts as a Predictor of Prognosis in Lung, Prostate, and Colon Cancer Patients

https://www.nature.com/articles/s41598-018-25019-1

Mallick lab paper investigating temporal changes in platelets and their associations with cancer biology.

Krönke et al., 2014 - Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells

https://www.science.org/doi/10.1126/science.1244851

Seminal paper describing selective protein degradation caused by lenalidomide.

Fink and Ebert 2015 - The novel mechanism of lenalidomide activity

https://ashpublications.org/blood/article/126/21/2366/34644/The-novel-mechanism-of-lenalidomide-activity

Review of research elucidating the mechanisms of lenalidomide activity

Ndoja et al., 2025 - COP1 Deficiency in BRAFV600E Melanomas Confers Resistance to Inhibitors of the MAPK Pathway

https://www.mdpi.com/2073-4409/14/13/975

Describe links between kinase inhibitor vemurafenib and changes in ETV transcription factor degradation

Song et al., 2022 - RTK-Dependent Inducible Degradation of Mutant PI3Kα Drives GDC-0077 (Inavolisib) Efficacy

https://aacrjournals.org/cancerdiscovery/article/12/1/204/675622/RTK-Dependent-Inducible-Degradation-of-Mutant-PI3K

Use proteomics to discover that inavolisib acts through selective degradation of mutant PI3Kα

Canon et al., 2019 - The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity

https://www.nature.com/articles/s41586-019-1694-1

Covers the development of an inhibitor of KRAS mutant KRAS (G12C).

Schneider et al., 2024 - Feeding gut microbes to nourish the brain: unravelling the diet-microbiota-gut-brain axis

https://www.nature.com/articles/s42255-024-01108-6

Review on the gut-brain axis

Webpage for Johanna Lampe’s Lab at Fred Hutch Cancer Center

https://www.fredhutch.org/en/faculty-lab-directory/lampe-johanna.html

Guseh et al., 2020 - An expanded repertoire of intensity-dependent exercise-responsive plasma proteins tied to loci of human disease risk

https://www.nature.com/articles/s41598-020-67669-0

Work investigating the relationship between exercise, the plasma proteome, and health

Human Proteome Organization (HUPO) webpage with resources focused on proteomics in space

https://hupo.org/Human-Proteomics-at-Extreme-Conditions

Joly et al., 2025 - Large-scale single-molecule analysis of tau proteoforms

https://doi.org/10.1101/2025.06.26.660445

Nautilus preprint using Iterative Mapping of proteoforms to measure tau proteoforms in Alzheimer’s disease and related dementias samples.