This paper introduces SomaModules, a pathway enrichment approach for SomaScan data, showing improved enrichment compared to original gene sets in Alzheimer's Disease and mitochondrial pathway analyses.

Journal of Proteome Research · Aug 11, 2025Peer-reviewedBioinformatics

Synapse protein signatures in cerebrospinal fluid and plasma predict cognitive maintenance versus decline in Alzheimers disease

Hamilton Se‐Hwee Oh, Deniz Yagmur Urey, Linda Karlsson, Zeyu Zhu, Yuanyuan Shen, Amelia Farinas, Jigyasha Timsina, Michael R. Duggan, Jingsha Chen, Ian Hunter Guldner, Nader Morshed, Chengran Yang, Daniel Western, Muhammad Ali, Yann Le Guen, , Tony Wyss‐Coray

CSF YWHAG:NPTX2 synapse protein ratio, from proteomics of 3,416 individuals across six cohorts, explains cognitive impairment beyond amyloid and tau and predicts decline (hazard ratio 15.4).

Nature Medicine · Mar 31, 2025Peer-reviewedNeuroscience✦ In-depth digest

Variability of 7K and 11K SomaScan plasma proteomics assays

Julián Candia, Giovanna Fantoni, Francheska Delgado‐Peraza, Nader Shehadeh, Toshiko Tanaka, Ruin Moaddel, Keenan A. Walker, Luigi Ferrucci

Across Baltimore Longitudinal Study of Aging replicates, fully normalized SomaScan 11K has median inter-plate coefficient of variation 5% (7K: 4.5%), intra-plate 3%, 7K inter-batch 8%.

Journal of Proteome Research · Oct 30, 2024Peer-reviewedSystems Biology✦ In-depth digest

Assessment of Variability in the Plasma 7k SomaScan Proteomics Assay

Julián Candia, Gulzar N. Daya, Toshiko Tanaka, Luigi Ferrucci, Keenan A. Walker

Using inter-plate duplicates from 102 donors, a self-contained normalization of the 7k SomaScan plasma assay yields median CV 4.5% across 7,288 human-protein SOMAmers.

Scientific Reports · Oct 13, 2022Peer-reviewedMolecular Biology✦ In-depth digest