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Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer.
Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer. bioRxiv : the preprint server for biology Plubell, D. L., Remes, P. M., Wu, C. C., Jacob, C. C., Merrihew, G. E., Hsu, C., Shulman, N., MacLean, B. X., Heil, L., Poston, K., Montine, T., MacCoss, M. J. 2024Abstract
The development of targeted assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to large scale clinical studies. Targeted assays are currently unable to scale to hundreds or thousands of targets. We demonstrate the generation of large-scale assays using a novel hybrid nominal mass instrument. The scale of these assays is achievable with the Stellar™ mass spectrometer through the accommodation of shifting retention times by real-time alignment, while being sensitive and fast enough to handle many concurrent targets. Assays were constructed using precursor information from gas-phase fractionated (GPF) data-independent acquisition (DIA). We demonstrate the ability to schedule methods from an orbitrap and linear ion trap acquired GPF DIA library and compare the quantification of a matrix-matched calibration curve from orbitrap DIA and linear ion trap parallel reaction monitoring (PRM). Two applications of these proposed workflows are shown with a cerebrospinal fluid (CSF) neurodegenerative disease protein PRM assay and with a Mag-Net enriched plasma extracellular vesicle (EV) protein survey PRM assay.
View details for DOI 10.1101/2024.06.04.597431
View details for PubMedID 38895256
View details for PubMedCentralID PMC11185584