TMT proteomics differential abundance with msqrob2 mixed models, benchmarked on spike-in mixtures with known ground truth to measure ratio compression and the cost of ignoring the plex, and applied to a high fat diet study in mouse adipose tissue.
bioinformatics r bioconductor proteomics mass-spectrometry multiplexing mixed-models batch-effects reporter-ions tmt proteome-discoverer qfeatures isobaric-labeling differential-abundance msqrob2 spike-in-benchmark tandem-mass-tags ratio-compression sps-ms3 reference-channels
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Updated
Sep 23, 2026 - R