Inspecting the quality of isobaric labeling proteomic data in a Jupyter notebook. Data output from Proteome Discoverer.
Workflow to perform unbiased site-to-protein normalization in multiplex proteomics by accounting for ratio compression effects due to ion interference
Workflow to perform interference modeling and interference correction for MS2-based multiplex proteomics data
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.
Workflow to perform unbiased site-to-protein normalization in multiplex proteomics by accounting for ratio compression effects due to ion interference
Workflow to perform interference modeling and interference correction for MS2-based multiplex proteomics data
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