tmt topic
PAW_pipeline
A Comet-based, best practices proteomics pipeline.
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
TMT_analysis_examples
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
MSstatsTMT
R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
IRS_normalization
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.