optTMT: optimizing any experimental design to minimize false positives caused by TMT reporter ion interference

Summary To enable multiplexing in large-scale proteomics experiment, TMT-plex isobaric tag has been the gold standard. However, tandem mass tag (TMT) reporter ion interference, also named cross-label isotopic impurity, can occur from manufacture level impurities and experimental error. Such interference increases the risk of false positive after differential analysis, even more so on high intensity peptide further leading to wrong conclusions. However, by planning the right experimental design beforehand these interferences can be minimized by solving an optimization problem. In this work, I present a user-friendly interface to allow the proteomics community to find any optimal TMT experimental designs. Availability The Shiny application is available as an executable file at https://zenodo.org/records/14883262 for Windows users and at https://marc-antoinegerault.shinyapps.io/TMT_optimization/. Code and documentation are freely available on github at https://github.com/mgerault/optTMT. The package is written in R and a vignette shows its use in an R command line workflow. Supplementary information Supplementary data are available at Bioinformatics Advances online.