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

Human induced pluripotent stem cell (iPSC) technology holds great potential for therapeutic and research purposes, by providing improved models of disease and for studying mechanisms regulating differentiation. The Human Induced Pluripotent Stem Cell Initiative (HipSci) was established to generate large panel of high-quality human iPSC lines from both healthy donors and disease cohorts for the research community. Here I present a reanalysis of the resource data published by (Kilpinen et al. 2017, Nature) which features a comprehensive proteomic analysis of >200 human iPSC lines obtained from >100 different donors. This dataset has identified in total >16,000 proteins expressed in iPSCs, with expression levels spanning 7 orders of magnitude. Raw files from this dataset were published by (Brenes et al. 2019, Molecular & Cellular Protemics) and can be found on ProteomeXchange with the identifier PXD010557. The ones used for this analysis were corresponding to 21 batches out of the 24 provided by (Brenes et al. 2019, Molecular & Cellular Protemics); their raw files were also deposited in this repository. This reanalysis was performed with the aim to evaluate the impact of TMT reporter ion interference and the impact of TMT quantification corection on it. Each PD results files with the mention '_woQuanCorrection' didn't have any TMT quantification correction applied while the one with the mention '_wQuanCorrection' did. The product data sheet used for applying such correction is the one provided by ThermoFisher Scientific for the TNT10-plex reagent product number 90110, lot number UL298812.