Example data used for the vignette about structural analysis. The data was obtained from Cappelletti et al. 2021 (doi:10.1016/j.cell.2020.12.021 ) and corresponds to two separate experiments. Both experiments were limited proteolyis coupled to mass spectrometry (LiP-MS) experiments conducted on purified proteins. The first protein is phosphoglycerate kinase 1 (pgk) and it was treated with 25mM 3-phosphoglyceric acid (3PG). The second protein is phosphoenolpyruvate-protein phosphotransferase (ptsI) and it was treated with 25mM fructose 1,6-bisphosphatase (FBP). From both experiments only peptides belonging to either protein were used for this data set. The ptsI data set contains precursor level data while the pgk data set contains peptide level data. The pgk data can be obtained from supplementary table 3 from the tab named "pgk+3PG". The ptsI data is only included as raw data and was analysed using the functions of this package.
ptsi_pgkA data frame containing differential abundances and adjusted p-values for peptides/precursors of two proteins.
Cappelletti V, Hauser T, Piazza I, Pepelnjak M, Malinovska L, Fuhrer T, Li Y, Dörig C, Boersema P, Gillet L, Grossbach J, Dugourd A, Saez-Rodriguez J, Beyer A, Zamboni N, Caflisch A, de Souza N, Picotti P. Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell. 2021 Jan 21;184(2):545-559.e22. doi:10.1016/j.cell.2020.12.021 . Epub 2020 Dec 23. PMID: 33357446; PMCID: PMC7836100.