A recent "Bioinformatics Advances" paper by the Picotti lab (IMSB) introduces their R package for data analysis of LiP-MS and bottom-up proteomics data.
Novel bottom-up proteomics approaches such as LiP-MS, phosphoproteomics and other PTM-centric experiments require flexible software tools to facilitate analysis and interpretation of their large and often diverse data structures. Existing R packages either offer fixed analysis pipelines or are not suited for specific user needs.
We introduce an R package "protti" that is user-friendly and easy to implement even for inexperienced R users. The R package is suitable for the analysis of peptide- and protein-centric data and can use various quantitative data matrices as its input. protti can be used for quality control, statistical analyses and data interpretation. While protti does not provide a graphical user interface, its design principles - based on tidyverse packages - and its documentation make it easy to understand and accessible to novice users.
Link to the paper in Bioinformatics Advancescall_made
