Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools R package protti version 1.0.0 CRAN Task View: Omics (https://CRAN.R-project.org/view=Omics) Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions. Software Depends: R (>= 4.0) Imports: rlang, dplyr, stringr, magrittr, data.table, janitor, progress, purrr, tidyr, ggplot2, forcats, tibble, plotly, ggrepel, utils, grDevices, curl, readr, lifecycle, httr, methods, R.utils, stats Suggests: testthat, covr, knitr, rmarkdown, shiny, r3dmol, proDA, limma, dendextend, pheatmap, heatmaply, furrr, future, parallel, seriation, drc, igraph, stringi, STRINGdb, iq, scales, farver, ggforce, xml2, jsonlite, missForest Jan-Philipp Quast <jpquast.software@gmail.com> Comprehensive R Archive Network (CRAN) Jan-Philipp Quast [aut, cre] (ORCID: <https://orcid.org/0000-0003-2713-778X>), Dina Schuster [aut] (ORCID: <https://orcid.org/0000-0001-6611-8237>), ETH Zurich [cph, fnd] MIT + file LICENSE (https://CRAN.R-project.org/package=protti/LICENSE) 2026-01-14 application/tgz https://CRAN.R-project.org/package=protti doi:10.32614/CRAN.package.protti