protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

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.

Version: 0.2.0
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
Suggests: testthat, covr, knitr, rmarkdown, proDA, limma, dendextend, pheatmap, heatmaply, viridis, iq, furrr, future, parallel, seriation, drc, httr, igraph, stringi, STRINGdb
Published: 2021-09-17
Author: Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast at>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: README NEWS
CRAN checks: protti results


Reference manual: protti.pdf
Vignettes: Dose-Response Data Analysis Workflow
Single Dose Treatment Data Analysis Workflow
Input Preparation Workflow
Qualtiy control (QC) workflow


Package source: protti_0.2.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): protti_0.2.0.tgz, r-release (x86_64): protti_0.2.0.tgz, r-oldrel: protti_0.2.0.tgz
Old sources: protti archive


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