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: 0.6.0
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, 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
Published: 2023-01-20
Author: Jan-Philipp Quast ORCID iD [aut, cre], Dina Schuster ORCID iD [aut], ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast at>
License: MIT + file LICENSE
NeedsCompilation: no
Citation: protti citation info
Materials: README NEWS
In views: Omics
CRAN checks: protti results


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


Package source: protti_0.6.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): protti_0.6.0.tgz, r-oldrel (arm64): protti_0.6.0.tgz, r-release (x86_64): protti_0.6.0.tgz, r-oldrel (x86_64): protti_0.6.0.tgz
Old sources: protti archive

Reverse dependencies:

Reverse suggests: MACP


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