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LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Bioconductor version: Release (3.19)

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

Author: Devon Kohler [aut, cre], Tsung-Heng Tsai [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Valentina Cappelletti [aut], Liliana Malinovska [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at>

Citation (from within R, enter citation("MSstatsLiP")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

MSstatsLiP Proteolytic Workflow HTML R Script
MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats
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Follow Installation instructions to use this package in your R session.

Source Package MSstatsLiP_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) MSstatsLiP_1.10.0.tgz
macOS Binary (arm64) MSstatsLiP_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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