MSstatsConvert

MSstatsConvert is an R/Bioconductor package that imports reports from a wide range of mass spectrometry signal-processing tools into the standardized format used by MSstats and MSstatsTMT for statistical analysis. It provides the shared converter functions — one row per feature, run, and condition — used across the MSstats ecosystem, along with a common three-step import pipeline (MSstatsImport(), MSstatsClean(), MSstatsPreprocess()) that reads, cleans, and reformats each tool's output. Because MSstats and its companion packages call these converters internally, most users interact with MSstatsConvert indirectly, but the functions can also be used directly for custom or scripted workflows.

MSstatsConvert is part of the MSstats family of packages, developed and maintained by the Vitek Lab at Northeastern University. The package and its documentation are also available at msstats.org.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSstatsConvert")

The development version can be installed directly from this repository:

remotes::install_github("Vitek-Lab/MSstatsConvert")

Quick Start

library(MSstatsConvert)

# Read your search tool's report, then convert it to MSstats format.
# Example: a Skyline report exported as CSV
raw <- data.table::fread("Skyline_report.csv")
msstats_input <- SkylinetoMSstatsFormat(raw)

head(msstats_input)

The converted data frame is then passed to MSstats::dataProcess() (or MSstatsTMT::proteinSummarization() for the *toMSstatsTMTFormat() converters). See the data-format vignette for the columns each converter produces and the options it accepts.

Supported Converters

Label-free / label-based (for use with MSstats):

Search tool / format	Converter function
Skyline	`SkylinetoMSstatsFormat()`
MaxQuant	`MaxQtoMSstatsFormat()`
Progenesis	`ProgenesistoMSstatsFormat()`
Spectronaut	`SpectronauttoMSstatsFormat()`
Proteome Discoverer	`PDtoMSstatsFormat()`
DIA-NN	`DIANNtoMSstatsFormat()`
DIA-Umpire	`DIAUmpiretoMSstatsFormat()`
FragPipe	`FragPipetoMSstatsFormat()`
OpenMS	`OpenMStoMSstatsFormat()`
OpenSWATH	`OpenSWATHtoMSstatsFormat()`
Metamorpheus	`MetamorpheusToMSstatsFormat()`
MZmine	`MZMinetoMSstatsFormat()`

Isobaric labeling (for use with MSstatsTMT):

Search tool / format	Converter function
MaxQuant	`MaxQtoMSstatsTMTFormat()`
OpenMS	`OpenMStoMSstatsTMTFormat()`
Proteome Discoverer	`PDtoMSstatsTMTFormat()`
Philosopher / FragPipe	`PhilosophertoMSstatsTMTFormat()`
Protein Prospector	`ProteinProspectortoMSstatsTMTFormat()`
SpectroMine	`SpectroMinetoMSstatsTMTFormat()`

Documentation

MSstats data format vignette — the required MSstats input format and how converters produce it
Official website: msstats.org
Bioconductor package page and reference manual

Getting Help / Reporting Bugs

Questions about usage, statistical methods, or troubleshooting: please post to the MSstats Google Group. This is monitored by the development team and searchable, so it's the fastest way to get help and to see if your question has already been answered.
Bug reports and feature requests for this repository: please open a GitHub issue.

References

MSstatsConvert provides the converters used by the MSstats workflow. If you use it, please cite the MSstats publication(s):

Kohler D, Staniak M, Tsai TH, Huang T, Shulman N, Bernhardt OM, MacLean BX, Nesvizhskii AI, Reiter L, Sabido E, Choi M, Vitek O. MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale. J Proteome Res. 2023;22(5):1466-1482. DOI: 10.1021/acs.jproteome.2c00834
Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics. 2014;30(17):2524-2526. DOI: 10.1093/bioinformatics/btu305

Funding

MSstats development has been supported by the Chan Zuckerberg Initiative's Essential Open Source Software for Science.

License

MSstatsConvert is released under the Artistic-2.0 license.