MSstatsBig

MSstatsBig is an R/Bioconductor package for preprocessing mass spectrometry-based proteomics experiments that are larger than a standard computer's memory. Modern acquisition protocols — most often data-independent acquisition (DIA) with a large number of MS runs — can produce quantitative reports that the standard MSstats converters cannot load into RAM. MSstatsBig provides drop-in replacement converters that filter each tool's PSM report down to the data required for differential analysis using out-of-memory backends (Arrow / Spark), so the result fits in memory. Once a converter has run, the standard MSstats workflow (dataProcess(), groupComparison()) can be followed as usual.

MSstatsBig 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("MSstatsBig")

The development version can be installed directly from this repository:

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

Quick Start

library(MSstatsBig)

# Example FragPipe msstats.csv output bundled with the package
input <- system.file("extdata", "fgexample.csv", package = "MSstatsBig")

# Convert out-of-memory using the Arrow backend; writes to output_file.csv
converted <- bigFragPipetoMSstatsFormat(input,
                                        "output_file.csv",
                                        backend = "arrow",
                                        max_feature_count = 20)

# Collect the Arrow object into an in-memory data.frame
converted <- as.data.frame(dplyr::collect(converted))

# Continue with the standard MSstats workflow
library(MSstats)
summarized <- dataProcess(converted, use_log_file = FALSE)

Users can also feed data into the underlying MSstatsPreprocessBig() function directly — either from a tool's native export format or by converting raw data chunk by chunk — to support other tools. See the workflow vignette for details.

Supported Converters

MSstatsBig provides larger-than-memory replacements for the standard MSstats converters. After a converter runs, its output is used with MSstats:

Search tool / format	Converter function
FragPipe	bigFragPipetoMSstatsFormat()
Spectronaut	bigSpectronauttoMSstatsFormat()
DIA-NN	bigDIANNtoMSstatsFormat()
Generic MSstats-format data	MSstatsPreprocessBig()

The MSstatsAddAnnotationBig() helper attaches experimental-design annotation to converted data. See the MSstatsBig workflow vignette for the required input files and options for each converter.

Documentation

• MSstatsBig workflow — full worked example from raw data to results
• 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

MSstatsBig prepares data for the standard MSstats workflow. If you use it, please cite the MSstats publication(s):

1. 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
2. Kohler D, Vitek O, et al. An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing. Nat Protoc. 2024;19:2915-2938. DOI: 10.1038/s41596-024-01000-3

Funding

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

License

MSstatsBig is released under the Artistic-2.0 license.