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An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing

Nature Protocols volume 19, pages 2915–2938 (2024)Cite this article

Subjects

Abstract

Technological advances in mass spectrometry and proteomics have made it possible to perform larger-scale and more-complex experiments. The volume and complexity of the resulting data create major challenges for downstream analysis. In particular, next-generation data-independent acquisition (DIA) experiments enable wider proteome coverage than more traditional targeted approaches but require computational workflows that can manage much larger datasets and identify peptide sequences from complex and overlapping spectral features. Data-processing tools such as FragPipe, DIA-NN and Spectronaut have undergone substantial improvements to process spectral features in a reasonable time. Statistical analysis tools are needed to draw meaningful comparisons between experimental samples, but these tools were also originally designed with smaller datasets in mind. This protocol describes an updated version of MSstats that has been adapted to be compatible with large-scale DIA experiments. A very large DIA experiment, processed with FragPipe, is used as an example to demonstrate different MSstats workflows. The choice of workflow depends on the user’s computational resources. For datasets that are too large to fit into a standard computer’s memory, we demonstrate the use of MSstatsBig, a companion R package to MSstats. The protocol also highlights key decisions that have a major effect on both the results and the processing time of the analysis. The MSstats processing can be expected to take 1–3 h depending on the usage of MSstatsBig. The protocol can be run in the point-and-click graphical user interface MSstatsShiny or implemented with minimal coding expertise in R.

Key points

  • Technological advances in bottom-up mass spectrometry-based proteomics have resulted in a substantial increase in the volume and complexity of the resulting data, and for comparative studies, large numbers of samples are required to get statistically meaningful results.

  • MSstats can be used to perform statistical analysis of the data after the peptides and proteins have been identified and quantified. MSstatsBig is a variant specifically designed to manage very large datasets.

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Fig. 1: Overview of the protocol workflow.
Fig. 2: Overview of the plots available in MSstats after data pre-processing and summarization.
Fig. 3: Overview of modeling plots available in MSstats.
Fig. 4: Example sample size calculation plot produced by MSstats.

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Data availability

The dataset used in this protocol is freely available at https://pdc.cancer.gov/pdc/study/PDC000200 and MassIVE (https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=6847574c13964a1f9482ee4d71f33eb1. The quantification results from FragPipe and the MSstats processed data at each step are available in the MassIVE.quant Reanalysis RMSV000000696.1. Source data are provided with this paper.

Code availability

All analysis scripts to recreate Procedure 2 can be found in the same MassIVE.quant Reanalysis RMSV000000696.1.

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Acknowledgements

We thank J. Carver for his help in setting up the MassIVE container that allowed us to share the datasets and analysis code for this paper. This work was supported by awards NSF-BIO/DBI-1759736 (to O.V.), NSF-BIO/DBI-1950412 (to O.V.) and NIH-NLM-1R01LM013115 (to O.V.), the Chan-Zuckerberg Foundation (to O.V.) and National Institutes of Health grants R01-GM-094231 and U24-CA271037 (to A.I.N.). M.S. was partially financially supported by the National Science Centre, Poland, grant Preludium 2020/37/N/ST6/04070.

Author information

Authors and Affiliations

  1. Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA

    Devon Kohler & Olga Vitek

  2. Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA, USA

    Devon Kohler & Olga Vitek

  3. University of Wrocław, Wrocław, Poland

    Mateusz Staniak

  4. Department of Pathology, University of Michigan, Ann Arbor, MI, USA

    Fengchao Yu & Alexey I. Nesvizhskii

  5. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA

    Alexey I. Nesvizhskii

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Contributions

D.K. analyzed the data in MSstats and wrote the relevant MSstats sections of the manuscript. D.K. and O.V. wrote the introduction for the manuscript. M.S. implemented the methods in MSstatsBig. F.Y. analyzed the data by using FragPipe and wrote the relevant FragPipe sections of the paper. F.Y. and A.I.N. determined the experimental dataset for the manuscript. A.I.N., O.V. and D.K. conceptually developed and scoped the manuscript. All authors provided feedback and edited the manuscript.

Corresponding author

Correspondence to Olga Vitek.

Ethics declarations

Competing interests

A.I.N. and F.Y. receive royalties from the University of Michigan for the sale of MSFragger and IonQuant software licenses to commercial entities. All license transactions are managed by the University of Michigan Innovation Partnerships office, and all proceeds are subject to the university technology transfer policy. The other authors declare no competing interests.

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Nature Protocols thanks Chu Wang, Witold Wolski and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

Key references using this protocol

Kohler, D. et al. J. Proteome Res. 22, 1466–1482 (2023)

Kohler, D. et al. J. Proteome Res. 22, 551–556 (2023)

Kong, A. et al. Nat. Methods 14, 513–520 (2017)

Yu, F. et al. Nat. Commun. 14, 4154 (2023)

Clark, D. J. et al. Cell 179, 964–983 (2019)

Extended data

Supplementary information

Supplementary Information

Supplementary Methods 1 and 2, Figs. 1–9 and Tables 1 and 2

Source data

Source Data Fig. 2

Statistical source data for Fig. 2b–d

Source Data Fig. 3

Statistical source data for Fig. 3a–c

Source Data Fig. 4

Statistical source data for Fig. 4

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Kohler, D., Staniak, M., Yu, F. et al. An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing. Nat Protoc 19, 2915–2938 (2024). https://doi.org/10.1038/s41596-024-01000-3

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