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plexDIA: Multiplexed data-independent acquisition

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Perspective: Derks, J., Slavov N., Strategies for increasing the depth and throughput of protein analysis by plexDIA, 10.1101/2022.11.05.515287, GitHub J. Proteome Res. 22(10):3149-3158 10.1021/acs.jproteome.3c00177

 

Requirements

This application has been tested on R >= 3.5.0, OSX 10.14 / Windows 7/8/10. R can be downloaded from the main R Project page or downloaded with the RStudio Application.


Reproducing the data analysis

  1. Download all the data reports from the "search" section of MassIVE MSV000089093.

  2. Download the two meta files from the "metadata" section of MassIVE (specifically, "Meta_SingleCell.tsv" and "Meta_Bulk_benchmarking.tsv") MSV000089093.

  3. Create a new R project, and copy the .Rmd, .R, .py, and .txt files from the Code section (https://github.com/SlavovLab/plexDIA) to it. Note: The main functions are in plexDIA_Functions.R, but it uses the other functions in the code directory, so please download all.

  4. Please update the file paths in the .Rmd.

  5. Run!

About the project

The manuscript is freely available on bioRxiv: Derks et al., 2022 (version 2). The peer reviewed version is available at Nature Biotechnology: Derks et al., 2022

For more information, contact Slavov Laboratory or directly Prof. Nikolai Slavov

License

The plexDIA code is distributed by an MIT license.

Contributing

Please feel free to contribute to this project by opening an issue or pull request.


Help!

For any bugs, questions, or feature requests, please use the GitHub issue system to contact the developers.

About

Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.

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