DO-MS

Data-Driven Optimization of Mass Spectrometry Methods

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• BioArxiv Preprint

Getting Started

Please read our detailed getting started guides:

• Getting started with DIA preprocessing
• Getting started with DIA reports
• Getting started with DDA reports

Requirements

This application has been tested on R >= 3.5.0, OSX 10.14 / Windows 7/8/10/11. R can be downloaded from the main R Project page or downloaded with the RStudio Application. All modules are maintained for MaxQuant >= 1.6.0.16 and DIA-NN > 1.8.1.

The application suffers from visual glitches when displayed on unsupported older browsers (such as IE9 commonly packaged with RStudio on Windows). Please use IE >= 11, Firefox, or Chrome for the best user experience.

Running the Interactive Application

The easiest way to run the app is directly through RStudio, by opening the DO-MS.Rproj Rproject file

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and clicking the "Run App" button at the top of the application, after opening the server.R file. We recommend checking the "Run External" option to open the application in your default browser instead of the RStudio Viewer.

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You can also start the application by running the start_server.R script.

Customization

DO-MS is designed to be easily user-customizable for in-house proteomics workflows. Please see Building Your Own Modules for more details.

Hosting as a Server

Please see Hosting as a Server for more details.

Supporting other Search Engines

This application is currently maintained for (MaxQuant)[https://www.nature.com/articles/nbt.1511] >= 1.6.0.16 and (DIA-NN)[https://www.nature.com/articles/s41592-019-0638-x] >= 1.8. Adapting to other search engines is possible but not provided out-of-the-box. Please see Integrating Other Search Engines for more details.

Can I use this for Metabolomics, Lipidomics, etc... ?

While the base library of modules are based around bottom-up proteomics by LC-MS/MS, this project is fundamentally compatible with any delimited text files (CSV, TSV, etc). These implementations will require some programming work, but once it is done DO-MS gives you a extensible framework that can be used over-and-over again to generate shareable reports. See Integrating Other Search Engines for more details

About the project

The manuscript for this tool is published at the Journal of Proteome Research: https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00039 The manuscript for the extended version 2.0 can be found on bioArxiv: https://www.biorxiv.org/content/10.1101/2023.02.02.526809v1

Contact the authors by email: nslavov{at}northeastern.edu.

License

DO-MS is distributed by an MIT license.

Contributing

Please feel free to contribute to this project by opening an issue or pull request in the GitHub repository.

Help!

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