DO-MS

Data-Driven Optimization of Mass Spectrometry Methods

GitHub release GitHub

Get started now Download JPR Article GitHub Repository

Getting Started

Please read our detailed getting started guides:

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. All modules are maintained for MaxQuant >= 1.6.0.16.

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.

Installation

Install this application by downloading it from the release page.

Running

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

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.

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

Automated Report Generation

You can automatically generate PDF/HTML reports without having to launch the server by running the do-ms_cmd.R script, like so:

$ Rscript do-ms_cmd.R config_file.yaml

This requires a configuration file, and you can find an example one here. See Automating Report Generation for more details and instructions.

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.

Search Engines Other Than MaxQuant

This application is currently maintained for MaxQuant >= 1.6.0.16. 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 is also freely available on bioRxiv: https://www.biorxiv.org/content/10.1101/512152v1.

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.

Data

Figures/Analysis


Help!

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