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Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. Check out our manuscript describing EncyclopeDIA at Nature Communications (Searle et al, 2018) for more information. EncyclopeDIA contains Walnut, an implementation of the PECAN (Ting et al, 2017) scoring system, to enable chromatogram library generation from FASTA protein sequence databases when spectrum libraries are unavailable.

How do I get EncyclopeDIA?

EncyclopeDIA is open source under the Apache 2 licence, which means you can do what you like with the software, as long as you include the required notices. You can download the latest stable version or look at the manual.

You can check out a DIA quick start document you're interested in how to set up your instrument to collect DIA data or check out recommended starting settings for DIA on Thermo instruments. Finally, if you're doing work with Human samples (including tissue or cells), you can download an EncyclopeDIA-compatible version of the Pan-Human library created from the Rosenberger et al, 2014 dataset.

Stable versions: Release Date Major Changes (see changelog for full details)
encyclopedia-0.8.1 2019-01-13 new Window Scheme Wizard
encyclopedia-0.8.0 2019-01-04 improved file converters, new visualizations, update notifications
encyclopedia-0.6.14 2018-03-02 original upload used in Searle et al, 2018

Who do I talk to?

This is a MacCoss Lab project from the University of Washington, Department of Genome Sciences. For more information please contact Brian Searle (bsearle at systemsbiology dot org).

Contribution guidelines

Code contributions are welcome! However, any contribution must follow the coding style of the project, be presented with tests, and stand up to code review before it will be accepted.