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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. EncyclopeDIA also supports Prosit, a deep learning tool for generating peptide fragmentation spectra, as described in our new methods paper (Searle et al, 2020).

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.

Stable versions: Release Date Major Changes (see changelog for full details)
encyclopedia-0.9.5 2019-06-27 Added Thesaurus into the main build. Also additional options for Percolator, PTMs, the Window Scheme Wizard, and support for command line conversion
encyclopedia-0.9.0 2019-06-27 support for Prosit libraries, see this new paper! Also Maxquant, Spectronaut, and Progenesis
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

How do I start collecting DIA?

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. Our new "tutorial", Pino et al, 2020, is a great place to gain intuition about why these methods and settings make sense, and this content is consolidated in our ASMS 2020 talk, which has full lecture notes.

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. Alternatively, if you're doing work with non-human samples, you can download a pre-generated Prosit library or read our tutorial on developing new Prosit libraries using only a FASTA database.

How do I use EncyclopeDIA?

EncyclopeDIA is a cross-platform Java application that has been tested for Windows, Macintosh, and Linux. Specifically, we have tested it under Windows 8 and 10, Mac OS X 10.11-15, and RedHat Linux 4.4. The EncyclopeDIA GUI can be opened by double clicking on the EncyclopeDIA .JAR (e.g. EncyclopeDIA-0.9.0-executable.jar). EncyclopeDIA can also be used at the command line and there are more detailed instructions for this available in the FAQs.

EncyclopeDIA requires 64-bit Java 1.8. If you don’t already have it, you can download either the “Windows x64 Offline”, "Mac OS X x64 .DMG" or "Linux x64" link from the Java SE Runtime Environment 8 downloads website, depending on your specific operating system. The download and installation time should take only a few minutes.

Check here for FAQs.

Check here to report Issues.

Check here for file format guidelines.

Who do I talk to?

This is a Searle Lab and MacCoss Lab project from the Institute for Systems Biology and 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, and thank you to all code contributors! 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.