EncyclopeDIA - Galaxy Training Network

In proteomics research, data-independent acquisition (DIA), a mass spectrometry technique improves the depth of peptide and protein detection and quantitation. In one of the methods published by Searle et al, a narrow-window, gas-phase fractionated (GPF) DIA method is performed to acquire data on pooled samples from biological replicates. The EncyclopeDIA software (doi: 10.1038/s41467-018-07454-w), is used to generate a chromatogram library from GPF data for subsequent processing and searching of experimental datasets. Chromatogram library offers a) refined and accurate retention time information and b) recalibrates the spectral library to generate a library that represents detectable precursor/transitions for experimental analysis (doi: 10.1038/s41467-018-07454-w). We have deployed EncyclopeDIA in Galaxy, enabling processing of pooled GPF data and mining of DIA data. This enables quantitative data generation for: a) proteomics analysis (for single-organism datasets); b) proteogenomics analysis (integrating proteomics and RNA-Seq datasets) which will help detect rare sequence variants; c) metaproteomics analysis (integrating metagenomics and proteomics datasets) will aid in detecting key microbial proteins, functional groups, and taxa and d) using deep learning approach-based PROSIT-predicted library of fragmentation patterns and retention times for every peptide in a FASTA database (doi:10.1038/s41592-019-0426-7)