Library Searching for Data Independent Acquisition
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).