Hybrid-DIA is a new acquisition method that combines simultaneous targeted and discovery (DIA) proteomics strategies. HybridDIA is based on an Application Programming Interface, which enables the ability to combine targeted and discovery proteomics by intercalating DIA scans with accurate triggering of predefined peptide targets.
Hybrid-DIA data is obtained using the Moonshot iAPI from Thermo, which is available at API.
The pipeline to analyze HybridDIA files is comprised of three steps:
- Extract MSx Scans from the raw file. This step requires pymsfilereader and ProteoWizard.
- Upload to Skyline to extract the Fragment Intensities of the Heavy (Internal Standard or IS) and Light (Endogeneous or ENDO) peptides.
- Injection Time based intensity correction and data visualization.
You can find a complete guide in: Guide
Any of the code required to run this pipeline requires an standard computer.
This pipeline is supported and has been tested in Windows 10 systems.
Information about recommended packages and software versions used in this pipeline are included in Guide.
Demo files to execute the pipeline and expected outputs are available: Demo