Improving SWATH-MS data analysis using multi-omics approach

Proteomics research has relied on publicly accessible sequence databases for mining peptide fragmentation patterns and deriving biological information. The limitation of this approach is that databases are as good as genome annotation, which can be incomplete or not available for non-model organisms. A novel reference genome-independent proteomics pipeline termed DIA-Seq is introduced. The pipeline integrates the advancements of long-read RNA sequencing (Iso-Seq) and deep learning neural network tools for isoform-specific peptide spectra prediction and SWATH-MS based quantification. DIA-Seq pipeline developed in the study improves annotation of a well-characterized model organism. It has the potential to fast-track discoveries in non-model species