A reference database enabling in-depth proteome and PTM analysis of mouse immune cells

Abstract Spectral libraries fulfill multiple functions in biological and analytical applications. For biologists, these libraries provide a valuable resource to verify the presence and abundance of proteins or pathways within a selected cell type thus determine the feasibility of further experiments. Despite advances, existing libraries are incomplete and provide researchers only a limited amount of information. To address this, we introduce the reference database - Spectral Library of Immune Cells (SpLICe), a resource covering B-cells, CD4 and CD8 T-cells, macrophages and dendritic cells containing nearly 9,000 protein groups and 110,346 proteotypic peptides. Additionally, the database provides data on > 20,000 post-translationally modified proteotypic peptides (oxidation, phosphorylation, methylation, acetylation, deamidation and N-glycosylation) across the selected immune cell populations. SpLICe supports the quantification of more than half of total murine proteins annotated by UniProtKB/Swiss-Prot, enabling monitoring of selected proteins or pathways from Reactome pathways and Gene Ontology databases. The platform provides relative protein abundances and supports the generation of targeted mass spectrometry assays by identifying and scoring proteotypic peptides.