A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs

The domestic dog, Canis lupus familiaris, plays a vital role as companion or service animal, and the well-being and healthy aging of dogs is gaining importance. Proteins are key actors in cells, tissues and body fluids, and the ability to measure their composition and abundance is crucial to understand biological processes. We report a mass spectrometry-based proteomics approach analyzing canine tissues, plasma and urine obtained from Labrador retrievers to develop two comprehensive resources to advance the study of the dog proteome. Firstly, we developed a Labrador PeptideAtlas covering 49% of the predicted UniProtKB proteome and secondly, a Labrador spectral assay library for targeted applications by data-independent acquisition that enables the identification and quantification of 11,792 proteins (11,564 protein groups) of the dog proteome (56%). We demonstrate the performance of the library with gradients of different length and quantify 10,140 proteins in tissues and 385 proteins in plasma.