Updated project metadata. Companion dog care market is annually increasing. A relationship with a dog who lives with humans gives a lot of psychological stability. Therefore, companion dog's health is important to the owner. It would be of great help if a non-invasive method could monitor health through bodily fluids (urine, serum). In addition to this, it is principal to discover and verify protein biomarkers that can detect the presence or absence of disease. Despite the growing application of proteomics in biomarker research using canine serum or urine, there is no spectral assay library publicly available. Here, we set up spectral assay libraries for canine serum and urine samples using 24 midpH-fractionated samples to enable deep proteome coverage. The canine serum assay library includes 4,749 protein groups and 25,228 peptides and urine assay library contains 1,132 protein groups and 5,483 peptides.