This dataset is a label-free quantitation of proteins milk and dry secretions from the end of lactation through day 21 of the dry period using liquid chromatography with tandem mass spectrometry (LC-MS/MS). The data supplied in this article supports the accompanying publication entitled “Characterization of bovine mammary gland dry secretions and their proteome from the end of lactation through day 21 of the dry period”. The Thermo mass spectrometry raw files and MaxQuant files have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset number PXD017837. Resources in this dataset:Resource Title: Characterization of Bovine Dry Secretions and their Proteome from the End of Lactation Through Day 21 of the Dry Period - ProteomeXchange Consortium via the PRIDE partner repository, Project PXD017837. File Name: Web Page, url: https://www.ebi.ac.uk/pride/archive/projects/PXD017837 Thermo raw file code for Pride raw files and supplemental Excel files. The 3 technical replicates are denoted as a letter A, B and C. The number following is the cow identification number for 11 cows used. The final two-digit number after the underscore is the day sampled where _01 = day 1, _03 = day 3, _10 = day 10 and _21 = day 21 of dry period. For example, A1313_01 is technical replicate A for cow 1313 collected on day 1. B1313_03 is technical replicate B for cow 1313 collected on day 3. Details of sample and data processing protocols are provided.