For optimal results, and overcoming the limitations of incomplete, poorly annotated and highly redundant bovine protein databases, a customized protein database was created for the searches. The one protein sequence per gene version of the Bos taurus (taxon ID 9913) reference proteome (ID UP000009136) of 8 January 2022 was downloaded from UniProt (https://www.uniprot.org/proteomes/UP000009136) in FASTA format on 3 March 2022. This database was further processed by removing residual duplicate sequences (i.e. protein sequences with the same gene name), adding complete sequence where only fragment sequences were present, and updating the FASTA headers to the current headers of the date of download, i.e. 3 March 2022. Considering that the bovine immunoglobulins in UniProt were listed under the names “uncharacterized protein” or “Ig domain-containing protein”, functional bovine immunoglobulin heavy and light chain, constant and variable sequences were downloaded from the reference directory of the international ImMunoGeneTics information system (IMGT RefSeq, https://www.imgt.org/vquest/refseqh.html). The constant immunoglobulin heavy chain sequences were assembled from the respective fragment sequences of the constant heavy (CH) domains and hinge (H) regions. A single representative allele for each immunoglobulin gene sequence was kept in the working protein database. The contaminants FASTA file from the installation folder of the MaxQuant software was processed to remove all bovine contaminants. Database searches were performed on MaxQuant v 1.5.3.30 against the three databases described above combined, using default settings unless otherwise specified. The built-in contaminants feature of MaxQuant was deactivated. Digestion mode was set to specific against Trypsin/P and GluC, allowing a maximum of two missed cleavages. Methionine oxidation, protein N-terminus acetylation, and serine and threonine phosphorylation were searched as variable modifications. Cysteine carbamidomethylation was set as a fixed modification. Minimum peptide length was allowed at five amino acids, and maximum peptide mass was limited at 10,000 Da. Protein quantification was performed on a minimum of two unique + razor peptides. Label-free quantification was carried out using the intensity based absolute quantification (iBAQ) values. FTMS recalibration was activated. Following the database search, the protein groups table was further post-processed to remove non-bovine contaminants, reverse identifications, variable immunoglobulin sequences, proteins identified by less than two unique peptides, and proteins identified with an Andromeda score below 20. Supplementary Fig. S14 illustrates the shortcomings of commonly-used SwissProt and UniProt bovine protein databases, and the advantages of using our optimized bovine protein database.