Context Systemic events resulting from mother-embryo relation at the peri-implantation period may result in specific changes to the protein composition of serum and thus provide a source of biomarkers for early detection of pregnancy. Aims We set out to use two different quantitative proteomic approaches to test this hypothesis by comparing heifer serum at the peri-implantation period to that from cycling heifers. Methods Two-dimensional electrophoresis (2-DE) and isobaric tags were used for relative and absolute quantitation (iTRAQ) of proteins. Key results These methods yielded complementary data indicating biomarker candidate proteins. Conclusions Different proteomic methods provide different and complementary information that needs to be analysed in order to consider proteins as potential biomarkers. Implications In order to characterise the proteome under specific conditions, the use of complementary techniques is advisable.