Variation in the milk serum proteome within and between individual cows

The objective of this observational study was to determine the variation between and within cows for their milk serum proteome. We used two sample sets to investigate the individual variations in milk serum proteome. Sample set 1 were mature milk with 5 times points collected between 2 months after the start and 2 months before the end of lactation. The information of diet, SCC and parity were recorded. Sample set 2 consisted of 17 mature milk samples, being in the same range of lactation days. Sample sets were prepared using filter aided sample preparation, either label free (Sample set 1) or with dimethyl labelling (Sample set 2), followed by Orbitrap-LC-MS/MS for protein analysis. The results showed that the milk serum protein was very constant in mid lactation (Sample set 1). Sample set 2 showed significant variation in the milk serum proteins between individual cows. The most variable proteins were immune-related proteins, whereas proteins related to nutrient synthesis and transport were relatively constant.