Fast screening and quantitative evaluation of internally deleted goat αs1‐casein variants by mass spectrometric detection of the signature peptides

Currently, the internally deleted caprine α_s1‐casein (α_s1‐CN) variants F and G, associated with low casein expression, are detected by means of ordinary descriptive techniques. No relevant procedure is available to detect internally deleted goat α_s1‐CN in bulk milks. The availability of full‐length and α_s1‐CN F and G variants allowed us to further investigate this issue. Using matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry (MS) and high‐performance liquid chromatography (HPLC)/electrospray ionization (ESI)‐MS and ESI‐MS/MS, tryptic signature peptides α_s1‐CN F f59‐63/f43‐63, α_s1‐CN G f4‐20/f4‐21, α_s1‐CN B₂ f4‐22 Pro₁₆ and α_s1‐CN A f4‐22 Leu₁₆ were identified. This also helped to solve the interesting question of how the casein variants contribute to the composition of goat's bulk milk. Synthetic peptide analogues with ionization efficiency equivalent to that of tryptic junction peptides were used as internal standards to evaluate α_s1‐CN variants, either individually or globally, using bulk milk from a single goat breed as a model system. Here, α_s1‐CN F accounted for 0.15 ± 0.08% and the α_s1‐CN G variant was missing or below the 0.10% detection limit. The analysis of six samples confirmed that α_s1‐CN G was missing and that α_s1‐CN F occurred at a low frequency in hybrid and local breed bulk milks from Mediterranean areas. In conclusion, a quantitative MS‐based application of the signature peptides for full‐length and internally deleted variants in goat's casein is provided. The strategy is also suggested for the determination of splice variants in any biological sample. Copyright © 2009 John Wiley & Sons, Ltd.