Proteomic Analysis of White-tailed Deer

Mass spectra were searched against a protein database using the SEQUEST [25 (link)] algorithm in Bioworks 3.3 (Thermo Fisher Scientific). At the time of analysis, the C. virginianus known proteome contained fewer than 100 proteins so the reference proteome (RefSeq) for Gallus gallus containing 18,768 entries was downloaded from NCBI on September 29, 2009. The protein database was in silico trypsin digested and cysteine carbamidomethylation and methionine oxidations (single and double) were included in the search criteria. Precursor and fragment ion tolerances were set at 1.5 Daltons. A randomized decoy database was also searched with mass spectra using the same search criteria as described above to estimate the probability of peptide identifications being false positives. We used a peptide probability filter of p ≤ 0.05 for protein identifications. Identified proteins were evaluated for differential expression using Monte Carlo re-sampling statistics [26 (link)] at a p-value of ≤ 0.05. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001206.