In our experiments, the mass tolerance for decoys was set at 20 ppm, maximum missed cleavage number was set to 2, peptide variation was set at 200 Da and the number of decoys per target was set to 20.
Briefly, each cleavage site is labeled with a number, and the fragment ions arising from particular cleavages are shown next to each cleavage number with their associated m/ z values.
As can be seen in Figure 1, α- and β-cleavage pathways (numbered 1 and 2, respectively) converge on a further intramembrane γ-cleavage (numbered 3) by the PS-containing γ-secretase complex to release the variable length Aβ and P3 peptides and the variable length APP intracellular domain (AICD).
Six SNPs were found in the upstream region and one in the region close to the cleavage site (number 1 7 in figure 2, panel A).
The effect of the independent variable oocyte donor's breed on the different dependent variables -i.e. cleavage rate, number of cleaved beyond the 2-cell stage, number of blastocysts at day 7 and at day 8, and quality grade was tested using Logistic regression models with the intercept as random effect and batch as grouping variable.
Embryos were examined for cleavage (cell number) and grade, which includes cytoplastmic fragmentation.
CusA in C12M is also highly dynamic, explaining why AcrB and CusA have opposite crystallisation behaviours and diverging proteolytic profiles that cannot be explained by a higher cleavage site number in CusA sequence.
The search was carried out with default settings and thus the cleavage specificity, number of missed cleavages and mass tolerances were preset.
Other discriminative information includes the mass accuracy, presence of missed cleavage sites, number of peptide termini consistent with the enzymatic cleavage, and etc.
As citrullination of arginine abrogates the site of trypsin cleavage, the number of digested peptides diminishes with the rate of citrullination.
n is the cleavage cycle number, R v a and R u a are the maximum synthesis rates, D v a and D u a are the diffusion coefficients, and λ v a and λ u a are the decay rates for protein and mRNA of gene a.
