Accurately identifying modifications in protein sequences is a critical first step for PTM profiling, and thus our approach may benefit routine proteomic analysis.
As expected, this newly identified modification of IRF3 is not needed for its transcriptional activity (Chattopadhyay et al., 2016).
In order to evaluate the distribution of acetylation sites in the acetylated proteins of Y. lipolytica, we calculated the numbers of identified modification sites per protein.
We find that a modest alteration of an initially 'scale-free' network can usefully improve robustness against attack, particularly when the fraction of attacked nodes is small, and we identify modification schemes that are most effective for this purpose.
Based on these data each of the identified modification patterns is assigned a position index (Supplementary Table S1) in order to build the full depth-wise modification profile.
Histone modifications are most complex, as those occur at multiple sites within multiple genes, blurring assessment of biological impact of identified modification [ 54].
In the same data set, we recently identified modification by stress in the relation between bone lead and heart rate variability (Clougherty JE, Peters JL, Schwartz J, Kubzansky L, unpublished data).
Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites.
Including an interaction term to identify modification by centre was not possible, since we had 31 centres in this study in 16 European countries with unequal numbers of participants per centre or country.
A histone ubiquitin ligase determines the resistance to necrotrophic fungi [ 35], and the growing number of identified modification types makes it likely that more of them will also be connected with stress regulation.
