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Information for Design of Follow-Up Experiments

For follow-up experiments, candidate proteins and specific PTM sites are selected on the basis of confidence of sequence and PTM assignments, stoichiometry data, and their potential role in the biological context [131]. Analysis of proteomic data to filter them based on protein function can be achieved using Gene Ontology terms as reviewed by Schmidt et al. [132]. Evolutionary conservation of PTMs across members of a domain family can be used to predict functionally important regulatory regions: PTMs that are known or predicted to be regulated in vivo are more likely to be conserved across species than average sites, particularly those involved in PTM cross talk [133]. In silico data demonstrate that the majority of lysine acetylation sites have the potential to impact protein phosphorylation, methylation, and ubiquitination status [134]. Thus, analysis of protein acetylation and methylation should be considered in the context of other PTMs in terms of determining regulatory pathways and mechanisms.

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