I am investigating the proteome of human cancer samples and want to insert their genetic variations into the reference proteome fasta sequences to increase the sensitivity of my peptide/protein quantification.
Can you implement this "proteomeVariantInsertion()" in the VariantAnnotation package?
VariantAnnotation::predictCoding() function already translates codons at variant positions from a reference BSgenome object to assess the consequences of a variant. I would like to take all coding variants (or just non-synonymous SNVs for a start) and insert them into the reference proteome, then save the modified fasta file.
In principle the package customProDB is already doing this job. But from 11,000 genes with ~40k non-synonymous SNVs that were extracted using VariantAnnotation::predictCoding() only ~2k proteins are changed with at least one variant. There is too much loss.
The customProDB package works mostly on custom data.frames and could utilize the maintained Bioc objects on variants and sequences much more.
I would highly appreciate a "Bioconductor-native" solution for the customized proteome challenge.