I'm currently working on a proteogenomics project, and using customProDB to generate a custom protein database, it's a great R package and i find it really helpful.
However, I recently discovered a bug with the aaVariation function were Leucine is predicted as Methionine.
# R example :
txid genename txname proname chr strand pos refbase varbase pincoding rsid COSMIC_id refcode varcode
2 649 ENSG00000138593 ENST00000559471 ENSP00000453854 15 - 49325289 A C 537 rs11638215 <NA> CTT CTG
vartype aaref aapos aavar
2 non-synonymous L 179 M
Since the CTG codon gives leucine and not methionine after translation, i made a correction on the output while waiting for a permanent fix.