Table 1.

Recommended best practices for inter‐ and intra‐database integration for chemoproteomics datasets.

Entry	Recommendation
A	Support integration of quantitative chemoproteomics studies by (i) providing reference UniProtKB FASTA files alongside raw proteomic data files and (ii) including genomic coordinates for the codons of identified amino acids in the reference files
B	Perform proteomics database searches against reference database sequences that map to known transcript and gene coordinates (e.g., CCDS)
C	Perform sequence identity checks, which will identify and minimize mismapping caused by canonical sequence updates between UniProtKB releases
D	Map data to the appropriate genome assembly for downstream applications. Genome assembly updates can introduce or refine genome resolution and in doing so alter the genomic coordinates of codons. Not all downstream pathogenicity predictors are compatible with both GRCh37 and GRCh38 (Appendix Table S14)