PrecisionProDB online

PrecisionProDB (Precision protein database), a tool improving the proteomics performance for precision medicine.

To start, paste in the variants. Click start directly to test.

If input the variants, less than 1000 variants are allowed. If upload a file, the file size should be less than 10MB. Gzip file is also accepted.

PrecisionProDB is a Python package for proteogenomics, which can generate a customized protein database for peptide search in mass spectrometry.
Current models were: GENCODE v47, Ensembl v113, RefSeq GCF_000001405.40-RS_2024_08, RefSeq T2T-CHM13v2.0 GCF_009914755.1-RS_2024_08. For input variants, chromosome name like "chr1" or "1" is be auto-matched when gene model is from RefSeq. To use T2T-chm13, the variant positions should match the genome annoation! Liftover is required if variants were not called based on this version of genome. Users may test T2T-chm13 with this file. More examples are available.
Position of variant is 1-based, like in the GTF annotation and vcf file. Not 0-based like in the bed file!
The uploaded file must be in the tsv format (gzipped is OK). Check the instruction or check the example file here. It may took a long time to finish. The files will be deleted after 30 days. To process vcf file, it is suggested to run it locally. Or you may convert it to tsv file with vcf2mutation.py. Files be provided in the gzipped format. An example output page can be found here.
Open an issue if you have any questions or encounter any issues as we cannot anticipate all potential errors. For commercial use, please contact us for details.