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vasicek58 authored Apr 3, 2024
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## Using the database for proteomic searches
Once you obtain a list of peptide-spectrum matches (PSMs), you can use a pipeline provided in the \([PeptideAnnotator](https://github.com/ProGenNo/ProHap_PeptideAnnotator)\) repository to map the peptides back to the respective protein haplotype / variant sequences, and map the identified variants back to their genetic origin. For the usage and details, please refer to the following [wiki page](https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches).
Once you obtain a list of peptide-spectrum matches (PSMs), you can use a pipeline provided in the [PeptideAnnotator](https://github.com/ProGenNo/ProHap_PeptideAnnotator) repository to map the peptides back to the respective protein haplotype / variant sequences, and map the identified variants back to their genetic origin. For the usage and details, please refer to the following [wiki page](https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches).

## Output
The ProHap / ProVar pipeline produces three kinds of output files. Below is a brief description, please refer to the [wiki page](https://github.com/ProGenNo/ProHap/wiki/Output-files) for further details.
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