PepCentric is a tool that can search proteins and peptides against repository-scale MS/MS spectra (~2 billion spectra) within seconds. It also controls the global false-discovery rate (FDR) for the search results.
- Our public PepCentric website: http://peptidecentric.org/
- Our RESTful API
- Users can submit their peptide or protein sequences using the "input query" box or upload a file on the landing page
- Select the input type (protein or peptide)
- Select the enzyme type
- Fill in optional user information, including analysis name and email
- Click "submit"
- There will be a job ID displayed on the webpage. Please make a note of the ID in case you wish to revisit the results.
A query must be given either in the input box or as an uploaded file, not both. An uploaded file has to be smaller than 1 MB, and text typed into the input box may not exceed 100000 amino acids.
The "Get Results" link in the navigation bar can be used to retrieve old results based on the job ID.
There is also a "dump" button to export all results given a job ID. It might take a long time if there are many entries. Each result table can also be exported on its own, as CSV or as Excel.
Get the frontend and backend servers from the following links:
- Frontend server: https://github.com/Nesvilab/PepCentric-frontend
- Backend server: https://github.com/Nesvilab/PepCentric/releases/tag/latest
Set up the servers by following this tutorial
PepCentric Enables Fast Repository-Scale Proteogenomics Searches
Fengchao Yu, Andy T. Kong, Yi Hsiao, Alexey I. Nesvizhskii
bioRxiv, 2025, DOI: 10.1101/2025.02.24.639867