Patpat

Patpat stands for Proteomics Aiders Telescope, a public proteomics dataset search framework that simply passes in protein identifiers to search for relevant datasets and returns metadata to aid your research.

Installation

pip install patpat

Quickly Use

Load Patpat package and create runtime environment:

import patpat.hub as hub
import patpat.mapper as mapper
import patpat.utility as utility

utility.init()
utility.initiate_uniprot_proteome_catalog()

Directory structure of the runtime environment is as follows:

patpat_env/
    |-- logs/
    |-- tmp/
    |-- result/
    |-- proteome/
        |-- UP_README_yyyy-mm-dd

As an example, take the mouse protein P23950 (UniProt) and search for the peptide to be searched by QueryHub

identifier_ = 'P23950'
q = hub.QueryHub()
q.identifier = identifier_
q.simple_query()

Having checked that the corresponding FASTA file for Mus musculus does not exist locally, consider obtaining from UniProt:

Choose local peptide search.
The Mus musculus UP000000589 proteome file was not found locally.
Do you want to download it?(y/n)

Get the search configs:

conf_ = q.get_query_config()

Set up Mappers based on connectivity and add MapperHub's configuration, search and get results.:

mappers_ = hub.CheckerHub().checker()

m = hub.MapperHub(config=conf_,
                  mappers=mappers_,
                  )
m.mapping()

result_ = m.export()

Result files store in patpat_envs/result/<task_uuid>, you can find <task_uuid> by m.config

In its current version, Patpat supports both PRIDE, iProX and MassIVE databases. In addition, Patpat is an extensible framework and users are encouraged to extend it with databases of interest to Patpat or to build their processes.

For more information, see the Wiki.

Cite us

Weiheng Liao, Xuelian Zhang, Patpat: a public proteomics dataset search framework, Bioinformatics, Volume 39, Issue 2, February 2023, btad076, https://doi.org/10.1093/bioinformatics/btad076

Credits

This work is inseparable from the help of predecessors, and the list is listed in the references section of the article.