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Related Experiment Video

Updated: Oct 26, 2025

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

ppx: Programmatic Access to Proteomics Data Repositories.

William E Fondrie¹, Wout Bittremieux^2,3, William S Noble^1,4

¹Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.

Journal of Proteome Research

|August 3, 2021

Summary

This summary is machine-generated.

A new Python package, ppx, offers easy access to ProteomeXchange proteomics data for reproducible research. It integrates into workflows, enabling efficient data retrieval and analysis for computational tool development and validation.

Keywords:

FAIR Python bioinformatics data access data dissemination data sharing mass spectrometry proteomics repository reproducibility

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Last Updated: Oct 26, 2025

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

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Published on: August 19, 2025

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Area of Science:

Proteomics
Computational Biology
Bioinformatics

Background:

Public proteomics and mass spectrometry data repositories are rapidly expanding.
Open science practices necessitate accessible data for validation and tool development.

Purpose of the Study:

To introduce ppx, a Python package for programmatic access to ProteomeXchange data.
To demonstrate ppx's utility in enhancing reproducible research workflows.

Main Methods:

Developed ppx, a Python package and command-line tool.
Utilized ppx within a Snakemake workflow to reanalyze a published dataset.
Employed the ANN-SoLo tool for open modification searching.

Main Results:

ppx provides easy programmatic access to ProteomeXchange data (PRIDE, MassIVE).
The tool seamlessly integrates into computational workflows like Snakemake.
Reanalysis using ppx yielded results consistent with the original study, confirming reproducibility.

Conclusions:

ppx facilitates reproducible proteomics data analysis and tool development.
The package simplifies data retrieval for benchmarking and large-scale analyses.
ppx is an open-source tool promoting open science in proteomics.