# Percolator

> proteomics analysis software

**Wikidata**: [Q113089939](https://www.wikidata.org/wiki/Q113089939)  
**Source**: https://4ort.xyz/entity/percolator-q113089939

## Summary
Percolator is an open-source software tool designed for proteomics analysis, specifically for processing and validating data from mass spectrometry experiments. It is widely used in biomedical research to improve the accuracy of protein identification. Funded by the Chan Zuckerberg Initiative, the software has been actively maintained since its initial release in 2014.

## Key Facts
- **Funder**: Supported by the Chan Zuckerberg Initiative through the Essential Open Source Software for Science program grant.
- **Latest Stable Version**: Version 3.07, released on May 31, 2024.
- **Website**: http://percolator.ms/
- **Source Code Repository**: Hosted on GitHub at https://github.com/percolator/percolator.
- **Initial Release**: Version 2.05 debuted on February 10, 2014.
- **Classification**: Categorized as "software" with a focus on proteomics analysis.

## FAQs
### Q: What is Percolator primarily used for?
A: Percolator is used to analyze mass spectrometry data in proteomics, helping researchers validate protein identifications and reduce false positives.

### Q: Is Percolator open-source?
A: Yes, the software is open-source, with its code freely available on GitHub for community contribution and use.

### Q: Who funds Percolator’s development?
A: The Chan Zuckerberg Initiative supports Percolator through its Essential Open Source Software for Science program.

## Why It Matters
Percolator plays a critical role in proteomics by addressing the challenge of accurately interpreting complex mass spectrometry data. Its statistical validation algorithms help researchers distinguish true protein identifications from random matches, a key bottleneck in large-scale studies. As an open-source tool, it promotes accessibility and collaboration in the scientific community, driving advancements in fields like systems biology and disease research. Continuous updates since 2014, including recent versions like 3.07, reflect its evolving utility in handling modern datasets, ensuring it remains a foundational resource for proteomics workflows.

## Notable For
- **Open-Source Accessibility**: Freely available for use and modification, fostering transparency and community-driven improvements.
- **Long-Term Maintenance**: Actively updated since 2014, with consistent releases (e.g., versions 2.05 to 3.07) ensuring compatibility with advancing technologies.
- **Specialized Funding**: Supported by the Chan Zuckerberg Initiative, highlighting its importance in scientific infrastructure.
- **Integration with Workflows**: Compatible with tools like MSGF+ for seamless integration into proteomics analysis pipelines.

## Body
### Overview
Percolator is a software package tailored for proteomics, a field focused on large-scale study of proteins. It specializes in refining data from mass spectrometry, a technique used to identify and quantify proteins in complex mixtures. The tool employs statistical methods to validate peptide and protein identifications, reducing errors in experimental results.

### Development and Funding
- **Funding Source**: The Chan Zuckerberg Initiative (CZI) has supported Percolator through its Essential Open Source Software for Science program, emphasizing its role in scientific research.
- **Code Repository**: Hosted on GitHub (https://github.com/percolator/percolator), the project encourages community engagement and contributions.

### Key Features
- **Statistical Validation**: Uses algorithms to assess the confidence of protein identifications, minimizing false discoveries.
- **Integration**: Works with popular proteomics tools such as MSGF+ for comprehensive data analysis.
- **Cross-Platform Compatibility**: Designed to operate across various computing environments, enhancing usability.

### Version History
- **2.05 (2014-02-10)**: Initial release with core functionality for data validation.
- **2.09 (2015-04-03)**: Introduced improvements in processing speed and accuracy.
- **3.07 (2024-05-31)**: Latest stable version, incorporating updates for modern datasets and workflows.

## References

1. [Release 2.05. 2014](https://github.com/percolator/percolator/releases/tag/rel-2-05)
2. [Release 2.06. 2014](https://github.com/percolator/percolator/releases/tag/rel-2-06)
3. [Release 2.07. 2014](https://github.com/percolator/percolator/releases/tag/rel-2-07)
4. [Release 2.07.01. 2014](https://github.com/percolator/percolator/releases/tag/rel-2-07-01)
5. [Release 2.07.02. 2014](https://github.com/percolator/percolator/releases/tag/rel-2-07-02)
6. [Release 2.08. 2014](https://github.com/percolator/percolator/releases/tag/rel-2-08)
7. [Release 2.08.01. 2014](https://github.com/percolator/percolator/releases/tag/rel-2-08-01)
8. [Release 2.09. 2015](https://github.com/percolator/percolator/releases/tag/rel-2-09)
9. [Release 2.10. 2015](https://github.com/percolator/percolator/releases/tag/rel-2-10)
10. [Release 3.07. 2024](https://github.com/percolator/percolator/releases/tag/rel-3-07)
11. [Release 3.07.01. 2024](https://github.com/percolator/percolator/releases/tag/rel-3-07-01)
12. [Release 3.08. 2025](https://github.com/percolator/percolator/releases/tag/rel-3-08)
13. [Source](https://chanzuckerberg.com/eoss/proposals/)