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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: Jul 9, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Advancing proteomic discovery through optimized multi-stage scoring and deep learning-enhanced open search.

Chen Qian1,2, Kaifei Wang1,2, Pengzhi Mao1,2

  • 1Institute of Computing Technology, Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Beijing, 100190, China.

Bioinformatics (Oxford, England)
|July 7, 2026
PubMed
Summary

pFind+ enhances protein identification from mass spectrometry data. This new search engine improves sensitivity in both restricted and open searches, aiding in the discovery of unknown protein modifications.

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Related Experiment Videos

Last Updated: Jul 9, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Protein search engines are crucial for interpreting mass spectrometry data.
  • Existing tools struggle with sensitivity in complex datasets and lack unified deep learning integration for open searches.
  • Discovering unknown protein modifications remains a challenge.

Purpose of the Study:

  • To develop a high-performance protein search engine, pFind+, that enhances sensitivity and integrates deep learning for both restricted and open searches.
  • To enable comprehensive post-translational modification (PTM) discovery, including unknown modifications.
  • To optimize the search engine for practical deployment with hardware-aware inference.

Main Methods:

  • Developed pFind+, an extension of the pFind search engine for data-dependent acquisition (DDA) proteomics.
  • Implemented enhanced raw scoring for improved pre-filtering and a tailored acceleration strategy.
  • Integrated deep learning features into an enhanced rescoring framework for high-sensitivity open search.
  • Incorporated hardware-aware inference optimizations.

Main Results:

  • pFind+ demonstrates significantly improved sensitivity in restricted searches (12.7%-29.3% gain) and open searches (8.0%-38.4% gain) compared to existing tools.
  • The enhanced raw scoring improves pre-filtering ability while computational overhead is managed.
  • Deep learning integration enables high-sensitivity, DL-enhanced open search for comprehensive PTM discovery.
  • Evaluations across diverse datasets confirm the superior performance of pFind+.

Conclusions:

  • pFind+ offers a unified framework for high-performance proteomics data analysis.
  • The search engine achieves superior sensitivity, particularly for discovering unknown post-translational modifications.
  • pFind+ provides a practical and efficient solution for modern proteomics research.