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Related Experiment Video

Updated: May 4, 2026

Author Spotlight: Quantification of Complex Lipidomic Samples Using Stable Isotope Labeling
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SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods.

Cheng Chang1, Jiyang Zhang, Mingfei Han

  • 1Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China.

Bioinformatics (Oxford, England)
|December 18, 2013
PubMed
Summary
This summary is machine-generated.

SILVER is a new tool for analyzing stable isotope labeling mass spectrometry data. It offers accurate quantification and faster processing compared to existing software, with user-friendly features.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Stable isotope labeling is crucial for quantitative proteomics.
  • Existing tools may have limitations in accuracy, speed, or user-friendliness.

Purpose of the Study:

  • To introduce SILVER, an efficient software tool for processing stable isotope labeling mass spectrometry data.
  • To enhance the accuracy and speed of quantitative proteomics data analysis.

Main Methods:

  • SILVER employs novel quality control methods at spectrum, peptide, and protein levels.
  • It incorporates new quantification confidence filters and indices.
  • Performance was validated against MaxQuant and Proteome Discoverer using multiple datasets.

Main Results:

  • SILVER demonstrates high accuracy and robustness in quantitative proteomics.
  • It significantly reduces data processing time compared to established software.
  • The tool provides comprehensive features for analysis and validation.

Conclusions:

  • SILVER is an efficient and accurate tool for stable isotope labeling quantitative proteomics.
  • Its user-friendly interface and improved performance make it a valuable resource.
  • The software is freely available for research use.