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CIMAGE2.0: An Expanded Tool for Quantitative Analysis of Activity-Based Protein Profiling (ABPP) Data.

Jinjun Gao1,2, Yuan Liu1, Fan Yang1

  • 1Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.

Journal of Proteome Research
|September 8, 2021
PubMed
Summary

CIMAGE software enhances activity-based protein profiling (ABPP) quantification. The updated CIMAGE2.0 offers improved data analysis, ensuring accurate results for protein activity studies.

Keywords:
LC-MS/MSactivity-based protein profilingquantitative proteomicssoftware

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Area of Science:

  • Biochemistry
  • Proteomics
  • Chemical Biology

Background:

  • Activity-based protein profiling (ABPP) is vital for studying protein activity, modifications, and interactions.
  • Accurate quantification of probe labeling is essential in ABPP experiments.
  • Existing software may lack specialized features for comprehensive ABPP data analysis.

Purpose of the Study:

  • To introduce CIMAGE, an in-house software for ABPP data analysis.
  • To describe recent upgrades to CIMAGE, enhancing its functionality and compatibility.
  • To validate the accuracy and performance of the updated CIMAGE2.0 software.

Main Methods:

  • Development of CIMAGE with a relaxed peak extraction algorithm and stringent post-quantification checks.
  • Implementation of upgrades including database search engine interfacing, triplex quantification via reductive dimethylation, and isotopic envelope checking.
  • Benchmarking CIMAGE2.0 against SILAC data and MaxQuant for performance comparison.

Main Results:

  • CIMAGE provides efficient and accurate quantification for ABPP data.
  • The upgraded CIMAGE2.0 maintains high accuracy and depth in ABPP data quantification.
  • CIMAGE2.0 demonstrates comparable quantification performance to MaxQuant on SILAC data.

Conclusions:

  • CIMAGE2.0 is a powerful analytical tool for activity-based protein profiling studies.
  • The software's enhancements improve its versatility and reliability for researchers.
  • CIMAGE2.0 facilitates accurate visualization and analysis of complex proteomic data.