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

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

J Proteome Res

Synthetic 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.

Published: October 2021

AI Article Synopsis

  • Activity-based protein profiling (ABPP) is a high-throughput method used to analyze protein activity and interactions, with accurate quantification being essential for measuring probe labeling.
  • CIMAGE is a specialized software developed for ABPP data analysis, featuring a peak extraction algorithm and comprehensive quantification checks, along with visualization tools for results.
  • The recent upgrade of CIMAGE allows for integration with various database search engines, improved quantification methods, and accurate checks for chemical elements, maintaining high accuracy comparable to other quantification tools like MaxQuant.

Article Abstract

Activity-based protein profiling (ABPP) is a powerful chemical proteomic method for studying protein activity, modifications, and interactions in a high-throughput manner. In ABPP experiments, accurate quantification is crucial to determine the extent of probe labeling at the level of either target proteins or specific amino acid side chains. CIMAGE has been developed as an in-house quantification software specifically designed for ABPP data analysis that incorporates (1) a relaxed peak extraction algorithm and (2) stringent post-quantification checks for efficient and accurate quantification. It also can generate table and image data for users to conveniently visualize their results. Here we provide a retrospective introduction of the software and describe our recent upgrade efforts to enable (1) interfacing with different database search engines as input, (2) triplex quantification of ABPP data by reductive dimethylation, and (3) envelope checking for chemical elements with special isotopic distributions. We show that the updated CIMAGE can maintain its ability to quantify ABPP data with dramatic depth and high accuracy, and it also has similar quantification performance in benchmarked SILAC data as compared with MaxQuant. We believe that CIMAGE2.0 will continue to serve as a powerful analytical tool for ABPP studies.

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Source
http://dx.doi.org/10.1021/acs.jproteome.1c00455DOI Listing

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