SRMBuilder: a user-friendly tool for selected reaction monitoring data analysis

Area of Science:

• Proteomics
• Mass Spectrometry
• Biochemistry

Background:

• Selected Reaction Monitoring (SRM) is a sensitive and reproducible technique for targeted quantification in proteomics, lipidomics, and metabolomics.
• The increasing use of SRM necessitates user-friendly software for post-acquisition data analysis and result validation.

Purpose of the Study:

• To introduce SRMBuilder, a software tool designed to streamline SRM data analysis and quantification result validation.
• To provide a comprehensive solution for processing and validating SRM data across various mass spectrometry-based research areas.

Main Methods:

• SRMBuilder automatically parses SRM data from multiple file formats.
• The software assigns transitions to compounds and matches light/heavy transition/compound pairs.
• It offers a user-friendly graphical interface for manual validation at transition, compound, and sample levels.

Main Results:

• SRMBuilder facilitates the processing of post-acquisition SRM data files.
• The tool enables efficient validation of quantification results for SRM experiments.
• It supports targeted quantification of low abundance proteins and post-translational modifications.

Conclusions:

• SRMBuilder significantly simplifies and accelerates SRM data analysis and validation.
• This software is a valuable asset for researchers in proteomics, lipidomics, and metabolomics utilizing SRM.
• SRMBuilder is available as part of the ProteomicsTools suite for free download.