Investigation and Development of the BODIPY-Embedded Isotopic Signature for Chemoproteomics Labeling and Targeted...

Area of Science:

• Chemoproteomics
• Mass Spectrometry
• Chemical Biology

Background:

• Directly measuring protein-ligand conjugation sites is crucial but challenging in chemoproteomics.
• Low abundance of labeled proteins and identification difficulties hinder standard proteomics software.
• Reporter tags with signature fragments or isotopic encoding aid in preemptive labeled peptide discovery.

Purpose of the Study:

• To investigate BODIPY FL azide as a click chemistry reagent for chemoproteomics.
• To leverage boron's isotopic signature (¹⁰B:¹¹B) for identifying labeled peptides.
• To enhance the detection and site identification of small molecule-protein modifications.

Main Methods:

• Utilized BODIPY FL azide for click chemistry labeling of peptides.
• Developed an R script to filter MS1 spectra for boron's isotopic ratio (¹⁰B:¹¹B) and mass defect.
• Employed BODIPY's HF neutral loss signature to aid peptide identification.

Main Results:

• Achieved three times greater labeled peptide coverage in BSA samples compared to untargeted methods.
• Successfully identified BODIPY-labeled peptides using the boron isotopic signature.
• Demonstrated the method's applicability in a complex E. coli digest spiked with labeled BSA.

Conclusions:

• BODIPY FL azide provides a unique isotopic signature for pinpointing protein modification sites.
• This approach significantly improves labeled peptide coverage in mass spectrometry-based chemoproteomics.
• Offers potential for integrated UV or fluorescence detection alongside mass spectrometry analysis.