Discovery of Cysteine Carboxyalkylations by Real-Time Isotopic Signature Targeted Profiling

Data-dependent acquisition (DDA) is widely applied in shotgun proteomics. However, restricted by the scanning speed of mass spectrometry (MS) instruments, it remains challenging for DDA to directly detect peptides with low abundance. Herein, we developed a real-time targeted MS data acquisition method, “isoSTAR”, which identifies target peptides by their unique isotopic signatures during the stage of full-MS scanning and subjects them to targeted MS/MS scans immediately. The method showed dramatic improvement in sensitivity in identifying target peptides with low abundance compared to traditional MS acquisition methods. Using this method, we discovered a series of carboxyalkylations on cysteines during fatty acid metabolism and verified their modification structures using synthetic peptide standards. We envision that isoSTAR will become a powerful and versatile tool to enhance shotgun proteomics applications in profiling protein-centric modifications.