| Autor: |
Rojas Ramírez C; Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States., Espino JA; Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States., Jones LM; Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California 92093, United States., Polasky DA; Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States., Nesvizhskii AI; Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States. |
| Abstrakt: |
Monitoring protein structure before and after environmental alterations (e.g., different cell states) can give insights into the role and function of proteins. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry (MS) allows for monitoring of structural rearrangements by exposing proteins to OH radicals that oxidize solvent-accessible residues, indicating protein regions undergoing movement. Some of the benefits of FPOP include high throughput and a lack of scrambling due to label irreversibility. However, the challenges of processing FPOP data have thus far limited its proteome-scale uses. Here, we present a computational workflow for fast and sensitive analysis of FPOP data sets. Our workflow, implemented as part of the FragPipe computational platform, combines the speed of the MSFragger search with a unique hybrid search method to restrict the large search space of FPOP modifications. Together, these features enable more than 10-fold faster FPOP searches that identify 150% more modified peptide spectra than previous methods. We hope this new workflow will increase the accessibility of FPOP to enable more protein structure and function relationships to be explored. |
