Establishing and Streamlining Mass Spectrometry Workflows for Elucidating Cross-links for Protein Conformational Analysis
Conference Year
2024
Abstract
Chemical crosslinking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating protein-protein interactions and structural dynamics in complex biological systems. We present a comparative analysis of two prominent software tools, Proteome Discoverer’s Xlinkx and Kojak, for the analysis of Cytochrome C cross-linked by the cleavable Disuccinimidyl Sulfoxide (DSSO). Xlinkx identified nine unique peptides and fourteen crosslinks with a minimum score cut off at 40 from cytochrome c digested with trypsin. Kojak identified significantly more peptides and crosslinks, but with much lower confidence. We visualized our data through PyMOL, mapping the distance of the three highest scoring crosslinks.
Primary Faculty Mentor Name
Ying Wai Lam
Status
Undergraduate
Student College
College of Arts and Sciences
Program/Major
Biochemistry
Primary Research Category
Life Sciences
Establishing and Streamlining Mass Spectrometry Workflows for Elucidating Cross-links for Protein Conformational Analysis
Chemical crosslinking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating protein-protein interactions and structural dynamics in complex biological systems. We present a comparative analysis of two prominent software tools, Proteome Discoverer’s Xlinkx and Kojak, for the analysis of Cytochrome C cross-linked by the cleavable Disuccinimidyl Sulfoxide (DSSO). Xlinkx identified nine unique peptides and fourteen crosslinks with a minimum score cut off at 40 from cytochrome c digested with trypsin. Kojak identified significantly more peptides and crosslinks, but with much lower confidence. We visualized our data through PyMOL, mapping the distance of the three highest scoring crosslinks.