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ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry

submitted on 04.01.2021, 18:58 and posted on 05.01.2021, 12:38 by Carter Lantz, Muhammad A. Zenaidee, Benqian Wei, Zachary Hemminger, Rachel R. Ogorzalek Loo, Joseph Loo

Here we describe ClipsMS, an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation. Further, ClipsMS can be used to locate various modifications on the protein sequence. Using ClipsMS to assign TD-MS generated product ions, we demonstrate that for apo-myoglobin, the inclusion of internal fragments increases the sequence coverage up to 78%. Interestingly, many internal fragments cover complimentary regions to the terminal fragments that enhance the information that is extracted from a single top-down mass spectrum. Analysis of oxidized apo-myoglobin using terminal and internal fragment matching by ClipsMS confirmed the locations of oxidation sites on the two methionine residues. Internal fragments can be beneficial for top-down protein fragmentation analysis, and ClipsMS can be a valuable tool for assigning both terminal and internal fragments present in a top-down mass spectrum.


NIH R01GM103479


Email Address of Submitting Author


University of California, Los Angeles



ORCID For Submitting Author


Declaration of Conflict of Interest

no conflict of interest