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bioRxiv · 10.1101/2025.02.05.636727

Proteoform identification using multiplexed top-down mass spectra

Wang, Z.·Xiong, X.·Liu, X.
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Abstract

Top-down mass spectrometry (TDMS) is the method of choice for analyzing intact proteoforms, as well as their post-translational modifications and sequence variations. In TDMS experiments, multiple proteoforms are often co-fragmented in tandem mass spectrometry (MS/MS) analysis, resulting in multiplexed TD-MS/MS spectra. Since multiplexed TD-MS/MS spectra are more complex than common spectra generated from single proteoforms, these spectra pose a significant challenge for proteoform identification and quantification. Here we present TopMPI, a new computational tool specifically designed for the identification of multiplexed TD-MS/MS spectra. Experimental results demonstrate that TopMPI significantly increases proteoform identifications and reduces identification errors in multiplexed TD-MS/MS spectral analysis compared to existing tools.

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Wang, Z., Xiong, X., Liu, X.. 2025-02-08. Proteoform identification using multiplexed top-down mass spectra. https://doi.org/10.1101/2025.02.05.636727

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