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Related Experiment Video

Updated: Jan 18, 2026

Atom Probe Tomography Analysis of Exsolved Mineral Phases

Atom Probe Tomography Analysis of Exsolved Mineral Phases

Published on: October 25, 2019

Theropod: Software Tools to Analyze Externally Collected Selective Temporal Overview of Resonant Ions.

Timothy P Cleland¹, Michael G Trizna²

¹Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States.

Journal of the American Society for Mass Spectrometry

|January 16, 2026

Summary

Theropod software enables selective temporal overview of resonant ions (STORI) analysis for characterizing individual and mixed proteoforms. This tool accurately calculates uncharged protein masses and identifies post-translational modifications from mass spectrometry data.

Keywords:

charge detection mass spectrometry individual ion post-translational modifications proteoform

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Area of Science:

Mass Spectrometry
Proteomics
Computational Biology

Background:

Charge detection mass spectrometry (CDMS) enables characterization of individual proteoforms.
Orbitrap mass spectrometers are widely used for collecting ion data.
Analysis of complex proteoform mixtures requires advanced computational tools.

Purpose of the Study:

To introduce Theropod, a novel software suite for analyzing mass spectrometry transients.
To enable Selective Temporal Overview of Resonant Ions (STORI) analysis.
To facilitate the calculation of uncharged masses and identification of post-translational modifications.

Main Methods:

Development of Theropod software tools for STORI analysis.
Utilizing transients collected on an external digital oscilloscope.
Application of a wide charge correction method for mass calculation.

Main Results:

Successfully calculated the uncharged masses of ubiquitin, myoglobin, carbonic anhydrase, and enolase.
Characterized the Pierce Intact Protein Standard mixture.
Identified post-translational modifications in both individual proteins and mixtures.

Conclusions:

Theropod provides a robust method for proteoform characterization using CDMS data.
The software facilitates accurate mass determination and PTM identification.
Theropod is a valuable tool for proteomics research and is publicly available.