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FLASHQuant: A Fast Algorithm for Proteoform Quantification in Top-Down Proteomics
Jihyung Kim1,2, Kyowon Jeong1,2, Philipp T Kaulich3
1Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076 Tübingen, Germany.
Analytical Chemistry
|October 18, 2024
Summary
Accurate quantification of proteoforms using top-down proteomics (TDP) is improved with FLASHQuant. This new method resolves coeluting signals, boosting quantification accuracy and reproducibility in rapid LC-MS runs.
Area of Science:
- Proteomics
- Biochemistry
- Analytical Chemistry
Background:
- Accurate proteoform quantification is vital for understanding biological states.
- Top-down proteomics (TDP) using liquid chromatography-mass spectrometry (LC-MS) is a key method.
- Label-free quantification (LFQ) is preferred for its cost-effectiveness.
Purpose of the Study:
- To develop a method for accurate quantification of coeluting proteoforms in TDP.
- To improve the accuracy and reproducibility of MS1-level LFQ in TDP.
- To provide an open-source software solution for proteoform analysis.
Main Methods:
- Introduction of FLASHQuant software for MS1-level LFQ analysis in TDP.
- Utilizing automatic signal resolution for coeluting proteoforms.
- Employing the ConsensusFeatureGroupDetector algorithm for multi-run alignment.
Main Results:
- FLASHQuant accurately and reproducibly quantifies coeluting proteoforms in TDP.
- Resolving overlapping signals significantly enhances quantification accuracy.
- The method achieves high accuracy in short runtimes (minutes per LC-MS run).
Conclusions:
- FLASHQuant enhances the accuracy of LFQ in TDP by resolving coeluting proteoforms.
- The software provides a rapid and reliable solution for proteoform quantification.
- FLASHQuant is available as open-source software, promoting wider adoption.
