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Identification of Post-translational Modifications of Plant Protein Complexes
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MODplus: Robust and Unrestrictive Identification of Post-Translational Modifications Using Mass Spectrometry
Seungjin Na1, Jihyung Kim1, Eunok Paek1
1Department of Computer Science , Hanyang University , Seoul 04763 , South Korea.
Analytical Chemistry
|August 1, 2019
Summary
MODplus enables comprehensive analysis of mass spectrometry data for post-translational modifications. This tool improves identification rates and reliability by handling multiple modifications and correcting errors from missing precursor spectra.
Area of Science:
- Proteomics
- Mass Spectrometry
- Biochemistry
Background:
- Post-translational modifications (PTMs) are crucial for cellular functions.
- Detecting PTMs in mass spectrometry data is challenging.
- Current methods struggle with comprehensive and accurate PTM identification.
Purpose of the Study:
- To develop a software tool, MODplus, for unrestrictive PTM searches in mass spectrometry data.
- To enable the identification of multiple PTMs per peptide and across the entire proteome.
- To improve the accuracy and reliability of PTM identification by addressing issues like missing precursor spectra.
Main Methods:
- MODplus allows for hundreds of modifications, multiple modifications per peptide, and whole proteome database searches.
- It supports flexible search parameters, including any tolerant values.
- The tool was validated on large human datasets (HEK293 cells) and TMT-labeled phosphorylation enrichment data.
Main Results:
- MODplus successfully identified diverse PTMs at multiple sites in human cell datasets.
- The software accurately distinguishes real chemical and biological modifications from artifacts.
- MODplus recognized and corrected errors caused by missing precursor (MP) spectra, improving identification rates by up to 70% and enhancing reliability.
Conclusions:
- MODplus provides a practical solution for unrestrictive PTM searches in mass spectrometry.
- The tool significantly enhances the accuracy and efficiency of PTM discovery.
- MODplus is valuable for advancing research in cellular processes regulated by PTMs.
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