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Published on: April 17, 2012
Improved candidate biomarker detection based on mass spectrometry data using the Hilbert-Huang transform
Li-Ching Wu1, Ping-Heng Hsieh, Jorng-Tzong Horng
1Graduate Institute of System Biology and Bioinformatics, National Central University, JhongLi City, Taoyuan County, Taiwan. richard@mail.sybbi.ncu.edu.tw
Protein and Peptide Letters
|September 17, 2011
Summary
Enhanced HHTMass (E-HHTMass) improves mass spectrometry biomarker discovery for disease diagnosis. This method achieves a high peak appearance rate, identifying known and potential new biomarkers from MALDI-TOF and SELDI-TOF data.
Area of Science:
- Biomarker discovery
- Mass spectrometry
- Computational biology
Background:
- Mass spectrometry is crucial for disease diagnosis and understanding new diseases.
- Previous HHTmass method showed noise removal but lacked testing for peak reappearance and medical data application.
- Existing methods require improvement for accuracy and efficiency in biomarker identification.
Purpose of the Study:
- To develop an improved biomarker discovery method, Enhance HHTMass (E-HHTMass), for MALDI-TOF and SELDI-TOF mass spectrometry data.
- To integrate preprocessing and classification for identifying significant peaks.
- To enhance peak detection reliability and discover novel potential biomarkers.
Main Methods:
- Developed E-HHTMass, a modified biomarker discovery method.
- Removed interpolation and the biomarker discovery process from the original HHTMass.
- Integrated preprocessing and classification into a single workflow.
- Tested E-HHTMass on MALDI-TOF and SELDI-TOF mass spectrometry data.
Main Results:
- E-HHTMass identified most known biomarkers with a high peak appearance rate, outperforming MSCAP and the original HHTMass.
- The method demonstrated adaptability to spectra with small increasing intervals.
- New potential biomarkers were detected, requiring further validation.
- Achieved improved performance in peak detectability and reappearance rate.
Conclusions:
- E-HHTMass offers a robust and efficient approach for mass spectrometry biomarker discovery.
- The enhanced method improves diagnostic capabilities and aids in identifying novel disease characteristics.
- E-HHTMass provides a reliable tool for analyzing MALDI-TOF and SELDI-TOF data, advancing clinical diagnostics.
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