A two-phase clustering approach for peak alignment in mining mass spectrometry data

Lien Chin Chen*, Yu Cheng Liu, Chi Wei Liu, S. Tseng

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

In recent years, the mass spectrometry technologies emerge as useful tools for biomarker discovery through studying protein profiles in various biological specimens. In mining mass spectrometry datasets, peak alignment is a critical issue among the preprocessing steps that affect the quality of analysis results. In this paper, we proposed a novel algorithm named Two-Phases Clustering for peak Alignment (TPC-Align) to align mass spectrometry peaks across samples in the pre-processing phase. The TPC-Align algorithm sequentially considers the distribution of intensity values and the locations of mass-to-charge ratio values of peaks between samples. Moreover, TPC-Align algorithm can also report a list of significantly differential peaks between samples, which serve as the candidate biomarkers for further biological study. The proposed peak alignment method was compared to the current peak alignment approach based on one-dimension hierarchical clustering through experimental evaluations, and the results show that TPC-Align outperforms the traditional method on the real dataset.

Original languageEnglish
Title of host publicationProceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
Pages226-230
Number of pages5
DOIs
StatePublished - 1 Dec 2009
Event2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009 - Washington, DC, United States
Duration: 1 Nov 20094 Nov 2009

Publication series

NameProceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009

Conference

Conference2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
CountryUnited States
CityWashington, DC
Period1/11/094/11/09

Keywords

  • Biomarker discovery
  • Clustering
  • Mass spectrometry analysis
  • Peak alignment

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