Classification and cluster analysis of complex time-of-flight secondary ion mass spectrometry for biological samples

Xue Tian, Stephen E. Reichenbach, Qingping Tao, Alex Henderson

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

Identifying and separating subtly different biological samples is one of the most critical tasks in biological analysis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is becoming a popular and important technique in the analysis of biological samples, because it can detect molecular information and characterize chemical composition. ToF-SIMS spectra of biological samples are enormously complex with large mass ranges and many peaks. As a result the classification and cluster analysis are challenging. This study presents a new classification algorithm, the most similar neighbor with a probability-based spectrum similarity measure (MSNPSSM), which uses all the information in the entire ToFSIMS spectra. MSN-PSSM is applied to automatically classify bacterial samples which are major causal agents of urinary tract infections. Experimental results show that MSN-PSSM is an accurate classification algorithm. It outperforms traditional techniques such as decision trees, principal component analysis (PCA) with discriminant function analysis (DFA), and soft independent modeling of class analogy (SIMCA). This study also applies a modern clustering algorithm, normalized spectral clustering, to automatically cluster the bacterial samples at the species level. Experimental results demonstrate that normalized spectral clustering is able to show accurate quantitative separations. It outperforms traditional techniques such as hierarchical clustering analysis, kmeans, and PCA with k-means. Copyright

Original languageEnglish (US)
Title of host publicationInternational Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2009, BCBGC 2009
Pages78-85
Number of pages8
Publication statusPublished - Dec 1 2009
Event2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, BCBGC 2009 - Orlando, FL, United States
Duration: Jul 13 2009Jul 16 2009

Publication series

NameInternational Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2009, BCBGC 2009

Conference

Conference2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, BCBGC 2009
CountryUnited States
CityOrlando, FL
Period7/13/097/16/09

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ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Tian, X., Reichenbach, S. E., Tao, Q., & Henderson, A. (2009). Classification and cluster analysis of complex time-of-flight secondary ion mass spectrometry for biological samples. In International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2009, BCBGC 2009 (pp. 78-85). (International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2009, BCBGC 2009).