Peak selection from MALDI-TOF mass spectra using ant colony optimization.

Peak selection from MALDI-TOF mass spectra using ant colony optimization. Research Abstract Details 

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Peak selection from MALDI-TOF mass spectra using ant colony optimization. Abstract Text:

H W Ressom,R S Varghese,S K Drake,G L Hortin,M Abdel-Hamid,C A Loffredo,R Goldman,

MOTIVATION: Due to the large number of peaks in mass spectra of low-molecular-weight (LMW) enriched sera, a systematic method is needed to select a parsimonious set of peaks to facilitate biomarker identification. We present computational methods for matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectral data preprocessing and peak selection. In particular, we propose a novel method that combines ant colony optimization (ACO) with support vector machines (SVM) to select a small set of useful peaks. RESULTS: The proposed hybrid ACO-SVM algorithm selected a panel of eight peaks out of 228 candidate peaks from MALDI-TOF spectra of LMW enriched sera. An SVM classifier built with these peaks achieved 94% sensitivity and 100% specificity in distinguishing hepatocellular carcinoma from cirrhosis in a blind validation set of 69 samples. Area under the receiver operating characteristic (ROC) curve was 0.996. The classification capability of these peaks is compared with those selected by the SVM-recursive feature elimination method. AVAILABILITY: Supplementary material and MATLAB scripts to implement the methods described in this article are available at http://microarray.georgetown.edu/web/files/bioinf.htm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Peak selection from MALDI-TOF mass spectra using ant colony optimization. Publishing Authors By Initials

HW Ressom,RS Varghese,SK Drake,GL Hortin,M Abdel-Hamid,CA Loffredo,R Goldman,

For similar biological factors: biological markers: tumor markers, biological research abstracts see: biological factors: biological markers: tumor markers, biological research

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Peak selection from MALDI-TOF mass spectra using ant colony optimization. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: 619-26

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 19

MONTH: 01

YEAR: 2007

Peak selection from MALDI-TOF mass spectra using ant colony optimization. Information

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LANGUAGE: eng

NlmUniqueID: 9808944

Peak selection from MALDI-TOF mass spectra using ant colony optimization. Keywords Mesh Terms:

KEYWORDS: Tumor Markers, Biological

MESH TERMS: blood

Chemical & Substance for Abstract: Peak selection from MALDI-TOF mass spectra using ant colony optimization. Information

Substance Name: Tumor Markers, Biological

Registry Number: 0

Grant and Affiliation Information for Peak selection from MALDI-TOF mass spectra using ant colony optimization.

AFFILIATION: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA. hwr@georgetown.edu

Country: England

AGENCY: United States NCI

GRANT: 2R01CA85888

ACRONYM: CA

MEDLINETA: Bioinformatics

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