Peak selection from MALDI-TOF mass spectra using ant colony optimization
Peak selection from MALDI-TOF mass spectra using ant colony optimization
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DOI：
10.1093/bioinformatics/btl678
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发表时间：
2007-03-01
期刊：
影响因子：
5.8
通讯作者：
Goldman, R.
中科院分区：
文献类型：
--
作者：
Ressom, H. W.;Varghese, R. S.;Goldman, R.
动机：由于低分子量（LMW）富集血清的质谱中有大量的峰，因此需要一种系统的方法来选择一组简约的峰，以促进生物标志物的鉴定。我们提出了计算方法的基质辅助激光解吸/电离飞行时间（MALDI-TOF）光谱数据预处理和峰值选择。特别是，我们提出了一种新的方法，结合蚁群优化（ACO）与支持向量机（SVM）选择一个小的有用peaks.Results：建议的混合ACO-SVM算法选择了一个面板的8个峰的228个候选峰从MALDI-TOF光谱的LMW富集血清。用这些峰建立的SVM分类器在69个样本的盲验证集中区分肝细胞癌和肝硬化时达到了94%的灵敏度和100%的特异性。受试者工作特征（ROC）曲线下面积为0.996。这些峰的分类能力与SVM递归特征消除方法选择的峰进行比较。可用性：实现本文所述方法的补充材料和MATLAB脚本可在http://microarray.georgetown.edu/web/files/bioinf.htmContact：hwr@georgetown. edu获得补充信息：补充数据可在Bioinformatics online获得。
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.htmContact: hwr@georgetown.eduSupplementary information: Supplementary data are available at Bioinformatics online.