Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens

• Published in: Bioinformatics Vol. 20; no. 17; pp. 3128 - 3136
• Main Authors: Satten, Glen A., Datta, Somnath, Moura, Hercules, Woolfitt, Adrian R., Carvalho, Maria da G., Carlone, George M., De, Barun K., Pavlopoulos, Antonis, Barr, John R.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 22-11-2004; Oxford Publishing Limited (England)
• Subjects: Algorithms; Artificial Intelligence; Bacteria - classification; Bacteria - isolation & purification; Bacteria - metabolism; Bacterial Proteins - analysis; Biological and medical sciences; Biomarkers - analysis; Escherichia coli - isolation & purification; Escherichia coli - metabolism; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - standards; High throughput screening; Tissue; Sample; Classification; Standardization; Bacteria; Web site; Bioinformatics; Algorithm; Mass spectrometry; Protein
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bth372

Motivation: Application of mass spectrometry in proteomics is a breakthrough in high-throughput analyses. Early applications have focused on protein expression profiles to differentiate among various types of tissue samples (e.g. normal versus tumor). Here our goal is to use mass spectra to differentiate bacterial species using whole-organism samples. The raw spectra are similar to spectra of tissue samples, raising some of the same statistical issues (e.g. non-uniform baselines and higher noise associated with higher baseline), but are substantially noisier. As a result, new preprocessing procedures are required before these spectra can be used for statistical classification. Results: In this study, we introduce novel preprocessing steps that can be used with any mass spectra. These comprise a standardization step and a denoising step. The noise level for each spectrum is determined using only data from that spectrum. Only spectral features that exceed a threshold defined by the noise level are subsequently used for classification. Using this approach, we trained the Random Forest program to classify 240 mass spectra into four bacterial types. The method resulted in zero prediction errors in the training samples and in two test datasets having 240 and 300 spectra, respectively. Availability: Fortran code for standardization and denoising is available at the supplementary information website. Supplementary information: http://www.stat.uga.edu/~datta/Massspec/supp.html