Machine-Learning Classification of Bacteria Using Two-Dimensional Tandem Mass Spectrometry

Abstract

Biothreat detection has continued to gain attention. Samples suspected to fall into any of the CDC's biothreat categories require identification by processes that require specialized expertise and facilities. Recent developments in analytical instrumentation and machine learning algorithms offer rapid and accurate classification of Gram-positive and Gramnegative bacterial species. This is achieved by analyzing the negative ions generated from bacterial cell extracts with a modified linear quadrupole ion-trap mass spectrometer fitted with twodimensional tandem mass spectrometry capabilities (2D MS/MS). The 2D MS/MS data domain of a bacterial cell extract is recorded within five s using a five-scan average after sample preparation by a simple extraction. Bacteria were classified at the species level by their lipid profiles using the random forest, k-nearest neighbor, and multilayer perceptron machine learning models. 2D MS/MS data can also be treated as image data for use with image recognition algorithms such as convolutional neural networks. The classification accuracy of all models tested was greater than 99%. Adding to previously published work on the 2D MS/MS analysis of bacterial growth and the profiling of sporulating bacteria, this study demonstrates the utility and information-rich nature of 2D MS/MS in the identification of bacterial pathogens at the species level when coupled with machine learning.

Discrimination of Common E. coli Strains in Urine by Liquid Chromatography–Ion Mobility–Tandem Mass Spectrometry and Machine Learning

“…In fact, machine learning in combination with LC-MS/MS has been used for fast and accurate bacteria identification at the species level in urine specimens . Random forest classification (RFC), k-nearest neighbor (KNN), multilayer perceptron (MLP), and convolution neural network (CNN) are examples of classifiers that extract the most informative features for accurate classification …”