MicrobeMS - A MATLAB Toolbox for Microbial Identification Based on Mass Spectrometry

1.Over the last two decades, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) has become the standard method for identifying bacteria and has found a wide range of applications, especially in clinical microbiology. The methods high taxonomic resolution, minimal sample preparation, and complete, ready-to-use commercial systems, which include instrumentation, experimental protocols, spectral databases, and identification analysis software, were key factors in the success of MALDI-ToF MS as the standard for identifying microorganisms in routine diagnostic laboratories. However, despite the availability of these commercial solutions, there is also a growing need for efficient, cost-effective, vendor-neutral databases and analysis tools. These tools would enable the compilation of user-defined mass spectral databases and the testing of new analysis methods and algorithms, particularly in an academic context. To this end, MicrobeMS software has been developed to cover all stages of MALDI-ToF MS-based identification analysis. MicrobeMS is an easy-to-use desktop application for analyzing mass spectra from microorganisms and performing tasks related to spectrum database compilation. It includes routines for direct data import and export, biomarker peak searches, management of spectrum metadata, testing of spectrum quality, supervised and unsupervised identification analysis and intuitive result display. MicrobeMS is implemented in MATLAB and is freely available as MATLAB pcode for Windows and Linux, as well as a standalone application. Over the last fifteen years, the software has undergone continuous development and is now used routinely in various settings at the Centre for Biological Threats and Special Pathogens (ZBS) at the Robert Koch Institute (RKI) in Berlin, Germany, for example in supporting spectrum database compilation, to identify special or rare pathogenic bacteria by advanced identification analysis concepts, or to test in silico MALDI-ToF MS databases derived from microbial genomes. In this software publication the versatility and capabilities of MicrobeMS are demonstrated using a test data set from highly pathogenic bacteria (HPB) which has been obtained as part of a published European Union (EU)-funded External Quality Assurance Exercise (EQAE). MicrobeMS and HPB test data can both be downloaded from https://wiki.microbe-ms.com/. The goal of this software publication is twofold: to raise awareness of MicrobeMS within the scientific community and to encourage the testing of the software and custom-developed MALDI-ToF MS databases of the RKI, which are published at the ZENODO data repository (https://doi.org/10.5281/zenodo.7702374).