This package provides R functions to classify mass spectra in known categories, and to determine discriminant mass-to-charge values. It was developed with the aim of identifying very similar species or phenotypes of bacteria from mass spectra obtained by Matrix Assisted Laser Desorption Ionisation - Time Of Flight Mass Spectrometry (MALDI-TOF MS). However, the different functions of this package can also be used to classify other categories associated to mass spectra; or from mass spectra obtained with other mass spectrometry techniques. It includes easy-to-use functions for pre-processing mass spectra, functions to determine discriminant mass-to-charge values (m/z) from a library of mass spectra corresponding to different categories, and functions to predict the category (species, phenotypes, etc.) associated to a mass spectrum from a list of selected mass-to-charge values.
If you use this package in your research, please cite the associated publication: tools:::Rd_expr_doi("10.1016/j.eswa.2025.128796").
For a comprehensive guide, additional applications, and detailed examples of using this package, please visit our GitHub repository: here.
No return value. Package description.
Alexandre Godmer, Quentin Giai Gianetto
Alexandre Godmer, Yahia Benzerara, Emmanuelle Varon, Nicolas Veziris, Karen Druart, Renaud Mozet, Mariette Matondo, Alexandra Aubry, Quentin Giai Gianetto, MSclassifR: An R package for supervised classification of mass spectra with machine learning methods, Expert Systems with Applications, Volume 294, 2025, 128796, ISSN 0957-4174, tools:::Rd_expr_doi("10.1016/j.eswa.2025.128796").