Abstract
Motivation Classification of mass spectra is essential for identifying microorganisms from matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. However, spectrally close organisms remain difficult to identify. In this context, we developed the MSclassifR R package to improve the classification of mass spectra. Its open code strengthens the reproducibility of analyzes in the community.
Results We applied the functions of our package to raw mass spectra from three different laboratories. The best workflow available in MSclassifR package achieves near 100% accuracy in all three datasets. Thus, MSclassifR constitutes an interesting alternative for reliable MALDI-TOF based diagnosis.
Availability MSclassifR is freely available online from CRAN repository https://cran.r-project.org/web/packages/MSclassifR/index.html. Two vignettes illustrating how to use the functions of this package from real data sets are also available online to help users.
Contact alexandre.godmer{at}aphp.fr
Supplementary information Supplementary material is available at Bio-informatics online.
Competing Interest Statement
The authors have declared no competing interest.
