%0 Unpublished work %T MSclassifR: an R package for supervised classification of mass spectra with machine learning methods %+ Centre d'Immunologie et des Maladies Infectieuses (CIMI) %+ CHU Saint-Antoine [AP-HP] %+ Plateforme de Protéomique / Proteomics platform %+ CHU Pitié-Salpêtrière [AP-HP] %+ Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB %A Godmer, Alexandre %A Benzerara, Yahia %A Veziris, Nicolas %A Matondo, Mariette %A Aubry, Alexandra %A Gianetto, Quentin Giai %8 2023-05-10 %D 2023 %R 10.1101/2022.03.14.484252 %Z Life Sciences [q-bio] %Z Statistics [stat]Preprints, Working Papers, ... %X 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. %G English %2 https://pasteur.hal.science/pasteur-04093599/document %2 https://pasteur.hal.science/pasteur-04093599/file/2022.03.14.484252v1.full.pdf %L pasteur-04093599 %U https://pasteur.hal.science/pasteur-04093599 %~ PASTEUR %~ CNRS %~ APHP %~ CIMI %~ INC-CNRS %~ SORBONNE-UNIVERSITE %~ SORBONNE-UNIV %~ SU-MEDECINE %~ SU-MED %~ UNIV-PARIS %~ UNIVERSITE-PARIS %~ SU-TI %~ ALLIANCE-SU %~ FRANCE-GENOMIQUE %~ BIOINFO_BIOSTAT_HUB