Version 1
: Received: 12 February 2024 / Approved: 15 February 2024 / Online: 15 February 2024 (12:11:52 CET)
How to cite:
Ben Hamouda, R.; Estellon, B.; Himet, K.; Cherif, A.; Marthinet, H.; Loreau, J.; Texier, G.; Granjeaud, S.; ALMERAS, L. MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra. Preprints2024, 2024020852. https://doi.org/10.20944/preprints202402.0852.v1
Ben Hamouda, R.; Estellon, B.; Himet, K.; Cherif, A.; Marthinet, H.; Loreau, J.; Texier, G.; Granjeaud, S.; ALMERAS, L. MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra. Preprints 2024, 2024020852. https://doi.org/10.20944/preprints202402.0852.v1
Ben Hamouda, R.; Estellon, B.; Himet, K.; Cherif, A.; Marthinet, H.; Loreau, J.; Texier, G.; Granjeaud, S.; ALMERAS, L. MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra. Preprints2024, 2024020852. https://doi.org/10.20944/preprints202402.0852.v1
APA Style
Ben Hamouda, R., Estellon, B., Himet, K., Cherif, A., Marthinet, H., Loreau, J., Texier, G., Granjeaud, S., & ALMERAS, L. (2024). MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra. Preprints. https://doi.org/10.20944/preprints202402.0852.v1
Chicago/Turabian Style
Ben Hamouda, R., Samuel Granjeaud and Lionel ALMERAS. 2024 "MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra" Preprints. https://doi.org/10.20944/preprints202402.0852.v1
Abstract
In the early 2000s, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) emerged as a performant and relevant tool for identifying micro-organisms. Since then, it has become practically essential for identifying bacteria in microbiological diagnostic laboratories. In the last decade, it was successfully applied for arthropod identification allowing to distinguish vectors from non-vectors of infectious diseases. However, identification failures are not rare, hampering it widely use. Failure is generally attributed either to the absence of respective counter species MS spectra in the database, or to the insufficient quality of query MS spectra (i.e. lower intensity and diversity of MS peaks detected). To avoid matching errors due to non-compliant spectra, the development of a strategy for detecting and excluding outlier MS profiles became compulsory. To this end, we created MSProfileR, an R package leading to a bioinformatics tool through a simple installation, integrating the control quality system of MS spectra and an analysis pipeline including peak detection and MS spectra comparisons. MSProfileR can also add metadata concerning the sample that the spectra are derived from. MSProfileR has been developed in the R environment and offers a user-friendly web interface using the R Shiny framework. It is available on Microsoft Windows as a web browser application by simply navigation using the link of the package on the Github. MSProfileR is therefore accessible to non-computer specialists and is freely available to the scientific community. We evaluated MSProfileR using two datasets including exclusively MS spectra from arthropods. In addition to coherent sample classification, outlier MS spectra were detected in each dataset confirming the value of MSProfileR.
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
