{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:09:34Z","timestamp":1760144974114,"version":"build-2065373602"},"reference-count":67,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T00:00:00Z","timestamp":1717632000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006021","name":"D\u00e9l\u00e9gation G\u00e9n\u00e9rale pour l\u2019Armement","doi-asserted-by":"publisher","award":["PDH-2-NRBC-2-B-2201"],"award-info":[{"award-number":["PDH-2-NRBC-2-B-2201"]}],"id":[{"id":"10.13039\/501100006021","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Informatics"],"abstract":"<jats:p>In the early 2000s, matrix-assisted laser desorption ionization\u2013time 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 researchers to distinguish vectors from non-vectors of infectious diseases. However, identification failures are not rare, hampering its wide 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 a 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 simple navigation using the link of the package on Github v.3.10.0. 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.<\/jats:p>","DOI":"10.3390\/informatics11020039","type":"journal-article","created":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T08:45:37Z","timestamp":1717663537000},"page":"39","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["MSProfileR: An Open-Source Software for Quality Control of Matrix-Assisted Laser Desorption Ionization\u2013Time of Flight Spectra"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-2921-036X","authenticated-orcid":false,"given":"Refka","family":"Ben Hamouda","sequence":"first","affiliation":[{"name":"Aix Marseille University, SSA, AP-HM, RITMES, 13005 Marseille, France"},{"name":"IHU M\u00e9diterran\u00e9e Infection, 13005 Marseille, France"},{"name":"Unit\u00e9 Parasitologie et Entomologie, D\u00e9partement Microbiologie et Maladies Infectieuses, Institut de Recherche Biom\u00e9dicale des Arm\u00e9es, 13005 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertrand","family":"Estellon","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Informatique et Syst\u00e8mes, Aix-Marseille University, CNRS, 13013 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khalil","family":"Himet","sequence":"additional","affiliation":[{"name":"Aix Marseille University, SSA, AP-HM, RITMES, 13005 Marseille, France"},{"name":"IHU M\u00e9diterran\u00e9e Infection, 13005 Marseille, France"},{"name":"Unit\u00e9 Parasitologie et Entomologie, D\u00e9partement Microbiologie et Maladies Infectieuses, Institut de Recherche Biom\u00e9dicale des Arm\u00e9es, 13005 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2378-7611","authenticated-orcid":false,"given":"Aimen","family":"Cherif","sequence":"additional","affiliation":[{"name":"Aix Marseille University, SSA, AP-HM, RITMES, 13005 Marseille, France"},{"name":"IHU M\u00e9diterran\u00e9e Infection, 13005 Marseille, France"},{"name":"Unit\u00e9 Parasitologie et Entomologie, D\u00e9partement Microbiologie et Maladies Infectieuses, Institut de Recherche Biom\u00e9dicale des Arm\u00e9es, 13005 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugo","family":"Marthinet","sequence":"additional","affiliation":[{"name":"French Armed Forces Center for Epidemiology and Public Health (CESPA), SSA, Camp de Sainte Marthe, 13568 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Marie","family":"Loreau","sequence":"additional","affiliation":[{"name":"Aix Marseille University, SSA, AP-HM, RITMES, 13005 Marseille, France"},{"name":"IHU M\u00e9diterran\u00e9e Infection, 13005 Marseille, France"},{"name":"French Armed Forces Center for Epidemiology and Public Health (CESPA), SSA, Camp de Sainte Marthe, 13568 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9242-1018","authenticated-orcid":false,"given":"Ga\u00ebtan","family":"Texier","sequence":"additional","affiliation":[{"name":"Aix Marseille University, SSA, AP-HM, RITMES, 13005 Marseille, France"},{"name":"IHU M\u00e9diterran\u00e9e Infection, 13005 Marseille, France"},{"name":"French Armed Forces Center for Epidemiology and Public Health (CESPA), SSA, Camp de Sainte Marthe, 13568 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9245-1535","authenticated-orcid":false,"given":"Samuel","family":"Granjeaud","sequence":"additional","affiliation":[{"name":"CRCM Integrative Bioinformatics Platform, Centre de Recherche en Canc\u00e9rologie de Marseille, INSERM, U1068, Institut Paoli-Calmettes, CNRS, UMR7258, Aix-Marseille Universit\u00e9 UM 105, 13009 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0490-5774","authenticated-orcid":false,"given":"Lionel","family":"Almeras","sequence":"additional","affiliation":[{"name":"Aix Marseille University, SSA, AP-HM, RITMES, 13005 Marseille, France"},{"name":"IHU M\u00e9diterran\u00e9e Infection, 13005 Marseille, France"},{"name":"Unit\u00e9 Parasitologie et Entomologie, D\u00e9partement Microbiologie et Maladies Infectieuses, Institut de Recherche Biom\u00e9dicale des Arm\u00e9es, 13005 Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1002\/mas.21359","article-title":"MALDI TOF MS Profiling of Bacteria at the Strain Level: A Review","volume":"32","author":"Sandrin","year":"2013","journal-title":"Mass Spectrom. 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