mineMS2 preprint

THEVENOT Etienne · THEVENOT Etienne · commit d333f0baac5d · 2025-03-13T13:22:47.000+01:00
diff --git a/index.Rmd b/index.Rmd
@@ -4,8 +4,8 @@ title: "Odiscé"
 
 ## Welcome to the "Metabolomics Data Sciences for Health" team website
 
-For more than 15 years, our team based at **CEA Saclay** has been developing innovative methods and software in **metabolomic data science for health**. Our know-how and the digital ecosystem we have built cover all steps from **signal processing** of **mass spectrometry data**, **machine learning**, **feature selection**, **data integration**, **annotation** and up to reproducible **workflow management**.
+For more than 15 years, our team based at [**CEA Saclay**](https://www.cea.fr/paris-saclay/Pages/Accueil.aspx) in the [**LI-MS**](https://joliot.cea.fr/drf/joliot/en/Pages/research_entities/medicines_healthcare_technologies/spi/lims.aspx) laboratory (Laboratory of innovations in mass spectrometry for health), member of the [**MetaboHUB**](https://www.metabohub.fr/home.html) infrastructure in metabolomics and fluxomics, has been developing innovative computational methods and software libraries applied to **metabolomic data science for health**. Our know-how and the digital ecosystem we have built cover all steps from **signal processing** of **mass spectrometry data**, **machine learning**, **feature selection**, **data integration**, **cheminformatics** and up to reproducible **workflow management**.
 
 <center>![](images/odisce.png){width="673"}</center>
 
-###### Last update: 2024-09-25
+###### Last update: 2025-03-13
diff --git a/index.html b/index.html
@@ -288,19 +288,26 @@ <h1 class="title toc-ignore">Odiscé</h1>
 class="section level2">
 <h2>Welcome to the “Metabolomics Data Sciences for Health” team
 website</h2>
-<p>For more than 15 years, our team based at <strong>CEA Saclay</strong>
-has been developing innovative methods and software in
+<p>For more than 15 years, our team based at <a
+href="https://www.cea.fr/paris-saclay/Pages/Accueil.aspx"><strong>CEA
+Saclay</strong></a> in the <a
+href="https://joliot.cea.fr/drf/joliot/en/Pages/research_entities/medicines_healthcare_technologies/spi/lims.aspx"><strong>LI-MS</strong></a>
+laboratory (Laboratory of innovations in mass spectrometry for health),
+member of the <a
+href="https://www.metabohub.fr/home.html"><strong>MetaboHUB</strong></a>
+infrastructure in metabolomics and fluxomics, has been developing
+innovative computational methods and software libraries applied to
 <strong>metabolomic data science for health</strong>. Our know-how and
 the digital ecosystem we have built cover all steps from <strong>signal
 processing</strong> of <strong>mass spectrometry data</strong>,
 <strong>machine learning</strong>, <strong>feature selection</strong>,
-<strong>data integration</strong>, <strong>annotation</strong> and up to
-reproducible <strong>workflow management</strong>.</p>
+<strong>data integration</strong>, <strong>cheminformatics</strong> and
+up to reproducible <strong>workflow management</strong>.</p>
 <center>
 <img src="images/odisce.png" width="673" />
 </center>
-<div id="last-update-2024-09-25" class="section level6">
-<h6>Last update: 2024-09-25</h6>
+<div id="last-update-2025-03-13" class="section level6">
+<h6>Last update: 2025-03-13</h6>
 </div>
 </div>
 
diff --git a/news.Rmd b/news.Rmd
@@ -2,6 +2,8 @@
 title: "News"
 ---
 
+-   March 2025: **mineMS2 preprint** on ChemRxiv (<https://doi.org/10.26434/chemrxiv-2025-3c9z1>)
+
 -   Aug. 2024: **DIA-NMF publication** at the EUSIPCO Conference (<https://eurasip.org/Proceedings/Eusipco/Eusipco2024/pdfs/0002387.pdf>)
 
 -   Feb. 2024: **Spec2Annot package** to annotate and query mass spectra on our GitHub (<https://github.com/odisce>)
diff --git a/news.html b/news.html
@@ -284,6 +284,9 @@ <h1 class="title toc-ignore">News</h1>
 
 
 <ul>
+<li><p>March 2025: <strong>mineMS2 preprint</strong> on ChemRxiv (<a
+href="https://doi.org/10.26434/chemrxiv-2025-3c9z1"
+class="uri">https://doi.org/10.26434/chemrxiv-2025-3c9z1</a>)</p></li>
 <li><p>Aug. 2024: <strong>DIA-NMF publication</strong> at the EUSIPCO
 Conference (<a
 href="https://eurasip.org/Proceedings/Eusipco/Eusipco2024/pdfs/0002387.pdf"
diff --git a/publications.Rmd b/publications.Rmd
@@ -2,6 +2,8 @@
 title: "Selected publications"
 ---
 
+-   Delabrière A., Gianfrotta G., Dechaumet S., Damont A., Hautbergue T., Roger P., Jamin E.L., Puel O., Junot C., Fenaille F. and Thévenot E.A. (2025) mineMS2: Annotation of spectral libraries with exact fragmentation patterns. *ChemRxiv*, Preprint (<https://doi.org/10.26434/chemrxiv-2025-3c9z1>)
+
 <!-- -   Lefebvre T., Eguether T., Thévenot E., Poli A., Chu-Van E., Krasniqi P., Schmitt C., Talbi N., Nicolas G., Puy H., Junot C., Lamazière A., Castelli F., Gouya L. and Fenaille F. (2025) Nontargeted urine metabolomic analysis of acute intermittent porphyria reveals novel interactions between bile acids and heme metabolism: New promising biomarkers for the long-term management of patients. *Journal of Inherited Metabolic Disease*, **48**:1 (<https://doi.org/10.1002/jimd.12809>) -->
 
 -   Karaki D., Dechaumet S., Damont A., Colsch B., Fenaille F., Souloumiac A. and Thévenot E.A. (2024) Non-Negative Matrix Factorization of SWATH DIA Data Improves Global Metabolite Identification. In, *European Signal Processing Conference (EUSIPCO)*. Lyon (<https://eurasip.org/Proceedings/Eusipco/Eusipco2024/pdfs/0002387.pdf>)
diff --git a/publications.html b/publications.html
@@ -283,6 +283,15 @@ <h1 class="title toc-ignore">Selected publications</h1>
 </div>
 
 
+<ul>
+<li>Delabrière A., Gianfrotta G., Dechaumet S., Damont A., Hautbergue
+T., Roger P., Jamin E.L., Puel O., Junot C., Fenaille F. and Thévenot
+E.A. (2025) mineMS2: Annotation of spectral libraries with exact
+fragmentation patterns. <em>ChemRxiv</em>, Preprint (<a
+href="https://doi.org/10.26434/chemrxiv-2025-3c9z1"
+class="uri">https://doi.org/10.26434/chemrxiv-2025-3c9z1</a>)</li>
+</ul>
+<!-- -   Lefebvre T., Eguether T., Thévenot E., Poli A., Chu-Van E., Krasniqi P., Schmitt C., Talbi N., Nicolas G., Puy H., Junot C., Lamazière A., Castelli F., Gouya L. and Fenaille F. (2025) Nontargeted urine metabolomic analysis of acute intermittent porphyria reveals novel interactions between bile acids and heme metabolism: New promising biomarkers for the long-term management of patients. *Journal of Inherited Metabolic Disease*, **48**:1 (<https://doi.org/10.1002/jimd.12809>) -->
 <ul>
 <li><p>Karaki D., Dechaumet S., Damont A., Colsch B., Fenaille F.,
 Souloumiac A. and Thévenot E.A. (2024) Non-Negative Matrix Factorization
diff --git a/team.Rmd b/team.Rmd
@@ -2,9 +2,9 @@
 title: "Team"
 ---
 
--   Pinart Paul-Henri
+-   Anaghim Temtem
 
--   Ninon Robin
+-   Pinart Paul-Henri
 
 -   Coline Gianfrotta
 
@@ -20,6 +20,8 @@ title: "Team"
 
 ## **Alumni**
 
+-   Ninon Robin
+
 -   Oneeb Nasir
 
 -   Maria Teresa Avella
diff --git a/team.html b/team.html
@@ -284,8 +284,8 @@ <h1 class="title toc-ignore">Team</h1>
 
 
 <ul>
+<li><p>Anaghim Temtem</p></li>
 <li><p>Pinart Paul-Henri</p></li>
-<li><p>Ninon Robin</p></li>
 <li><p>Coline Gianfrotta</p></li>
 <li><p>Diana Karaki</p></li>
 <li><p>Dylan Saunier</p></li>
@@ -298,6 +298,7 @@ <h1 class="title toc-ignore">Team</h1>
 <div id="alumni" class="section level2">
 <h2><strong>Alumni</strong></h2>
 <ul>
+<li><p>Ninon Robin</p></li>
 <li><p>Oneeb Nasir</p></li>
 <li><p>Maria Teresa Avella</p></li>
 <li><p>Eric Venot</p></li>
