A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples.
Identifieur interne : 000187 ( Main/Exploration ); précédent : 000186; suivant : 000188A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples.
Auteurs : Tobias Boskamp [Allemagne] ; Delf Lachmund [Allemagne] ; Janina Oetjen [Allemagne] ; Yovany Cordero Hernandez [Allemagne] ; Dennis Trede [Allemagne] ; Peter Maass [Allemagne] ; Rita Casadonte [Allemagne] ; Jörg Kriegsmann [Allemagne] ; Arne Warth [Allemagne] ; Hendrik Dienemann [Allemagne] ; Wilko Weichert [Allemagne] ; Mark Kriegsmann [Allemagne]Source :
- Biochimica et biophysica acta [ 0006-3002 ] ; 2016.
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) shows a high potential for applications in histopathological diagnosis, and in particular for supporting tumor typing and subtyping. The development of such applications requires the extraction of spectral fingerprints that are relevant for the given tissue and the identification of biomarkers associated with these spectral patterns. We propose a novel data analysis method based on the extraction of characteristic spectral patterns (CSPs) that allow automated generation of classification models for spectral data. Formalin-fixed paraffin embedded (FFPE) tissue samples from N=445 patients assembled on 12 tissue microarrays were analyzed. The method was applied to discriminate primary lung and pancreatic cancer, as well as adenocarcinoma and squamous cell carcinoma of the lung. A classification accuracy of 100% and 82.8%, resp., could be achieved on core level, assessed by cross-validation. The method outperformed the more conventional classification method based on the extraction of individual m/z values in the first application, while achieving a comparable accuracy in the second. LC-MS/MS peptide identification demonstrated that the spectral features present in selected CSPs correspond to peptides relevant for the respective classification. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
DOI: 10.1016/j.bbapap.2016.11.003
PubMed: 27836618
Affiliations:
- Allemagne
- Bade-Wurtemberg, Bavière, Brême (Land), District de Haute-Bavière, District de Karlsruhe
- Brême, Heidelberg, Munich
- Université Louis-et-Maximilien de Munich
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Center for Histology, Cytology and Molecular Diagnostic, Trier, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Proteopath GmbH, Trier, Germany; Center for Histology, Cytology and Molecular Diagnostic, Trier</wicri:regionArea><wicri:noRegion>Trier</wicri:noRegion><wicri:noRegion>Trier</wicri:noRegion><wicri:noRegion>Trier</wicri:noRegion></affiliation></author><author><name sortKey="Warth, Arne" sort="Warth, Arne" uniqKey="Warth A" first="Arne" last="Warth">Arne Warth</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Pathology, Heidelberg University Hospital, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Dienemann, Hendrik" sort="Dienemann, Hendrik" uniqKey="Dienemann H" first="Hendrik" last="Dienemann">Hendrik Dienemann</name><affiliation wicri:level="3"><nlm:affiliation>Thoraxklinik Heidelberg, University of Heidelberg, Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Thoraxklinik Heidelberg, University of Heidelberg, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Weichert, Wilko" sort="Weichert, Wilko" uniqKey="Weichert W" first="Wilko" last="Weichert">Wilko Weichert</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Pathology, Technical University of Munich, Munich, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Pathology, Technical University of Munich, Munich</wicri:regionArea><placeName><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Haute-Bavière</region><settlement type="city">Munich</settlement></placeName><orgName type="university">Université Louis-et-Maximilien de Munich</orgName></affiliation></author><author><name sortKey="Kriegsmann, Mark" sort="Kriegsmann, Mark" uniqKey="Kriegsmann M" first="Mark" last="Kriegsmann">Mark Kriegsmann</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Pathology, Heidelberg University Hospital, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author></analytic><series><title level="j">Biochimica et biophysica acta</title><idno type="ISSN">0006-3002</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) shows a high potential for applications in histopathological diagnosis, and in particular for supporting tumor typing and subtyping. The development of such applications requires the extraction of spectral fingerprints that are relevant for the given tissue and the identification of biomarkers associated with these spectral patterns. We propose a novel data analysis method based on the extraction of characteristic spectral patterns (CSPs) that allow automated generation of classification models for spectral data. Formalin-fixed paraffin embedded (FFPE) tissue samples from N=445 patients assembled on 12 tissue microarrays were analyzed. The method was applied to discriminate primary lung and pancreatic cancer, as well as adenocarcinoma and squamous cell carcinoma of the lung. A classification accuracy of 100% and 82.8%, resp., could be achieved on core level, assessed by cross-validation. The method outperformed the more conventional classification method based on the extraction of individual m/z values in the first application, while achieving a comparable accuracy in the second. LC-MS/MS peptide identification demonstrated that the spectral features present in selected CSPs correspond to peptides relevant for the respective classification. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.</div></front></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Bade-Wurtemberg</li><li>Bavière</li><li>Brême (Land)</li><li>District de Haute-Bavière</li><li>District de Karlsruhe</li></region><settlement><li>Brême</li><li>Heidelberg</li><li>Munich</li></settlement><orgName><li>Université Louis-et-Maximilien de Munich</li></orgName></list><tree><country name="Allemagne"><region name="Brême (Land)"><name sortKey="Boskamp, Tobias" sort="Boskamp, Tobias" uniqKey="Boskamp T" first="Tobias" last="Boskamp">Tobias Boskamp</name></region><name sortKey="Casadonte, Rita" sort="Casadonte, Rita" uniqKey="Casadonte R" first="Rita" last="Casadonte">Rita Casadonte</name><name sortKey="Cordero Hernandez, Yovany" sort="Cordero Hernandez, Yovany" uniqKey="Cordero Hernandez Y" first="Yovany" last="Cordero Hernandez">Yovany Cordero Hernandez</name><name sortKey="Dienemann, Hendrik" sort="Dienemann, Hendrik" uniqKey="Dienemann H" first="Hendrik" last="Dienemann">Hendrik Dienemann</name><name sortKey="Kriegsmann, Jorg" sort="Kriegsmann, Jorg" uniqKey="Kriegsmann J" first="Jörg" last="Kriegsmann">Jörg Kriegsmann</name><name sortKey="Kriegsmann, Mark" sort="Kriegsmann, Mark" uniqKey="Kriegsmann M" first="Mark" last="Kriegsmann">Mark Kriegsmann</name><name sortKey="Lachmund, Delf" sort="Lachmund, Delf" uniqKey="Lachmund D" first="Delf" last="Lachmund">Delf Lachmund</name><name sortKey="Maass, Peter" sort="Maass, Peter" uniqKey="Maass P" first="Peter" last="Maass">Peter Maass</name><name sortKey="Oetjen, Janina" sort="Oetjen, Janina" uniqKey="Oetjen J" first="Janina" last="Oetjen">Janina Oetjen</name><name sortKey="Trede, Dennis" sort="Trede, Dennis" uniqKey="Trede D" first="Dennis" last="Trede">Dennis Trede</name><name sortKey="Warth, Arne" sort="Warth, Arne" uniqKey="Warth A" first="Arne" last="Warth">Arne Warth</name><name sortKey="Weichert, Wilko" sort="Weichert, Wilko" uniqKey="Weichert W" first="Wilko" last="Weichert">Wilko Weichert</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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