title: FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.
abstract: High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM). We introduce a metabolite-signal match score and a target-decoy FDR estimate for spatial metabolomics.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Andrew
authors.initials: A
authors.lastname: Palmer
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Prasad
authors.identifier: 0000-0002-9487-597X
authors.initials: P
authors.lastname: Phapale
authors.affiliation: Center for Industrial Mathematics, University of Bremen, Bremen, Germany.
authors.forename: Ilya
authors.initials: I
authors.lastname: Chernyavsky
authors.affiliation: Protim, Inserm U1085, IRSET, Rennes, France.|Université de Rennes I, Rennes, France.
authors.forename: Regis
authors.initials: R
authors.lastname: Lavigne
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Dominik
authors.initials: D
authors.lastname: Fay
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Artem
authors.initials: A
authors.lastname: Tarasov
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Vitaly
authors.initials: V
authors.lastname: Kovalev
authors.affiliation: Bruker Daltonik GmbH, Bremen, Germany.
authors.forename: Jens
authors.identifier: 0000-0003-3947-7677
authors.initials: J
authors.lastname: Fuchser
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.|National Research University Higher School of Economics, St. Petersburg, Russia.|Higher Institute of Information Technologies and Information Systems, Kazan Federal University, Kazan, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Nikolenko
authors.affiliation: Protim, Inserm U1085, IRSET, Rennes, France.|Université de Rennes I, Rennes, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Pineau
authors.affiliation: Bruker Daltonik GmbH, Bremen, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Becker
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.|SCiLS GmbH, Bremen, Germany.|Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA.
authors.forename: Theodore
authors.identifier: 0000-0001-9464-6125
authors.initials: T
authors.lastname: Alexandrov
mesh_terms: D000818:Animals; D001921:Brain / Q000166:cytology / Q000378:metabolism*; D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods*; D005189:False Positive Reactions; D005260:Female; D013058:Mass Spectrometry / Q000379:methods*; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D051379:Mice; D008810:Mice, Inbred C57BL; D057054:Molecular Imaging / Q000379:methods*; D012984:Software