Integrative analysis of multimodal mass spectrometry data in MZmine 3

被引:351
作者
Schmid, Robin [1 ,2 ,3 ]
Heuckeroth, Steffen [2 ]
Korf, Ansgar [2 ]
Smirnov, Aleksandr [4 ]
Myers, Owen [4 ]
Dyrlund, Thomas S. [5 ]
Bushuiev, Roman [3 ]
Murray, Kevin J. [6 ]
Hoffmann, Nils [7 ]
Lu, Miaoshan [8 ]
Sarvepalli, Abinesh [9 ]
Zhang, Zheng [1 ]
Fleischauer, Markus [10 ]
Duehrkop, Kai [10 ]
Wesner, Mark [2 ]
Hoogstra, Shawn J. [11 ]
Rudt, Edward [2 ]
Mokshyna, Olena [3 ]
Brungs, Corinna [3 ]
Ponomarov, Kirill [3 ]
Mutabdzija, Lana [3 ]
Damiani, Tito [3 ]
Pudney, Chris J. [12 ]
Earll, Mark [13 ]
Helmer, Patrick O. [2 ]
Fallon, Timothy R. [14 ]
Schulze, Tobias [15 ]
Rivas-Ubach, Albert [16 ]
Bilbao, Aivett [17 ]
Richter, Henning [18 ]
Nothias, Louis-Felix [19 ]
Wang, Mingxun [20 ]
Oresic, Matej [21 ,22 ,23 ]
Weng, Jing-Ke [24 ,25 ]
Boecker, Sebastian [10 ]
Jeibmann, Astrid [26 ]
Hayen, Heiko [2 ]
Karst, Uwe [2 ]
Dorrestein, Pieter C. [1 ]
Petras, Daniel [27 ]
Du, Xiuxia [4 ]
Pluskal, Tomas [3 ]
机构
[1] Univ Calif San Diego, Collaborat Mass Spectrometry Innovat Ctr, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA USA
[2] Univ Munster, Inst Inorgan & Analyt Chem, Munster, Germany
[3] Czech Acad Sci, Inst Organ Chem & Biochem, Prague, Czech Republic
[4] Univ North Carolina Charlotte, Dept Bioinformat & Genom, Charlotte, NC USA
[5] Steno Diabet Ctr Copenhagen, Gentofte, Denmark
[6] Univ Minnesota Twin Cities, Dept Biochem Mol Biol & Biophys, Minneapolis, MN USA
[7] Forschungszentrum Julich, Inst Bio & Geosci IBG 5, Julich, Germany
[8] Westlake Univ, Sch Engn, Hangzhou, Peoples R China
[9] San Diego Supercomp Ctr, BlockLab, Ctr Large Datasyst Res, La Jolla, CA USA
[10] Friedrich Schiller Univ Jena, Chair Bioinformat, Jena, Germany
[11] Agr & Agri Food Canada, London Res & Dev Ctr, London, ON, Canada
[12] Datacraft Technol, Mosman Pk, Washington, WA, Australia
[13] Jealotts Hill Int Res Ctr, Analyt Solut Grp, Prod Technol & Engn, Bracknell, England
[14] Univ Calif San Diego, Ctr Marine Biotechnol & Biomed, Scripps Inst Oceanog, La Jolla, CA USA
[15] UFZ Helmholtz Ctr Environm Res, Dept Effect Directed Anal, Leipzig, Germany
[16] Inst Forest Sci ICIFOR INIA CSIC, Ecol & Forest Genet, Madrid, Spain
[17] Pacific Northwest Natl Lab, Earth & Biol Sci Directorate, Richland, WA USA
[18] Univ Zurich, Clin Diagnost Imaging, Diagnost Imaging Res Unit DIRU, Zurich, Switzerland
[19] Univ Geneva, Sch Pharmaceut Sci, Geneva, Switzerland
[20] Univ Calif Riverside, Dept Comp Sci, Riverside, CA USA
[21] Orebro Univ, Sch Med Sci, Orebro, Sweden
[22] Univ Turku, Turku Biosci Ctr, Turku, Finland
[23] Abo Akad Univ, Turku, Finland
[24] Whitehead Inst Biomed Res, Cambridge, MA USA
[25] MIT, Dept Biol, Cambridge, MA USA
[26] Univ Hosp Munster, Inst Neuropathol, Munster, Germany
[27] Univ Tubingen, CMFI Cluster Excellence, Tubingen, Germany
基金
美国国家科学基金会; 英国生物技术与生命科学研究理事会; 瑞士国家科学基金会; 欧盟地平线“2020”;
关键词
VISUALIZATION;
D O I
10.1038/s41587-023-01690-2
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
引用
收藏
页码:447 / 449
页数:3
相关论文
共 17 条
  • [1] Global chemical analysis of biology by mass spectrometry
    Aksenov, Alexander A.
    da Silva, Ricardo
    Knight, Rob
    Lopes, Norberto P.
    Dorrestein, Pieter C.
    [J]. NATURE REVIEWS CHEMISTRY, 2017, 1 (07)
  • [2] Du XX, 2020, METHODS MOL BIOL, V2104, P25, DOI 10.1007/978-1-0716-0239-3_3
  • [3] SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
    Duhrkop, Kai
    Fleischauer, Markus
    Ludwig, Marcus
    Aksenov, Alexander A.
    Melnik, Alexey V.
    Meusel, Marvin
    Dorrestein, Pieter C.
    Rousu, Juho
    Bocker, Sebastian
    [J]. NATURE METHODS, 2019, 16 (04) : 299 - +
  • [4] Complementing Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging with Chromatography Data for Improved Assignment of Isobaric and Isomeric Phospholipids Utilizing Trapped Ion Mobility-Mass Spectrometry
    Helmer, Patrick O.
    Nordhorn, Ilona D.
    Korf, Ansgar
    Behrens, Arne
    Buchholz, Rebecca
    Zubeil, Florian
    Karst, Uwe
    Hayen, Heiko
    [J]. ANALYTICAL CHEMISTRY, 2021, 93 (04) : 2135 - 2143
  • [5] MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
    Katajamaa, M
    Miettinen, J
    Oresic, M
    [J]. BIOINFORMATICS, 2006, 22 (05) : 634 - 636
  • [6] Lipid Species Annotation at Double Bond Position Level with Custom Databases by Extension of the MZmine 2 Open-Source Software Package
    Korf, Ansgar
    Jeck, Viola
    Schmid, Robin
    Helmer, Patrick O.
    Hayen, Heiko
    [J]. ANALYTICAL CHEMISTRY, 2019, 91 (08) : 5098 - 5105
  • [7] Parallel Accumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device
    Meier, Florian
    Beck, Scarlet
    Grassl, Niklas
    Lubeck, Markus
    Park, Melvin A.
    Raether, Oliver
    Mann, Matthias
    [J]. JOURNAL OF PROTEOME RESEARCH, 2015, 14 (12) : 5378 - 5387
  • [8] Feature-based molecular networking in the GNPS analysis environment
    Nothias, Louis-Felix
    Petras, Daniel
    Schmid, Robin
    Duehrkop, Kai
    Rainer, Johannes
    Sarvepalli, Abinesh
    Protsyuk, Ivan
    Ernst, Madeleine
    Tsugawa, Hiroshi
    Fleischauer, Markus
    Aicheler, Fabian
    Aksenov, Alexander A.
    Alka, Oliver
    Allard, Pierre-Marie
    Barsch, Aiko
    Cachet, Xavier
    Caraballo-Rodriguez, Andres Mauricio
    Da Silva, Ricardo R.
    Dang, Tam
    Garg, Neha
    Gauglitz, Julia M.
    Gurevich, Alexey
    Isaac, Giorgis
    Jarmusch, Alan K.
    Kamenik, Zdenek
    Kang, Kyo Bin
    Kessler, Nikolas
    Koester, Irina
    Korf, Ansgar
    Le Gouellec, Audrey
    Ludwig, Marcus
    Martin H., Christian
    McCall, Laura-Isobel
    McSayles, Jonathan
    Meyer, Sven W.
    Mohimani, Hosein
    Morsy, Mustafa
    Moyne, Oriane
    Neumann, Steffen
    Neuweger, Heiko
    Nguyen, Ngoc Hung
    Nothias-Esposito, Melissa
    Paolini, Julien
    Phelan, Vanessa V.
    Pluskal, Tomas
    Quinn, Robert A.
    Rogers, Simon
    Shrestha, Bindesh
    Tripathi, Anupriya
    van der Hooft, Justin J. J.
    [J]. NATURE METHODS, 2020, 17 (09) : 905 - +
  • [9] MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights
    Pang, Zhiqiang
    Chong, Jasmine
    Zhou, Guangyan
    Morais, David Anderson de Lima
    Chang, Le
    Barrette, Michel
    Gauthier, Carol
    Jacques, Pierre-Etienne
    Li, Shuzhao
    Xia, Jianguo
    [J]. NUCLEIC ACIDS RESEARCH, 2021, 49 (W1) : W388 - W396
  • [10] MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
    Pluskal, Tomas
    Castillo, Sandra
    Villar-Briones, Alejandro
    Oresic, Matej
    [J]. BMC BIOINFORMATICS, 2010, 11