Your browser doesn't support javascript.
loading
Guiding the choice of informatics software and tools for lipidomics research applications.
Ni, Zhixu; Wölk, Michele; Jukes, Geoff; Mendivelso Espinosa, Karla; Ahrends, Robert; Aimo, Lucila; Alvarez-Jarreta, Jorge; Andrews, Simon; Andrews, Robert; Bridge, Alan; Clair, Geremy C; Conroy, Matthew J; Fahy, Eoin; Gaud, Caroline; Goracci, Laura; Hartler, Jürgen; Hoffmann, Nils; Kopczyinki, Dominik; Korf, Ansgar; Lopez-Clavijo, Andrea F; Malik, Adnan; Ackerman, Jacobo Miranda; Molenaar, Martijn R; O'Donovan, Claire; Pluskal, Tomás; Shevchenko, Andrej; Slenter, Denise; Siuzdak, Gary; Kutmon, Martina; Tsugawa, Hiroshi; Willighagen, Egon L; Xia, Jianguo; O'Donnell, Valerie B; Fedorova, Maria.
Afiliação
  • Ni Z; Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
  • Wölk M; Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
  • Jukes G; Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
  • Mendivelso Espinosa K; Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
  • Ahrends R; Department of Analytical Chemistry, University of Vienna, Vienna, Austria.
  • Aimo L; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
  • Alvarez-Jarreta J; Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
  • Andrews S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • Andrews R; Babraham Institute, Babraham Research Campus, Cambridge, UK.
  • Bridge A; Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
  • Clair GC; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
  • Conroy MJ; Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA.
  • Fahy E; Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
  • Gaud C; Department of Bioengineering, University of California, San Diego, CA, USA.
  • Goracci L; Babraham Institute, Babraham Research Campus, Cambridge, UK.
  • Hartler J; Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.
  • Hoffmann N; Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria.
  • Kopczyinki D; Field of Excellence BioHealthe-University of Graz, Graz, Austria.
  • Korf A; Center for Biotechnology, University of Bielefeld, Bielefeld, Germany.
  • Lopez-Clavijo AF; Department of Analytical Chemistry, University of Vienna, Vienna, Austria.
  • Malik A; Bruker Daltonics GmbH & Co. KG, Bremen, Germany.
  • Ackerman JM; Babraham Institute, Babraham Research Campus, Cambridge, UK.
  • Molenaar MR; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • O'Donovan C; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
  • Pluskal T; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Shevchenko A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • Slenter D; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
  • Siuzdak G; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
  • Kutmon M; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
  • Tsugawa H; Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA, USA.
  • Willighagen EL; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
  • Xia J; Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands.
  • O'Donnell VB; Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.
  • Fedorova M; RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
Nat Methods ; 20(2): 193-204, 2023 02.
Article em En | MEDLINE | ID: mdl-36543939
ABSTRACT
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
Assuntos
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Biologia Computacional / Lipidômica Idioma: En Ano de publicação: 2023 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Biologia Computacional / Lipidômica Idioma: En Ano de publicação: 2023 Tipo de documento: Article