Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/springer-journals/metabolite-imager-customized-spatial-analysis-of-metabolite-jnuIhewcvY
References (50)
-
M Sud, E Fahy, D Cotter, A Brown, EA Dennis, CK Glass, AH Merrill, RC Murphy, CRH Raetz, DW Russell, S Subramaniam (2007)
LMSD: LIPID MAPS structure databaseNucleic Acids Research, 35
-
PJ Horn, CN James, S Gidda, A Kilaru, JM Dyer, RT Mullen, JB Ohlrogge, K Chapman (2013)
Identification of a new class of lipid droplet-associated proteins in plantsPlant Physiology, 162
-
K Dettmer, PA Aronov, BD Hammock (2007)
Mass spectrometry-based metabolomicsMass Spectrometry Reviews, 26
-
M Hattori, Y Okuno, S Goto, M Kanehisa (2003)
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathwaysJournal of the American Chemical Society, 125
-
S Kaspar, M Peukert, A Svatos, A Matros, H-P Mock (2011)
MALDI-imaging mass spectrometry—An emerging technique in plant biologyProteomics, 11
-
O Fiehn (2002)
Metabolomics—the link between genotypes and phenotypesPlant Molecular Biology, 48
-
S Guenther, M Koestler, O Schulz, B Spengler (2010)
Laser spot size and laser power dependence of ion formation in high resolution MALDI imagingInternational Journal of Mass Spectrometry, 294
-
DS Wishart (2008)
Quantitative metabolomics using NMRTrAC, Trends in Analytical Chemistry, 27
-
R Welti, J Shah, W Li, M Li, J Chen, JJ Burke, ML Fauconnier, K Chapman, ML Chye, X Wang (2007)
Plant lipidomics: Discerning biological function by profiling plant complex lipids using mass spectrometryFront Biosci, 12
-
A Walch, S Rauser, S-O Deininger, H Höfler (2008)
MALDI imaging mass spectrometry for direct tissue analysis: A new frontier for molecular histologyHistochemistry and Cell Biology, 130
-
C Whittern, E Miller, D Pratt (1984)
Cottonseed flavonoids as lipid antioxidantsJournal of the American Oil Chemists Society, 61
-
DC Perdian, YJ Lee (2010)
Imaging MS methodology for more chemical information in less data acquisition time utilizing a hybrid linear ion trap—Orbitrap mass spectrometerAnalytical Chemistry, 82
-
PJ Horn, AR Korte, PB Neogi, E Love, J Fuchs, K Strupat, L Borisjuk, V Shulaev, Y-J Lee, KD Chapman (2012)
Spatial mapping of lipids at cellular resolution in embryos of cottonPlant Cell, 24
-
Q Hu, RJ Noll, H Li, A Makarov, M Hardman, R Graham Cooks (2005)
The Orbitrap: A new mass spectrometerJournal of Mass Spectrometry, 40
-
T Tohge, AR Fernie (2009)
Web-based resources for mass-spectrometry-based metabolomics: A user’s guidePhytochemistry, 70
-
TA Wagner, J Liu, RD Stipanovic, LS Puckhaber, AA Bell (2012)
Hemigossypol, a constituent in developing glanded cottonseed (Gossypium hirsutum)Journal of Agricultural and Food Chemistry, 60
-
P Källback, M Shariatgorji, A Nilsson, PE Andrén (2012)
Novel mass spectrometry imaging software assisting labeled normalization and quantitation of drugs and neuropeptides directly in tissue sectionsJournal of Proteomics, 75
-
A Scalbert, L Brennan, O Fiehn, T Hankemeier, B Kristal, B Ommen, E Pujos-Guillot, E Verheij, D Wishart, S Wopereis (2009)
Mass-spectrometry-based metabolomics: Limitations and recommendations for future progress with particular focus on nutrition researchMetabolomics, 5
-
M Sturm, A Bertsch, C Gropl, A Hildebrandt, R Hussong, E Lange, N Pfeifer, O Schulz-Trieglaff, A Zerck, K Reinert, O Kohlbacher (2008)
OpenMS—an open-source software framework for mass spectrometryBMC Bioinformatics, 9
-
PJ Horn, KD Chapman (2012)
Lipidomics in tissues, cells and subcellular compartmentsThe Plant Journal, 70
-
Y Mao, S Lu, L Wang, X Chen (2006)
Biosynthesis of gossypol in cottonCAB Reviews: Perspective in Agriculture, Veterinary Science, Nutrition and Natural Resources, 49
-
PGA Pedrioli, JK Eng, R Hubley, M Vogelzang, EW Deutsch, B Raught, B Pratt, E Nilsson, RH Angeletti, R Apweiler, K Cheung, CE Costello, H Hermjakob, S Huang, RK Julian, E Kapp, ME McComb, SG Oliver, G Omenn, NW Paton, R Simpson, R Smith, CF Taylor, W Zhu, R Aebersold (2004)
A common open representation of mass spectrometry data and its application to proteomics researchNature Biotechnology, 22
-
AB Canelas, A Pierick, C Ras, RM Seifar, JC Dam, WM Gulik, JJ Heijnen (2009)
quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomicsAnalytical Chemistry, 81
-
CN James, PJ Horn, CR Case, SK Gidda, D Zhang, RT Mullen, JM Dyer, RGW Anderson, KD Chapman (2010)
Disruption of the Arabidopsis CGI-58 homologue produces Chanarin–Dorfman-like lipid droplet accumulation in plantsProceedings of the National Academy of Sciences, 107
-
RC Murphy, JA Hankin, RM Barkley (2009)
Imaging of lipid species by MALDI mass spectrometryJournal of Lipid Research, 50
-
DS Wishart, D Tzur, C Knox, R Eisner, AC Guo (2007)
HMDB: The human metabolome databaseNucleic Acids Research, 35
-
T Kind, O Fiehn (2006)
Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppmBMC Bioinformatics, 7
-
R Caspi, T Altman, JM Dale, K Dreher, CA Fulcher, F Gilham, P Kaipa, AS Karthikeyan, A Kothari, M Krummenacker, M Latendresse, LA Mueller, S Paley, L Popescu, A Pujar, AG Shearer, P Zhang, PD Karp (2010)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databasesNucleic Acids Research, 38
-
PJ Horn, NR Ledbetter, CN James, WD Hoffman, CR Case, GF Verbeck, KD Chapman (2011)
Visualization of lipid droplet composition by direct organelle mass spectrometryJournal of Biological Chemistry, 286
-
L Chae, I Lee, J Shin, SY Rhee (2012)
Towards understanding how molecular networks evolve in plantsCurrent Opinion in Plant Biology, 15
-
LA McDonnell, A Remoortere, N Velde, RJM Zeijl, AM Deelder (2010)
Imaging mass spectrometry data reduction: Automated feature identification and extractionJournal of the American Society for Mass Spectrometry, 21
-
R Goodacre, S Vaidyanathan, WB Dunn, GG Harrigan, DB Kell (2004)
Metabolomics by numbers: Acquiring and understanding global metabolite dataTrends in Biotechnology, 22
-
JOR Gustafsson, MK Oehler, A Ruszkiewicz, SR McColl, P Hoffmann (2011)
MALDI imaging mass spectrometry (MALDI-IMS)—application of spatial proteomics for ovarian cancer classification and diagnosisInternational Journal of Molecular Sciences, 12
-
YJ Lee, DC Perdian, Z Song, ES Yeung, BJ Nikolau (2012)
Use of mass spectrometry for imaging metabolites in plantsThe Plant Journal, 70
-
CA Smith, EJ Want, G O’Maille, R Abagyan, G Siuzdak (2006)
XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identificationAnalytical Chemistry, 78
-
H Wu, AD Southam, A Hines, MR Viant (2008)
High-throughput tissue extraction protocol for NMR- and MS-based metabolomicsAnalytical Biochemistry, 372
-
T Schramm, A Hester, I Klinkert, J-P Both, RMA Heeren, A Brunelle, O Laprévote, N Desbenoit, M-F Robbe, M Stoeckli, B Spengler, A Römpp (2012)
imzML—A common data format for the flexible exchange and processing of mass spectrometry imaging dataJournal of Proteomics, 75
-
X Xiong, W Xu, L Eberlin, J Wiseman, X Fang, Y Jiang, Z Huang, Y Zhang, RG Cooks, Z Ouyang (2012)
Data processing for 3D mass spectrometry imagingJournal of the American Society for Mass Spectrometry, 23
-
R Adams, TA Geissman, JD Edwards (1960)
Gossypol, a pigment of cottonseedChemical Reviews, 60
-
RD Stipanovic, AA Bell, CR Benedict (1999)
Biologically active natural products: Agrochemicals -
M Sugimoto, M Kawakami, M Robert, T Soga, M Tomita (2012)
Bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysisCurrent Bioinformatics, 7
-
J Boccard, J-L Veuthey, S Rudaz (2010)
Knowledge discovery in metabolomics: An overview of MS data handlingJournal of Separation Science, 33
-
S Dietmair, NE Timmins, PP Gray, LK Nielsen, JO Krömer (2010)
Towards quantitative metabolomics of mammalian cells: Development of a metabolite extraction protocolAnalytical Biochemistry, 404
-
LA Mueller, P Zhang, SY Rhee (2003)
AraCyc: A biochemical pathway database for arabidopsisPlant Physiology, 132
-
K Dodou (2005)
Investigations on gossypol: Past and present developmentsExpert Opinion on Investigational Drugs, 14
-
PA Hedin, WL Parrott, JN Jenkins (1992)
Relationships of glands, cotton square terpenoid aldehydes, and other allelochemicals to larval growth of Heliothis virescens (Lepidoptera: Noctuidae)Journal of Economic Entomology, 85
-
P Chaurand, SA Schwartz, ML Reyzer, RM Caprioli (2005)
Imaging mass spectrometry: Principles and potentialsToxicologic Pathology, 33
-
X Han, RW Gross (2005)
Shotgun lipidomics: Electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samplesMass Spectrometry Reviews, 24
-
PEM Verhaert, MH Pinkse, K Strupat, MP Conaway (2010)
Mass spectrometry imaging -
Z Zhou, S Marepally, D Nune, P Pallakollu, G Ragan, M Roth, L Wang, G Lushington, M Visvanathan, R Welti (2011)
LipidomeDB data calculation environment: Online processing of direct-infusion mass spectral data for lipid profilesLipids, 46
- Publisher
- Springer Journals
- Copyright
- Copyright © 2013 by Springer Science+Business Media New York
- Subject
- Life Sciences; Biochemistry, general; Molecular Medicine; Cell Biology; Developmental Biology; Biomedicine, general
- ISSN
- 1573-3882
- eISSN
- 1573-3890
- DOI
- 10.1007/s11306-013-0575-0
- Publisher site
- See Article on Publisher Site
Abstract
Mass spectrometry (MS) is currently the most utilized analytical instrument for evaluating the metabolite composition of a biological sample at both the qualitative and quantitative level. The exponential growth of raw data generated through increasingly versatile mass spectrometers requires sophisticated algorithms to process and visualize the raw data to address biological questions. The structural and quantitative diversity of a single species’ metabolome (e.g. all metabolite species) under different experimental conditions itself forms a very large and complex dataset to analyze. We have developed a free, Java-based metabolomics application “Metabolite Imager” ( www.metaboliteimager.com ) that enables customized analysis and visualization of the metabolite distributions in tissues acquired through MS-based imaging approaches. Metabolite Imager algorithms perform customized targeted searching of metabolites through user-defined and publicly-available databases enabling the analysis of spatial distributions of large metabolite numbers in tissue sections. Metabolite Imager’s automated, two-dimensional image generator has several customizable features for producing high-resolution images. Additional Metabolite Imager algorithms support identifying targeted and unknown detected metabolites in selected tissue regions using spatially-based enrichment analysis that could impact metabolic engineering strategies. Co-localization algorithms of metabolites and selected ions by m/z enable analysis of precursor-product relationships in situ that will be important for expanding the biological context of metabolic pathways.
Journal
Metabolomics – Springer Journals
Published: Aug 15, 2013