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The HUPO-PSI standardized spectral library format

Autor: Gabriels, Ralf, Bandeira, Nuno, Bittremieux, Wout, Carver, Jeremy J, Chambers, Matthew, Kawano, Shin, Lam, Henry, Mak, Tytus, Perez-Riverol, Yasset, Pullman, Benjamin J, Sharma, Vagisha, Shofstahl, Jim, Van Den Bossche, Tim, Vizcaino, Juan Antonio, Zhu, Yunping, Deutsch, Eric W

Publikováno v: EuBIC 2020 developers' meeting

More and more proteomics datasets are becoming available in public repositories. The knowledge embedded in these datasets can be used to improve peptide identification workflows. Spectral library searching provides a straightforward method to boost i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bce080ddb087b68e307570a48925c214
https://biblio.ugent.be/publication/8643839/file/8643840

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Autor: Wang, Mingxun, Carver, Jeremy J, Phelan, Vanessa V, Sanchez, Laura M, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Porto, Carla, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Dutton, Rachel J, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Michelsen, Charlotte F, Jelsbak, Lars, Sohlenkamp, Christian, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Murphy, Brian T, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Sedio, Brian E, Klitgaard, Andreas, Larson, Charles B, P, Cristopher A Boya, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric JN, Granatosky, Eve A, Glukhov, Evgenia, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Kharbush, Jenan J, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Nielsen, Kristian Fog, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Silva, Ricardo R, Mascuch, Samantha J, Tomasi, Sophie, Jenkins, Stefan, Macherla, Venkat, Hoffman, Thomas, Agarwal, Vinayak, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Gurr, Joshua, Rodríguez, Andrés MC, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad

Publikováno v: Nature biotechnology, vol 34, iss 8

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published pape

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::22a2dbbfb2f6b06896d77b0b03835653
https://escholarship.org/uc/item/8q63m69f

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plantMASST - Community-driven chemotaxonomic digitization of plants.

Autor: Gomes PWP; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Mannochio-Russo H; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Schmid R; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic., Zuffa S; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Damiani T; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic., Quiros-Guerrero LM; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland.; School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland., Caraballo-Rodríguez AM; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Zhao HN; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Yang H; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; College of Pharmacy, Kangwon National University, Chuncheon, Republic of Korea., Xing S; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Charron-Lamoureux V; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Chigumba DN; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA., Sedio BE; Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.; Smithsonian Tropical Research Institute, Republic of Panama., Myers JA; Department of Biology, Washington University in St. Louis, St. Louis, MO, USA., Allard PM; Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland., Harwood TV; The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, United States., Tamayo-Castillo G; Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica.; Escuela de Química, Universidad de Costa Rica, 2061 San José, Costa Rica., Kang KB; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea., Defossez E; Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.; Botanical garden of Neuchâtel., Koolen HHF; University of the State of Amazonas, Manaus, Brazil., da Silva MN; Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil.; Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil., E Silva CYY; Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil.; Institute of Health Sciences, Faculty of Pharmacy, Federal University of Pará, Belém 66075-110, Brazil., Rasmann S; Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland., Walker TWN; Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland., Glauser G; Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000 Neuchâtel, Switzerland., Chaves-Fallas JM; Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica.; Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO 63121, USA., David B; Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, 3 Avenue Hubert Curien, BP 13562, 31562 Toulouse, France., Kim H; College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea., Lee KH; College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea., Kim MJ; College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea., Choi WJ; College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea., Keum YS; College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea., de Lima EJSP; University of the State of Amazonas, Manaus, Brazil., de Medeiros LS; Federal University of São Paulo, Diadema, Brazil.; Department of Chemistry, Federal University of São Paulo, Diadema, SP, 09972-270, Brazil., Bataglion GA; Federal University of Amazonas, Manaus, Brazil., Costa EV; Federal University of Amazonas, Manaus, Brazil., da Silva FMA; Federal University of Amazonas, Manaus, Brazil., Carvalho ARV; Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil.; Institute of Health Sciences, Faculty of Pharmacy, Federal University of Pará, Belém 66075-110, Brazil., Reis JDE; Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil.; Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil., Pamplona S; Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil.; Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil., Jeong E; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea., Lee K; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea., Kim GJ; Department of Pharmacology, College of Medicine, Dongguk University, Gyeongju, Gyeongsangbuk-do, Republic of Korea.; Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea., Kil YS; College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea.; College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gimhae, Gyeongnam 50834, Republic of Korea., Nam JW; College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea.; Core Research Support Center for Natural Products and Medical Materials, Yeungnam University, Gyeongsan, Republic of Korea., Choi H; College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea.; Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea.; Core Research Support Center for Natural Products and Medical Materials, Yeungnam University, Gyeongsan, Republic of Korea., Han YK; College of Pharmacy, Korea University, Sejong, Republic of Korea., Park SY; College of Pharmacy, Korea University, Sejong, Republic of Korea., Lee KY; College of Pharmacy, Korea University, Sejong, Republic of Korea., Hu C; Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA., Dong Y; Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA., Sang S; Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA., Morrison CR; Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.; Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX, USA., Borges RM; Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil., Teixeira AM; Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil., Lee SY; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea., Lee BS; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea., Jeong SY; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea., Kim KH; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea., Rutz A; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland.; School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland.; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Gaudry A; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland.; School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland., Bruelhart E; Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland., Kappers IF; Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands., Karlova R; Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands., Meisenburg M; Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands., Berdaguer R; Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands., Tello JS; Latin America Department, Missouri Botanical Garden, St. Louis, MO, USA., Henderson D; Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.; Missouri Botanical Garden, St. Louis, MO, USA., Cayola L; Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia., Wright SJ; Smithsonian Tropical Research Institute, Balboa, Republic of Panama., Allen DN; Department of Biology, Middlebury College, Middlebury, VT, USA., Anderson-Teixeira KJ; Conservation Ecology Center, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA., Baltzer JL; Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada., Lutz JA; Department of Wildland Resources, Utah State University, Logan, UT, USA., McMahon SM; Smithsonian Environmental Research Center, Edgewater, MD, USA.; Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Panama., Parker GG; Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA., Parker JD; Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA., Northen TR; Environmental Genomics and Systems Biology Division and the DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States., Bowen BP; Environmental Genomics and Systems Biology Division and the DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States., Pluskal T; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic., van der Hooft JJJ; Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, the Netherlands.; Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa., Carver JJ; Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States., Bandeira N; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA., Pullman BS; Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States., Wolfender JL; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland.; School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland., Kersten RD; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA., Wang M; Department of Computer Science, University of California Riverside, Riverside, CA, 92521, United States., Dorrestein PC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 May 14. Date of Electronic Publication: 2024 May 14.