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Schmidt T, Samaras P, Frejno M, et al. ProteomicsDB. Nucleic Acids Res. 2018;46:D1271-D1281doi: 10.1093/nar/gkx1029.
Schmidt, T., Samaras, P., Frejno, M., Gessulat, S., Barnert, M., Kienegger, H., Krcmar, H., Schlegl, J., Ehrlich, H. C., Aiche, S., Kuster, B., & Wilhelm, M. (2018). ProteomicsDB. Nucleic acids research, 46D1271-D1281. https://doi.org/10.1093/nar/gkx1029
Schmidt, Tobias, et al. "ProteomicsDB." Nucleic acids research vol. 46 (2018): D1271-D1281. doi: https://doi.org/10.1093/nar/gkx1029
Schmidt T, Samaras P, Frejno M, Gessulat S, Barnert M, Kienegger H, Krcmar H, Schlegl J, Ehrlich HC, Aiche S, Kuster B, Wilhelm M. ProteomicsDB. Nucleic Acids Res. 2018 Jan 04;46:D1271-D1281. doi: 10.1093/nar/gkx1029. PMID: 29106664; PMCID: PMC5753189.
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Nucleic Acids Res. 2018 Jan 04;46:D1271-D1281. doi: 10.1093/nar/gkx1029.

ProteomicsDB.

Nucleic acids research

Tobias Schmidt, Patroklos Samaras, Martin Frejno, Siegfried Gessulat, Maximilian Barnert, Harald Kienegger, Helmut Krcmar, Judith Schlegl, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Kuster, Mathias Wilhelm

Affiliations

  1. Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, 85354 Bavaria, Germany.
  2. Innovation Center Network, SAP SE, Potsdam 14469, Germany.
  3. Chair for Information Systems, Technical University of Munich (TUM), Garching 85748, Germany.
  4. SAP University Competence Center, Technical University of Munich (TUM), Garching 85748, Germany.
  5. PI HANA Platform Core, SAP SE, Walldorf 69190, Germany.
  6. Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, 85354 Bavaria, Germany.

PMID: 29106664 PMCID: PMC5753189 DOI: 10.1093/nar/gkx1029

Abstract

ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines. We recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e.g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically.

© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

References

  1. Nat Methods. 2017 Mar;14 (3):259-262 - PubMed
  2. Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56 - PubMed
  3. Nat Chem Biol. 2016 Feb;12(2):109-16 - PubMed
  4. Mol Cell Proteomics. 2012 Mar;11(3):M111.014068 - PubMed
  5. Curr Opin Chem Biol. 2008 Oct;12(5):483-90 - PubMed
  6. Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169 - PubMed
  7. Proteomics. 2015 Mar;15(5-6):930-49 - PubMed
  8. Proteomics. 2017 Nov;17 (21):null - PubMed
  9. Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6 - PubMed
  10. Nature. 2014 May 29;509(7502):582-7 - PubMed
  11. Genome Res. 2003 Nov;13(11):2498-504 - PubMed
  12. Science. 2014 Oct 3;346(6205):1255784 - PubMed
  13. J Proteome Res. 2004 Nov-Dec;3(6):1234-42 - PubMed
  14. Mol Cell Proteomics. 2012 Aug;11(8):492-500 - PubMed
  15. Cell. 2016 Jul 28;166(3):740-754 - PubMed
  16. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8 - PubMed
  17. Mol Cell Proteomics. 2012 Nov;11(11):1500-9 - PubMed
  18. Nucleic Acids Res. 2017 Jan 4;45(D1):D177-D182 - PubMed
  19. Mol Cell Proteomics. 2015 Sep;14(9):2394-404 - PubMed
  20. Mol Cell Proteomics. 2011 Jul;10(7):M111.009993 - PubMed
  21. Nat Biotechnol. 2007 Sep;25(9):1035-44 - PubMed
  22. Nature. 2003 Mar 13;422(6928):198-207 - PubMed
  23. Nature. 2012 Mar 28;483(7391):603-7 - PubMed
  24. Proteomics. 2009 Oct;9(20):4653-63 - PubMed
  25. Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361 - PubMed
  26. Nat Commun. 2015 Apr 30;6:7002 - PubMed
  27. Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):5048-53 - PubMed
  28. J Proteome Res. 2013 Apr 5;12(4):1723-31 - PubMed
  29. Annu Rev Anal Chem (Palo Alto Calif). 2009;2:265-77 - PubMed
  30. Anal Bioanal Chem. 2007 Oct;389(4):1017-31 - PubMed

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