NORMAN MassBank and beyond Status and future of activities regarding mass spectral databases
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1 NORMAN MassBank and beyond Status and future of activities regarding mass spectral databases NORMAN Annual General Assembly Meeting Vienna, 30 November - 01 December 2016 commons.wikimedia.org Tobias Schulze, Emma Schymanski, Steffen Neumann, Juliane Hollender, Jaroslav Slobodnik, Werner Brack UFZ Leipzig, Eawag Dübendorf, IPB Halle, EI tobias.schulze@ufz.de, emma.schymanski@eawag.ch
2 Proposed activities 2016 Establishment of isotope peak annotation in RMassBank (RMB) Implementation of tentative / unknown compound processing in RMB Inclusion of data independent analysis to address new MS technologies Regularly update a download page for MassBank in NIST mass spectral library format Fostering discussions with MassBank developers community and MassBank of North America Server relaunch includes setup of so-called SVN repository for easy download / update of open access MassBank spectra tobias.schulze@ufz.de, emma.schymanski@eawag.ch
3 Proposed activities Progress Establishment of isotope peak annotation in RMassBank (RMB) DONE! Contributions from Uni. Athens with annotated isotope pattern tobias.schulze@ufz.de, emma.schymanski@eawag.ch
4 Proposed activities Progress Implementation of tentative / unknown compound processing in RMB DONE! Several Eawag tentative collections with tentative/unknowns Following the Schymanski et al 2014 Eawag Level System tobias.schulze@ufz.de, emma.schymanski@eawag.ch
5 Proposed activities Progress Implementation of tentative / unknown compound processing in RMB DONE! Several Eawag tentative collections with tentative/unknowns Following the Schymanski et al 2014 Eawag Level System 1 Gulde et al. 2016: TPs already found in GNPS! Rösch et al (see below) tobias.schulze@ufz.de, emma.schymanski@eawag.ch
6 Proposed activities Progress Inclusion of data independent analysis to address new MS technologies In progress limited use cases at the moment Regularly update a download page for MassBank in NIST mass spectral library format In progress code in development; NIST busy with 2017 release Fostering discussions with MassBank developers community and MoNA Very successful see next slides (SPLASH) Server relaunch includes setup of so-called SVN repository for easy download / update of open access MassBank spectra Needs to shift to 2017; postdoc at IPB starts Nov tobias.schulze@ufz.de, emma.schymanski@eawag.ch
7 Additional Activities in 2016 Refactoring of RMassBank to better integrate other workflows (M. Stravs) Maintenance & relaunch of the European MassBank server Upload of new spectra (Eawag, UoA, UoT), all under CC-BY license University of Tübingen with the Agilent converter (Sascha Lege) Implementation of massbank.eu search in MZmine (v2.19) Implementation of the SPLASH (see next slides) Networking activities Non-target conference Monte Verita, Switzerland SWEMA workshop Garching, Germany US EPA CompTox Dashboard Early Member Network MS Library Webinar (E. Schymanski) or
8 MassBank.EU Status 2016 o 16,020 MS/MS spectra; 1,232 substances from NORMAN members o Tentative/unknown/literature spectra on massbank.eu (not massbank.jp) tobias.schulze@ufz.de, emma.schymanski@eawag.ch
9 Networking and awareness Citations of MassBank (Google and Google Scholar hits) hits 2800 hits 408 hits MassBank.jp MassBank.eu MoNA (Google Scholar, accessed ) MassBank.eu includes NORMAN MassBank and massbank.ufz.de queries tobias.schulze@ufz.de, emma.schymanski@eawag.ch
10 MassBank and other libraries *excluding GC-MS and in silico spectra. Data from various sources incl. Vinaixa et al., 2016, TrAC, 78:23-35, DOI: /j.trac Source: E. Schymanski EMN webinar:
11 at this stage YES! Do we need all these libraries? = HMDB, GNPS, MassBank, ReSpect Substance overlap between major libraries excluding stereochemistry Compound lists provided by: S. Stein, R. Mistrik, Agilent Vinaixa et al. 2016, TrAC, DOI: /j.trac
12 SPLASH: Communicate Between Different Libraries It is not trivial to find similar mass spectra in different libraries Vinaixa et al. Search by peak list? Search by mass spectra? Wohlgemuth et al., 2016, Nature Biotechnology 34, Vinaixa et al. 2016, TrAC, DOI: /j.trac
![spectrum] http://mona.fiehnlab.ucdavis.](/docs-images/76/74210190/images/13-3.jpg "edu/#/spectra/splash/splash10-0002-0900000000-b112e4e059e1ecf98c5f https://www.google.ch/search?")
13 SPLASH: Why SPectraL hash? splash b112e4e059e1ecf98c5f [version] - [top10] - [histogram] - [hash of full spectrum] Wohlgemuth et al Nature Biotechnology, 34, doi: /nbt
14 SPLASH: Why SPectraL hash? Wohlgemuth et al Nature Biotechnology, 34, doi: /nbt.3689
![Non-target m/z [M+H]+ = 267.1719 E.](/docs-images/76/74210190/images/15-4.jpg "Schymanski et al. in prep. emma.")
15 Mass Spectral Libraries now in MetFrag2.3 Example from Rhine Case Study Non-target m/z [M+H]+ = E. Schymanski et al. in prep. emma.schymanski@eawag.ch
16 Proposed activities 2017 Further development and curation of RMassBank Further development of MassBank server platform Fostering the integration of MassBank with external mass spectral and metadata platforms (e.g. MoNA, Chemspider, US EPA CompTox) Fostering the discussions with vendors for better integration of MassBank in vendor s software (import / export, integrated search functions) Upload of new spectra to MassBank tobias.schulze@ufz.de, emma.schymanski@eawag.ch
17 Acknowledgements
18 Questions?
19 Highlight: SPLASH, a hashed identifier for mass spectra Basics: What is a hash? A hash is a one-directional mapping between a long and potentially complex object and a typically much shorter hash string using a fixed length of characters and numbers Examples: Safe storage of passwords BadPassword Clear text 9fcf8a3217b2c75e43d5686ae0802de5 MD5 hashed Chemical structures InChI=1S/C14H11Cl2NO2/c (16)14(10) (12)8-13(18)19/h1-7,17H,8H2,(H,18,19) InChI code DCOPUUMXTXDBNB-UHFFFAOYSA-N InChIKey skeleton stereochemistry charge
20 SPLASH, a hashed identifier for mass spectra Goal Easy search and comparison of complex structures Example: Google search X InChI InChIKey InChI=1S/C14H11Cl2NO2/c (16)14(10) (12)8-13(18)19/h1-7,17H,8H2,(H,18,19) DCOPUUMXTXDBNB-UHFFFAOYSA-N DCOPUUMXTXDBNB 1,470 hits 24,200 hits 24,300 hits
21 SPLASH, a hashed identifier for mass spectra Goal Easy search and comparison of complex structures Example: Google search InChI X A hash is a mapping of a complex object The hash function is one-directed InChI=1S/C14H11Cl2NO2/c (16)14(10) (12)8-13(18)19/h1-7,17H,8H2,(H,18,19) The original object cannot be recovered 1,470 hits A hash InChIKeyis machine DCOPUUMXTXDBNB-UHFFFAOYSA-N readible, but not human 24,200 hits DCOPUUMXTXDBNB 24,300 hits
22 The SPectraL hash SPLASH, a hashed identifier for mass spectra splash10-0a d4ad f508 Block 1: Block 2: Block 3: Block 4: Encodes the semantic splash identifer, measurement type (e.g. 1 for MS) and version of splash Spectral summary histogram of reduced spectra with bins of 5 Da Spectral summary histogram of peak intensities with bins of 100 Da SHA256 hash of the full spectra Block 2 and 3 serve to prefilter and restrict searches Block 4 represents the full spectra and thus can be used for similarity search etc. Implemented in MassBank, MoNA, GNPS, HMDB, MetaboLights, mzcloud, MZmine, RMassBank; NIST discusses implementation in a later release Wohlgemuth et al., Nature Biotechnology 2016,
23 Block 1: The SPectraL hash SPLASH, a hashed identifier for mass spectra splash10-0a d4ad f508 Encodes the semantic splash identifer, measurement type (e.g. 1 for MS) and version of splash Block 2: Spectral summary histogram of reduced spectra with bins of 5 Da SPLASH allows easy search for mass spectra Block 3: Block 4: SPLASH is a new identifier to offer simple cross-database search for mass spectra with general purpose search engines Spectral summary histogram of peak intensities with bins of 100 Da SHA256 hash of the full spectra SPLASH does not replace complex queries based on mass spectral peak lists Block 2 and 3 serve to prefilter and restrict searches Block 4 represents the full spectra and thus can be used for similarity search etc. Implemented in MassBank, MoNA, GNPS, HMDB, MetaboLights, mzcloud, MZmine, RMassBank; NIST discusses implementation in a later release Wohlgemuth et al., Nature Biotechnology 2016,
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