MassBank for NORMAN. Achievements in 2011 and further proposed steps for identification of unknowns

Size: px

Start display at page:

Download "MassBank for NORMAN. Achievements in 2011 and further proposed steps for identification of unknowns"

Herbert Lindsey
6 years ago
Views:

1 MassBank for NRMAN Achievements in 2011 and further proposed steps for identification of unknowns Tobias Schulze NRMAN GA 2011, Stockholm November 2011

2 Background and objective of the activity Concept of NRMAN MassBank Conversion of EMPMAS to NRMAN MassBank Report from reviewers Proposed activities in 2012 utline Page 2

3 Background Identification in non-target screening and EDA no comprehensive and open-access database incorporating different instrument types for LC-MS n available many relevant compounds missing in commercial libraries Mass spectra database in NRMAN Comprehensive DB improved prediction and identification Improved identification supports prioritisation

4 Main objectives to implement NRMAN MassBank server as platform to collect and exchange mass spectral data to convert existing EMPMASS to NRMAN MassBank to adapt and develop procedures, tools and manuals for a coordinated and facile processing and upload of highquality mass spectra to collect and upload mass spectra from NRMAN partners to check the procedure Page 4

5 Concept of NRMAN MassBank public Public NRMAN MassBank data from standard compounds environ. knowns and unknowns internal Internal NRMAN DB data for internal evaluation (e.g. non-public unknowns) local UFZ Eawag Local database Local database Local database query data provider Page 5

6 From EMPMASS to MassBank records Search for additional and missing metadata EMPMASS DB Search for related raw spectra Raw chromatograms Extraction with AMDIS ChemSpider PubChem, CTS CAS#, SMILES InChI, CSID, CID, KEGG Merge PHP-script Matlab-script JChem KNIME workflow Raw mass spectra Match of scan #, retention time, base peak, BP intensity Mol files MSP files MassBank records riginal EMPMASS records Upload to NRMAN MassBank CTS: Chemical translation service Thanks to: Tony Koch, Martin Sand, Guido Schramm, Emma Schymanski Page 6

7 Example NRMAN MassBank record I Structure from Mol file Raw mass spectra General record information Compound related information links to: external DBs original mass spectrum (msp-file) original chromatogram (msfile) EMPMASS style record (html-file) Page 7

8 Example NRMAN MassBank record II Sample related information Analytical method related information Page 8

9 Example NRMAN MassBank record III Peak related information Peak information from EMPMASS Peak Information generated during record conversion from raw mass spektrum Page 9

Status of record conversion & upload Records uploaded to

peak list) Basis peak not found (Peak not in related peak

chromatogram available Revision of conversion process /

10 Status of record conversion & upload Records uploaded to MassBank (some artifacts) Low number of peaks (<4 peaks in peak list) Basis peak not found (Peak not in related peak list) Low numer of peaks / basis peak not found No raw chromatogram available Revision of conversion process / records Unfortunately not delivered to UFZ 19% 55% 11% 11% 4% Page 10

11 Supporting comments from reviews Lack of free available and suitable LC-MS n databases with high resolution accurate mass spectra, especially for emerging compounds. Learning from metabolomics community is a good idea. MassBank is a very flexible DB (e.g. search routines, open for any intrument type). Concept and setup of NRMAN MassBank achieved. Conversion and upload of EMPMASS data achieved (proof of concept). Thanks to: Prof. Zwiener (Tübingen, Ger), Dr. Michael Schlüssener (Koblenz, Ger) Dr. Ivan Spanik (Bratislava, Sk) Page 11

12 pen questions from reviews Instrument type open and standardised tools should be provided to encourage participation of many researchers Tools to process a large number of peaks automatically for the identification of unknowns in an user independent way? NRMAN MassBank workshop is demanded to demontrate the functions to stakeholders and to improve the generated tools Metadata should contain any information regarding sample background and analytical conditions, spatial information, quality control Concerns on loss of information during conversion? Thanks to: Prof. Zwiener (Tübingen, Ger), Dr. Michael Schlüssener (Koblenz, Ger) Dr. Ivan Spanik (Bratislava, Sk) Page 12

13 pen questions? MassBank was developed to mass spectra any kind of instrument types, thus provided tools could be adapted to other intruments / ionisation / fragmentation techniques. An one click tool to process a large number of peaks automatically could be developed in future, but we should now focus on basic problems, for example intercomparability of mass spectra of different intrument types. MassBank is open to any kind of metadata. However, metadata search / filters are not included yet to be discussed with MB developers No loss of information during conversion as shown above. Thanks to: Prof. Zwiener (Tübingen, Ger), Dr. Michael Schlüssener (Koblenz, Ger) Dr. Ivan Spanik (Bratislava, Sk) Page 13

14 EMPMASS records were transferred to MassBank records without loss of information. Records were extended by new related metadata (e.g., structure, links to external DBs, etc.). Information content of the mass spectra was enhanced, because raw spectra were included. Most of the records were not transferred due to missing raw chromatograms. Further tasks demanded by reviewers are achievable. Role of existing EMPMASS has to be defined. Summary Page 14

15 Tasks and Deliverables for 2011 and 2012 Task expected delivery achieved Manual upload of demonstration data to MassBank server of IPB Halle Concept, setup and configuration of NRMAN MassBank hostet at UFZ Conversion and upload of EMPMASS records to NRMAN MassBank (proof-of-concept) May 2011 May 2011 September 2011 Draft protocol for upload of mass spectra to NRMAN MassBank September 2011 Status report to NRMAN Steering Committee September 2011 Automated upload tools for rbitrap and other instruments ngoing Upload of rbitrap data UFZ ngoing Upload of partner standards (rbitrap / other instruments) ngoing 2012 Final tuning of data and upload tools / NRMAN MassBank customizing ngoing 2012 Final report to NRMAN 2012

16 MassBank for NRMAN Further proposed steps for identification of unknowns Tobias Schulze, Emma Schymanski et al. NRMAN GA 2011, Stockholm 22 November 2011

17 Proposed activities in 2012 Application of identification tools for the annotation of unknown compounds in existing GC-MS databases Unknown spectra from NRMAN EMPMASS (~700 spectra) and MDELKEY QPID (~6000 spektra) GC-MS databases Mass spectra quality and metadata evaluation Computer based identification of candidate structures Confirmation of tentatively-identified compounds using standards if commercially available Deliverables: Report to NRMAN, journal publication Partners: Emma Schymanski (Eawag), Jana Weiss (IVM), Peter swald (EI) Page 17

18 NIST MS Library MLGEN-MS Present: Absent: Substructure Information C(sat) CH 3 CH 2 Formulas C 9 H 8 2 C 8 H 4 3 C 7 4 Structure Generation H H

19 GC-MS Identification Strategy Structure Generation H H Boiling Point / Lee Retention Index (outside range BP = (LRI-31) to (LRI+71) ºC) Partitioning Coefficient log K ow (outside fraction log K ow range 1) Steric (MM2) Energy (MLGEN-QSPR > kcal/mol; ChemBio3D > kcal/mol) Spectral Match Value Details in: E.L. Schymanski et al. Analytical Chemistry, 2011, 83: 903 Page 19 E.L. Schymansik, C. Gallampois et al. Analytical Chemistry, in preparation

20 The End Thank you for your attention and many thanks to our colleagues for their contributions Emma Schymanski, Christine Hug, Merle Plaßmann Martin Krauss,Tony Koch, Martin Sand Guido Schramm, René Schreiber, Steffen Neumann contact: Page 20

NORMAN MassBank and beyond Status and future of activities regarding mass spectral databases

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,