1. Software Project MassAnalyst Roeland Luitwieler Marnix Kammer April 24, 2006

2. 2 Overview Introduction System requirements Our solution: Spectre Progress so far Conclusion

3. 3 Introduction Project initiator Scientific background The need for software tools

4. 4 Project initiator Dr. ir. Bas van Breukelen Department of Biomolecular Mass Spectrometry Utrecht University! WENT building Expert in: Bioinformatics Proteomics

5. 5 Scientific background: Proteomics Our body consists of cells Cell functionality and structure is offered by proteins Proteomics Main research areas: Identification of proteins Interaction of proteins Comparison of protein levels

6. 6 Protein identification How to identify proteins? Identity defined by their structure Protein structure Protein: sequence of peptides Peptide: sequence of amino acids 20 common types Consist of different atoms – have different masses Too small to see… but not to weigh Mass Spectrometry!

7. 7 Mass Spectrometry (MS) Technique using a mass spectrometer Input: sample of peptides Proteins have been split chemically Provides a.o. more accuracy, efficiency Most head / tail subsequences are present Output: mass spectrum Frequencies of particles of certain masses Full peptide sequence can be derived

8. 8

9. 9 Mass Spectrometry (MS) How does it work? Ionize particles Now particles have an electrical charge Accelerate them in an electric field Deflect them in a magnetic field Deflection depends on mass (F = m a) Measure how far they have been deflected

10. 10 Mass Spectrometry (MS) Improvements for better analysis (1) Use chromatography Spreads input over time: more details Output: a sequence of MS spectra

11. 11 Mass Spectrometry (MS) Improvements for better analysis (2) Use “recursive” mass spectrometry Called MS/MS (or MS 2 or tandem MS) Take part of the sample that produces a peak Usually concerns one certain peptide Output: MS spectra with related MS/MS spectra

12. 12 Mass Spectrometry (MS) Improvements for better analysis (3) Use bioinformatics All output is translated to mzXML A database is searched on MS/MS spectra Input: raw MS data Output: pepXML : peptide information Tools are used to e.g. display the data Lots of redundant / boring work is taken care of!

13. 13 Bioinformatics: what can be done? Remember the Proteomics research areas: Identification of proteins Interaction of proteins Comparison of protein levels Most research: differ one aspect at a time Requires interactive display of data Zooming, “stacking”, cross sections, etc. But not just display of data Filtering, “warping”, peak detection, etc.

14. 14 Bioinformatics: existing tools Tools exist, but… Lots of different tools to do different things Functionality not always as desired They also lack functionality Not easily extendable Example: Pep3D Nice visualization, but Only one sample at a time, only a single view Solution: develop new software

15. 15 System requirements Load raw spectrometry data Visualize the data Manipulate and analyze the data interactively Export data Extendibility Use in open community Open source

16. 16 Loading data mzXML : raw spectrometry data MS spectra Embedded MS/MS spectra pepXML : database of matches with peptides

17. 17 Visualizing the data List of loaded samples MS spectrum Cross sections of the MS spectrum MS/MS spectra Peptide information

18. 18 Manipulating and analyzing the data Stacking: toggle samples on/off Warping Zooming Peak detection More analysis, like ratio calculation

19. 19 Export data Lists of peak pairs Modified PepXML (i.e. with ratios) Images of spectra Modified samples

20. 20 Our solution: Spectre

21. 21 Opening a workspace

22. 22 Loading a workspace

23. 23 After the workspace is loaded

24. 24 Working in normal mode

25. 25 Zoom on selection mode

26. 26 After zooming in

27. 27 Zoom on click mode

28. 28 After zooming in

29. 29 The structure of Spectre Graph : MS spectra, cross sections, MS/MS spectra Workspace : a collection of samples and settings Sample : internal data structure for one sample GUI : the user interface Processor : the main link between parts of the program

30. 30 The structure of Spectre Processor GUI Workspace Sample Graph * * 4 1 1

31. 31 Systematic approach to the problem Phased development Three versions Lots of diagrams Application of courses MSO, PM HCI team and data layer team Later on: data visualization team Extreme Programming

32. 32 Progress so far First version will be due in week 18 Functionality: Loading raw data Visualization and user interface Basic interaction with zooming etc. Complete internal data structures Export of images Missing link between mzXML and pepXML!

33. 33 Further planning Version 2 – week 23 Warping Peak detection / analysis Export of calculated data Version 3 – week 27 Ratio calculation Modification of samples

34. 34 After completion of the project Web site Open source further maintaining extendable

35. 35 Conclusion Spectre: a modular and extendable program A combination of many different requirements Phased addition of features Any questions?

36. 36 The data structure MzTable Sample MzNode * 1 SampleParser SampleWriter MzParserPepParser ……