0
Peak Pick “A Modern, Computational Approach to Analyzing Protein Mass Spectra” Nelson Young Lab Presentation Dec 11,2003
M/Z – Proteometrics’ Solution (http://65.219.84.5/moverzDL.html)
PeakFinder – Efeckta's Solution (http://www.efeckta.com)
Peak Pick – MS Solution
Other Solutions <ul><li>PeakFinder – Efeckta's Solution (http://www.efeckta.com)   </li></ul><ul><li>Bruker’s Software (In...
Peak Pick – Algorithm <ul><li>Plot the mass spectrum based on the input text file </li></ul><ul><li>Draw the optimal basel...
Peak Pick – Algorithm (Cont’d) <ul><li>Point with the highest intensity determines the peak’s mz value </li></ul><ul><li>I...
Peak Pick – Scenarios 1.)What if baseline is too low that peaks are hidden and are consider as part of a larger peak (inte...
Peak Pick – Redefine Peak Region
Peak Pick – Redefine Peak Region
Peak Pick – Overview (Features) <ul><li>Rubber-band zoom / Undo zoom operations </li></ul><ul><li>Automatic peak labeling ...
Peak Pick – Overview (Input/Output)
Peak Pick – Overview (GUI)
Peak Pick – Overview (Export)
Peak Pick -- Advantages <ul><li>Highly portable to many different platforms </li></ul><ul><ul><li>Windows, Unix/Linux, Mac...
Peak Pick – Advantages (Cont’d) <ul><li>Simple, intuitive GUI </li></ul><ul><ul><li>No parameters or tolerances to set </l...
Peak Pick -- Disadvantages <ul><li>Need Java Runtime Environment (JRE) to run program </li></ul><ul><li>Show current zoom ...
Future Work <ul><li>Automate iterative zooms between adjacent peaks to improve peak picking algorithm </li></ul><ul><li>Ac...
Future Work (Cont’d) <ul><li>Create transparent images to facilitate overlaid and comparison of spectral images  </li></ul...
Acknowledgements <ul><li>Dr. David Wishart </li></ul><ul><li>Dr. Liang Li </li></ul><ul><li>Dr. Gary Van Domselaar </li></...
Upcoming SlideShare
Loading in...5
×

Download

252

Published on

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
252
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
1
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Transcript of "Download"

  1. 1. Peak Pick “A Modern, Computational Approach to Analyzing Protein Mass Spectra” Nelson Young Lab Presentation Dec 11,2003
  2. 2. M/Z – Proteometrics’ Solution (http://65.219.84.5/moverzDL.html)
  3. 3. PeakFinder – Efeckta's Solution (http://www.efeckta.com)
  4. 4. Peak Pick – MS Solution
  5. 5. Other Solutions <ul><li>PeakFinder – Efeckta's Solution (http://www.efeckta.com) </li></ul><ul><li>Bruker’s Software (Instrumental software) </li></ul><ul><li>Analyst QS – Biomics’ Solution http://www.biomics.co.kr/products/software/software_08.htm </li></ul>
  6. 6. Peak Pick – Algorithm <ul><li>Plot the mass spectrum based on the input text file </li></ul><ul><li>Draw the optimal baseline to filter out the background noise </li></ul><ul><ul><li>Typically, noise decreases gradually as m/z increases </li></ul></ul><ul><ul><li>Baseline changes w.r.t. noise and is always 1-2 times greater than noise. </li></ul></ul><ul><ul><li>Baseline determined by using the ‘windowing’ method </li></ul></ul><ul><ul><li>Test and trial to find the optimal size for the window </li></ul></ul><ul><li>Group the remaining clusters of points to form candidate peaks </li></ul><ul><li>Minimum peak width measuring from the base of the peak is 10 mz (usually over 100 pts!) </li></ul>
  7. 7. Peak Pick – Algorithm (Cont’d) <ul><li>Point with the highest intensity determines the peak’s mz value </li></ul><ul><li>If height of peak is 2-3 times greater than the height of baseline-noise, then label it as ‘valid’ peak. Peak-to-noise ratio decreases as m/z increases </li></ul><ul><li>Resolve internal peaks if necessary </li></ul><ul><ul><li>A labeled peak may contain multiple internal peaks if baseline is too low! </li></ul></ul><ul><li>Find the correlation among peaks (singly-charged, doubly-charged, triply-charged) </li></ul><ul><li>Peaks below 1000 mz are ignored – mostly instrumental noise </li></ul><ul><li>That’s it to the algorithm! Sounds easy, eh? Now, consider these scenarios …. </li></ul>
  8. 8. Peak Pick – Scenarios 1.)What if baseline is too low that peaks are hidden and are consider as part of a larger peak (internal peaks)? 2.)How to determine the base of the peaks? 3.)What if peak still fails to be labeled?
  9. 9. Peak Pick – Redefine Peak Region
  10. 10. Peak Pick – Redefine Peak Region
  11. 11. Peak Pick – Overview (Features) <ul><li>Rubber-band zoom / Undo zoom operations </li></ul><ul><li>Automatic peak labeling in bounded region </li></ul><ul><ul><li>Pick all the peaks if bounded region is whole spectrum </li></ul></ul><ul><li>Manually identify or erase peaks </li></ul><ul><li>Interactive display of mz and intensity values on mouse movement </li></ul><ul><li>Export spectrum on display in PNG image format </li></ul><ul><li>Export peak list in either text or MS Excel format </li></ul><ul><li>Color labeling for different types of peaks (singly - , doubly - , triply – charged ions) </li></ul><ul><li>Handle MS and MS/MS mass spectra </li></ul>
  12. 12. Peak Pick – Overview (Input/Output)
  13. 13. Peak Pick – Overview (GUI)
  14. 14. Peak Pick – Overview (Export)
  15. 15. Peak Pick -- Advantages <ul><li>Highly portable to many different platforms </li></ul><ul><ul><li>Windows, Unix/Linux, Macintosh, Solaris, SGI </li></ul></ul><ul><li>No installation required </li></ul><ul><ul><li>Window’s Drag&Drop </li></ul></ul><ul><ul><li>Console’s Command Line </li></ul></ul><ul><li>Fast startup </li></ul><ul><ul><li>No dependency of libraries </li></ul></ul><ul><li>Multiple simultaneous workspaces for spectral viewing and manipulation </li></ul><ul><li>Handle both types of mass spectra: MS and MS/MS </li></ul>
  16. 16. Peak Pick – Advantages (Cont’d) <ul><li>Simple, intuitive GUI </li></ul><ul><ul><li>No parameters or tolerances to set </li></ul></ul><ul><ul><li>No prior knowledge or expertise in analyzing mass spectra </li></ul></ul><ul><li>Effective, efficient peak picking algorithm (>95%) </li></ul><ul><ul><li>No fixed threshold across the spectrum, </li></ul></ul><ul><li>Textual and graphical outputs </li></ul><ul><li>‘ Smart’ correlated peak labeling schema </li></ul><ul><li>Manual and automatic peak labeling </li></ul>
  17. 17. Peak Pick -- Disadvantages <ul><li>Need Java Runtime Environment (JRE) to run program </li></ul><ul><li>Show current zoom position w.r.t. to the whole spectrum </li></ul><ul><li>Cannot read or write files to network </li></ul><ul><li>GUI – inconsistent with standard, commercial products </li></ul>
  18. 18. Future Work <ul><li>Automate iterative zooms between adjacent peaks to improve peak picking algorithm </li></ul><ul><li>Accept more file formats for input mass spectra </li></ul><ul><li>Process mass spectra in batch mode </li></ul><ul><li>More image formats for output </li></ul>
  19. 19. Future Work (Cont’d) <ul><li>Create transparent images to facilitate overlaid and comparison of spectral images </li></ul><ul><li>Allow reading and writing of files to network </li></ul><ul><li>Make it public, preferably a web application </li></ul><ul><ul><li>Applet front-end, servlet back-end </li></ul></ul><ul><ul><li>Online submission of mass spectra </li></ul></ul><ul><li>Toggle display of peak labels on/off </li></ul>
  20. 20. Acknowledgements <ul><li>Dr. David Wishart </li></ul><ul><li>Dr. Liang Li </li></ul><ul><li>Dr. Gary Van Domselaar </li></ul><ul><li>Haiyan Zhang </li></ul><ul><li>Hongzing </li></ul><ul><li>ShiLai </li></ul>
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×