FT-ICR and LabWindows CVI 7.0

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FT-ICR and LabWindows CVI 7.0

• Jesus Ivan Gonzalez
• University of Colorado at Denver
• Major Electrical Engineer
• July 30, 2004

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About my group

• FT-ICR Group
• Fourier Transform Ion Cyclotron Resonance
• Helps identify complex proteins and compounds to
  further medical research
• Comparing cancerous cells with healthy cells,
  identifying the effectiveness of medicine and
  find improvements

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Making A Complicated Procedure into Semi-Plain
English

• Inserting ions require techniques such as
  electron ionization and electrospray
• Goes through multiple stages using vacuums to
  decrease the atomic pressure in the ions (each
  stage is about 200X lighter than previous stage)
• At the magnet, ions feel that it is in space

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Making A Complicated Procedure into Semi-Plain
English(Part 2)

• Using AC voltages, the ions become excited as it
  become present with the magnetic field and will
  spin in a spiral motion until it barely hits the
  outer plates producing a current.
• The current is used in an RC circuit that can
  measure the energy used to help identify ion
  samples
• Applying an electric field to the ends of the
  magnet so now an ion is not only circles around
  in the magnet, but now it bounces back and forth.
  

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RC Circuit Layout
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Making A Complicated Procedure into Semi-Plain
English(Part 3)

• Results are now attained in a sinusoidal format
  due to the ions touching the places in a
  sinusoidal pattern
• Results are converted into a Fourier Transform
  where spikes represent complex compounds.

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Results in Sinusoidal Form
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Results in Fourier Transform
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What is Measured?

• Mass-to-charge ratio (m/z)
• Frequency
• Radius
• Magnetic Strength
• Kinetic Energy
• Trap Dimensions Different shapes makes for
  different results. Circular shape vs.
  Rectangular shape vs. Cube shape. Many answers
  for one question.

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Working with LabWindows CVI

• CVI helps measures data results using gauges,
  list boxes, ring choices, and switches
• Learned the rules and functionality of CVI.
  Written in C language. Learning a new program is
  easier said than done especially in a few weeks.
• Also worked with GUI (Graphical User Interface)
  which is basically programming with pictures.
• Skeleton code. The very complicated programming
  is done for you. Just fill in the functions to
  tell the computer what to do.

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CVI Example The GUI Part

• Example of GUI being used in CVI
• Usage of Gauges, Text Boxes, Timer, List Boxes
• Helped to get familiarized with CVI
• One out of 7 chapter examples. Hands On
  Experience is very valuable!

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CVI C Programming Example(A small piece of a
200 lines of code)

• int CVICALLBACK StartTestCB (int panel, int
  control, int event,
• void callbackData, int eventData1, int
  eventData2)
• switch (event)
• case EVENT_COMMIT
• TestRunNumber
• SetCtrlVal(TestHandle, TST_TEST_NUM,
  TestRunNumber)
• //Display the time on the panel
• SetCtrlVal(TestHandle, TST_TIME, TimeStr)
• response ConfirmPopup("WRITE TO FILE", Do
  you want to write data to the file?")
• if (response) //
• WriteToFile()
• DefaultCtrl(TestHandle, TST_RESULTS) //Clear
  Box
• Fmt(buf, "sltTime Temperature Result
  Pressure Result")
• InsertTextBoxLine(TestHandle, TST_RESULTS, -1,
  buf)

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Working with MASCOT option

• Mascot option allows users to store information
  by creating .pfl files
• Interacts with MASCOT website that helps identify
  compounds
• Different compounds are represented as spikes and
  shown (Upper Left)
• Identifying spikes and displays the m/z values
  found

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Using GUI for MASCOT option

• Profiles can be loaded and saved (Right side of
  screen)
• Name of the user and corresponding e-mail to
  deliver results of possible compounds (Upper left
  side)
• Corresponds with information from MASCOT website

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MASCOT Results Examplehttp//icr-mascot.com
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C Language Example 1 Reset Option

• int CVICALLBACK Reset_Profile_CB (int panel, int
  control, int event,
• void callbackData, int eventData1, int
  eventData2)
• switch (event)
• case EVENT_COMMIT
• DefaultCtrl(mascot_handle, MASCOT_SEARCH_TITLE)
  //Blanks out search title
• DefaultCtrl(mascot_handle, MASCOT_TAXONOMY) //
  Reset back to "All Entries"
• DefaultCtrl(mascot_handle, MASCOT_FIXED_MOD) /
  /Reset back to "AB_old_ICATdO (C)"
• DefaultCtrl(mascot_handle, MASCOT_VARIABLE_MOD)
  //Reset to "AB_old_ICADdO (C)"
• DefaultCtrl(mascot_handle, MASCOT_MISSED_CLEAVA
  GES) //Missed returned to 0
• DefaultCtrl(mascot_handle, MASCOT_PROTEIN_MASS)
  //reset to "0.000"
• DefaultCtrl(mascot_handle, MASCOT_ICAT) //ICAT
  is unchecked
• DefaultCtrl(mascot_handle, MASCOT_PEPTIDE_TOL)
  //peptide tolerance is 0
• DefaultCtrl(mascot_handle, MASCOT_PEPTIDE_TOL_S
  CALE) //reset to Da
• DefaultCtrl(mascot_handle, MASCOT_PEPTIDE_CHARG
  E) //Reset to 1
• DefaultCtrl(mascot_handle, MASCOT_PMZ) //Reset
  parent m/z to 0
• DefaultCtrl(mascot_handle, MASCOT_PCHARGE) //R
  eset parent charge to 0
• DefaultCtrl(mascot_handle, MASCOT_MS_MS_TOL) /
  /MS/MS tol is reset to 0

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C Language Example 2 Save Load Option

• int CVICALLBACK Load_Profile_CB (int panel, int
  control, int event,
• void callbackData, int eventData1, int
  eventData2) //Information loaded from memory
• char loadfile260
• int status
• switch (event)
• case EVENT_COMMIT
• status FileSelectPopup ("", ".", "", "Load
  File for Profile", VAL_LOAD_BUTTON, 0, 0, 1, 1,
  loadfile)
• break
• return 0
• int CVICALLBACK Store_Profile_CB (int panel, int
  control, int event, //Information stored into
  memory
• void callbackData, int eventData1, int
  eventData2)
• char filename260
• int status
• switch (event)
• case EVENT_COMMIT

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What Have I Learned

• How medical research corresponds with chemistry,
  engineering, computer science, and mathematics
• Learned how to interact with a program using GUI
  and how it uses skeleton code to do the grudge
  work
• Improved on programming techniques which needed
  to be improved

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Acknowledgements

• FT-ICR Staff
• Chris Hendrickson
• Greg Blakney
• CIRL Group
• Pat Dixon
• Gina LaFrazza
• Dave Sheaffer
• Carlos Villa
• Stacy Vanderlaan

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Questions?