Acquisition Software To-Do

http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/ToFAcqToDo.html

v1.7.0 -- Target 15-Sept-2006 DONE -- DISCUSSED DONE -- To BE DISCUSSED TO DO

1. !! CH2 Offscale Mode

2. !! Read data in "Image" mode for BFSP; transfer as Byte

3. !! 2-GHz Sampling

4. !! First draft tuning display * 1 sec spectra * Raw display of full spectrum with 4 peaks "windows" highlighted * Arrows(?) to move peak window * Gaussian Fit of Peaks in windows * Report FWHM, FW10%, and resolutions of peak in window

5. !! Test and Complete Cell-Phone Rejection

6. Menu Windows 1. Move Default Params to Menu Window or add Menu # Buttons to Default Window * If moved to Menu Window, need to discuss how to share values between similar ToF-type menus. 2. Timing Window: Saving calculator, display in menu: Gb hr-1, day-1, month-1 3. Button to load and compare any menu file to the active menu file * Useful for diagnosing problems or determining what has been changed

7. AP240 Settings Tab 1. All settings displayed in Bits and mV        2. Full Scale label should include mv/bit (i.e., FS/256)

8. m/z Calibration Window 1. Strategy for zooming out to determine if selected peak is correct m/z 2. Display slope and intercept 3. Acquire Mass Spectrum at load of m/z calib window. (Not wait for push of Acquire) 4. "Acquiring" label

9. m/z Ratio Window 1. Draw peaks for all thresholds; + offset peaks 1/10 of positive full scale, zero line on m/z ratio window

10. Mode Display Window 1. Zoom Windows: vertical lines to show center points 2. Zoom Windows: second tick mark on bottom axis for 1 Hydrogen Atom Greater 3. Zoom Windows: type center points below x axis 4. Zoom Windows: Change y units to bits/extraction 5. Zoom Windows: Eliminate check boxes, separate arrows for each box (?) 6. Zoom Windows: Leave on screen until next display is ready 7. Zoom Windows: Offset peaks in small right windows 1/10 of positive full scale, show negative, draw zero line. 8. Zoom Windows: Draw lines indicating position of integer masses. 9. Zoom Windows and PTOF: Minimum allowed full scale = 10 ions (in units of bits/extraction = 5*SIArea) 10. Label Ions per "extraction" instead of "pulse" 11. Autoscaling and scales for PTOF graphs * First PTOF display: All species except AB on same scale (?) * All displays: y axis to ions/extraction 12. Manual Servo Steps in Mode Display * G: closes on step * Shift G: opens one step * Reinitialize after each step * Mode label should change from eg "Chopper Chopped" to "Chopper Manual 62" 13. For real time display, insert some simple changes into how frag table, for example m/z 44 having CO2 from air subtracted out as fraction of m/z 28 (from Squirrel frag tables) 14. Draw lines indicating position of select masses (e.g. C4H9+ and C3H5O+ at m/z 57). 15. Use menu switching label to ALWAYS indicate active menu 16. For BFSP, display CPC values (if available) 17. For DAM, fix bug = Program hangs when trying to quit to switch menus manually

11. Servo Window 1. Add "Scan Wait After Servo Move" To Servo Window * MS AB as a function of Wait after servo move 2. label left axes 3. Add another 2 x 3 point scan at end of routine 4. Offset position scan to show 1/10 of FS as negative, add thick zero line 5. On servo position scan, spend a little more time on first fast (closed/chopped/open) scan, so that it can be determined whether the edge positions are ok.

12. Threshold Analysis Window 1. Report SI Area in bit-ns and mv-ns 2. Use sliding window to find SI               * 0.5(element) + 0.25(element-1) + 0.25(element+1) * Test with real data in Excel plots 3. Calculate "Bits to define Std SI" at front of peak acquisition loop. (Currently adjusted by user) * This will be threshold at which SI frequency 20x baseline frequency * Draw first plot blue line = SI Frequency with each Thresh as Bit to define Std SI, based on filtered data 4. Print FWHM of single ion to screen and to info files(?) 5. Add m/z ratio displays to threshold window. * Requires passing data between windows or reading most recent data file from ratio window. * If no ratio data exists, write "No Data Available" on top plot, direct to ratio window 6. Plot % SI Area Lost vs Threshold

13. Analog and Digital Controls 1. Use a TTL line (from 6024) to switch between pos./neg heater bias. * Requires bipolar TPS, as defined in ToFAMS_ID * Extended wait time after menu switch when changing polarity 2. Read CPC from analog in to InfoFile 3. Panel in ToF Menu Window to Control all Analog and Dig (now, just Analog in)

14. Data Saves 1. For each file (autosave and non-autosave), save total averaging time as info value * Necessary for averaging data on varied timescales in SQUIRREL * Or, derive from Duty Cycle values 2. Real-time data back-up * Can use transient functions, but need itx, HDF, and bin saves * Should not include the transient write feature "erase files when directory near full" * Test speed of acquisition w/ and w/out back-up active * Determine if USB is a bottle-neck * Set "day of save" at moment as 'secondsAtSave" when saving files.                     o In case data file save begins before midnight and ends after

15. Menu Parameters and Menu Files 1. Up to 6 Menu Files with Unique Names 2. Create unique file to hold only the run number * This will reduce number of time menu files are opened and saved * Synchronized with menu files at load of software, close of software, and exit of Parameter window * Also need to save m/z calibration values, which can change run to run 3. Make m/z for AB be a parameter in the menu (people may want to use, eg, 32 or 40)

16. TPS Control 1. Monitor Emission Current * Warnings if too high or too low