1. Squirrel Tutorial Post – Pre-Process Steps Airbeam correction PToF DVa, DC markers Fragmentation checks Donna Sueper Aerodyne, University of Colorado, Boulder ToF AMS Training, Aerodyne, Nov/Dec 2006

2. Tutorial Outline Squirrel Quick-Look Flow Chart Squirrel Complete Analysis Flow Chart Calculation discussion, Screen Shots Airbeam correction PToF DVa, DC markers Frag checks

3. Get Index Pre-Process HDF Index Tab PToF Tab time series, avg spectrum image, avg size dist, size binned spectrum _p data (DAQ sticks) MS Tab Squirrel Quick-Look Flow Chart

4. Get Index Pre-Process HDF Index Tab Quick-Look PToF Tab time series avgs, etc. size dist, mass spec, image, etc. _p data (DAQ sticks) Complete Analysis Pre-Process HDF Index Tab Get Index Check m/z calibration Corrections Tab _p data (recalc sticks) m/z fitting params MS Tab Check baseline baseline fitting params Squirrel Analysis Flow Charts PToF Tab time series avgs, etc. size dist, mass spec, image, etc. MS Tab Modify SI Ion_user Frag Checks Tab Tweak Frag table Do Corrections corr_fact Calc Loadings Airbeam PToF _p data (dc marker) Loading waves Diagnostics Plot

5. Complete Analysis > Corrections There are 3 subtabs: Errors (As of 1.36, the error calculation code is not completed.) PToF Airbeam Select the Corrections tab When the gold Do Corrections button is pressed, the actions as checked in each subtab will be performed. Airbeam PToF – DVa PToF – DC markers

6. Airbeam Correction Discussion In the diagnostics graph, we see the PToF and MS airbeam. For the moment we consider only the MS airbeam. We want to take an average of the airbeam at a specific region (airbeam reference value runs) and compute the ratio of this value to the airbeam values at all other runs. Correction factor = (airbeam avg/airbeam). The airbeam value is a measure of the overall amount of sample we measure. For each run the airbeam value (mass 28) changes, often by a relatively small amount.

7. Complete Analysis > Airbeam correction It is best to choose runs near a calibration period. If you are analyzing data with v/w mode switching, select reference runs with both v and w mode runs in it. On the Corrections tab, select the Airbeam (AB) tab Select airbeam reference runs by: Entering a run number series (380- 452) OR In a graph (one often uses the diagnostics graph), right – clicking a marquee and choosing ‘Set Airbeam Reference’ from the options. For this example we will use the Auto-set option.

8. Complete Analysis > Airbeam correction The airbeam correction factor should be near 1. It’s use in subsequent analyses is chosen by checkboxes in other tabs. Press the gold Do Corrections button. A graph of the airbeam correction factor will appear. Go to the PToF tab and make sure the Dva and DC markers checkboxes are unchecked.

9. Complete Analysis > Airbeam correction Airbeam Results: root:diagnostics:corr_fact Before pressing leaving the airbeam tab section, make sure that you have a good airbeam correction factor.

10. Complete Analysis > PToF Corrections In the Corrections tab, press the PToF subtab. There are 2 sections: DVa DC marker Performing the DVa or DC marker corrections can happen at any time after pre-process.

11. PToF DVa Discussion How do we convert PToF bin # to time, then size? Mass 4 123456500 0.01.10.20.50.4 0.3 …0.4 0.01.00.20.70.3 0.6 …0.1 0.10.11.22.52.1 3.3 …0.3. 4.00.10.50.00.0 0.10.0 integer amu bin number One run of PToF stick data set is a matrix. Let columns represent m/z dimension (0 – 500 amu), rows the different PToF size bins (90). 1 2 3 90

12. PToF DVa Discussion The formula for converting PToF time to size is: DVa = dx*((((vg - vl) / (vp - vl)) - 1) ^ (1/b)) Eqn A where vp=lc/t, dx, vg, vl, and b are inputs from the daq. The formula for converting PToF bin number to time is: PToF time = PToF_t0 + (bin number) * (PToF_step) Eqn B PToF_t0 incorporates any initial delays (delays from when chopper is open, first bin measurement, chopper slit center) PToF_step is a PToF bin width in units of time (consider coAdds) If doing calculations by hand, one needs to pay attention to units.

13. PToF DVa Discussion In practice, how does this work? 1 2 3 90 integer amu bin number 123500 0.01.10.2…0.4 0.01.00.2…0.1 0.10.11.2…0.3 4.00.10.5 …0.0 0.000327 0.000487 0.000647 0.014567 Measurement time (sec) PToF Size (nm) 1.0465 2.2553 4.4098 1390.4423 We don’t change the PToF stick matrix! Eqn AEqn B

14. PToF DVa One can set values in this window (blanks mean keep daq values) OR Press the simple graph aid button and set values here (one can explicitly see the daq values and the DVa calculation).

15. PToF DVa PToF DVa Results: 4 parameters vl, vg, dx, b Often these do not need to be changed from the settings as recorded by the daq. Before leaving the PToF DVa section make sure that these values are to your liking. The values will not be changed until the gold Do Corrections button is pushed!

16. PToF DC Markers Discussion Mass 4 123456500 0.01.10.20.50.4 0.3 …0.4 0.01.00.20.70.3 0.6 …0.1 0.10.11.22.52.1 3.3 …0.3. 4.00.10.50.00.0 0.10.0 integer amu bin number One run of PToF stick data set is a matrix. Let columns represent m/z dimension (0 – 500 amu), rows the different PToF size bins (90). 1 2 3 90

17. PToF DC Markers Discussion Region 2 Region 1 Mass 40 Define 2 regions. (size distribution at a mass) Find the average of the ptof sticks (for that mass) at each region. avg1 avg2 Find the average of both regions, and subtract this value from the entire mass size distribution trace. Avg = (avg1 + avg2)/2 Mass Size distribution -= Avg

18. PToF DC Markers Discussion In practice how does this work? Mass 28 0.01.10.20.50.4 0.01.00.20.70.6 0.10.11.22.5 3.3 4.00.10.50.0 0.1 integer amu bin number For each run, each mass (column), find 2 averages, subtract a value from this column This is very time consuming!! Mass 67

19. Complete Analysis > PToF DC Markers One can set values in this window OR Press the simple graph aid button and set values here. One can set the start and stop values for region 1 and 2 in PToF bin or time units. The same regions will be used for all runs and all masses except those indicated.

20. PToF DC Markers Results: Altered PToF stick matrix Before leaving the PToF DC marker section make sure that these values are to your liking. The values will not be changed until the gold Do Corrections button is pushed!

21. Frag Checks Discussion Press ‘Review Frags’ button. The loadings for most species are the sum of the fractional mass (fragment or frag, for short) of several integer sticks. Example: K has loading from the mass at 39 and at K’s isotope at 41 amu. It’s mass loading is a sum of the fractional mass at 39 and 41. Mass loading of K = 1*(entire peak at mass 39) + 0.0722*(entire peak at mass 39) This table encapsulates the linear combination of masses used to derive loadings. Formulas for some species (such as K) are unambiguous. Other formulas (such as nitrate) are complicated. Those with experience (!) can tweak the frag table to reflect conditions which are more consistent with their data.

22. Complete Analysis > Frag Checks One time-series wave for each species will be created. They are calculated in the same way as those found via the MS-tab, time series button. Press the Frag Checks tab. Review the species in the list and the airbeam checkbox. Press gold ‘Calculate…’ button.

23. Frag Checks Select species to examine. Press ‘Plot…’ button. Review results. As one become more familiar with fragmentation patterns, one can view these graphs to test the consistency with entries in the frag table.

24. Get Index Pre-Process HDF Index Tab Quick Look PToF Tab time series avgs, etc. size dist, mass spec, image, etc. _p data (DAQ sticks) Complete Analysis Pre-Process HDF Index Tab Get Index Check m/z calibration Corrections Tab _p data (recalc sticks) m/z fitting params MS Tab Check baseline baseline fitting params Squirrel Analysis Flow Charts PToF Tab time series avgs, etc. size dist, mass spec, image, etc. MS Tab Modify SI Ion_user Frag Checks Tab Tweak Frag table Do Corrections corr_fact Calc Loadings Airbeam PToF _p data (dc marker) Loading waves Diagnostics Plot The corrections and frag checks analysis steps are often iterative with the time series and other graphs.