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Squirrel Tutorial Post – Pre-Process Steps Airbeam correction PToF DVa, DC markers

Squirrel Tutorial Post – Pre-Process Steps Airbeam correction PToF DVa, DC markers Fragmentation checks. ToF AMS Training, Aerodyne, June, 2007. Donna Sueper. Aerodyne, University of Colorado, Boulder. Tutorial Outline. Squirrel Quick-Look Flow Chart

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Squirrel Tutorial Post – Pre-Process Steps Airbeam correction PToF DVa, DC markers

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  1. Squirrel Tutorial • Post – Pre-Process Steps • Airbeam correction • PToF DVa, DC markers • Fragmentation checks ToF AMS Training, Aerodyne, June, 2007 Donna Sueper Aerodyne, University of Colorado, Boulder

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

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

  5. Complete Analysis > Corrections Select the Corrections tab • There are 3 subtabs: • Errors • PToF • Airbeam • 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 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. 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).

  7. Complete Analysis > Airbeam correction On the Corrections tab, select the Airbeam (AB) tab For this example we will use the Auto-set option. • 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. 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.

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

  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? 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). integer amu Mass 4 1 2 3 4 5 6 500 0.0 1.1 0.2 0.5 0.4 0.3 … 0.4 0.0 1.0 0.2 0.7 0.3 0.6 … 0.1 0.1 0.1 1.2 2.5 2.1 3.3 … 0.3 . . 4.0 0.1 0.5 0.0 0.0 0.1 0.0 1 2 3 90 bin number

  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? Measurement time (sec) PToF Size (nm) integer amu 1 2 3 500 0.0 1.1 0.2 … 0.4 0.0 1.0 0.2 … 0.1 0.1 0.1 1.2 … 0.3 4.0 0.1 0.5 … 0.0 0.000327 0.000487 0.000647 0.014567 1 2 3 90 1.0465 2.2553 4.4098 1390.4423 bin number Eqn B Eqn A We don’t change the PToF stick matrix!

  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 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). integer amu Mass 4 1 2 3 4 5 6 500 0.0 1.1 0.2 0.5 0.4 0.3 … 0.4 0.0 1.0 0.2 0.7 0.3 0.6 … 0.1 0.1 0.1 1.2 2.5 2.1 3.3 … 0.3 . . 4.0 0.1 0.5 0.0 0.0 0.1 0.0 1 2 3 90 bin number

  17. PToF DC Markers Discussion Mass 40 Define 2 regions. Region 1 Find the average of the ptof sticks (for that mass) at each region. avg1 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 Region 2 avg2 (size distribution at a mass)

  18. PToF DC Markers Discussion In practice how does this work? Mass 28 integer amu Mass 67 0.0 1.1 0.2 0.5 0.4 0.0 1.0 0.2 0.7 0.6 0.1 0.1 1.2 2.5 3.3 4.0 0.1 0.5 0.0 0.1 bin number For each run, each mass (column), find 2 averages, subtract a value from this column This is very time consuming!!

  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 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) Press ‘Review Frags’ button. 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 Press the Frag Checks tab. Review the species in the list and the airbeam checkbox. Press gold ‘Calculate…’ button. 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.

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

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