Squirrel Tutorial

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• Squirrel Tutorial
• Post Pre-Process Steps
• Airbeam correction
• PToF DVa, DC markers
• Fragmentation checks

ToF AMS Training, Aerodyne, Nov/Dec 2006
Donna Sueper
Aerodyne, University of Colorado, Boulder
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Tutorial Outline

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

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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
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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)
Tweak Frag table
Calc Loadings
Loading waves
Frag Checks Tab
Diagnostics Plot
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Complete Analysis gt Corrections
Select the Corrections tab

• There are 3 subtabs
• Errors (As of 1.36, the error calculation code
  is not completed.)
• 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
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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).
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Complete Analysis gt 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.
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Complete Analysis gt 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. Its use in subsequent analyses is chosen by
checkboxes in other tabs.
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Complete Analysis gt Airbeam correction
Airbeam Results rootdiagnosticscorr_fact
Before pressing leaving the airbeam tab section,
make sure that you have a good airbeam correction
factor.
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Complete Analysis gt 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.
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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
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PToF DVa Discussion
The formula for converting PToF time to size
is DVa dx((((vg - vl) / (vp - vl)) - 1)
(1/b)) Eqn A where vplc/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.
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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 A
Eqn B
We dont change the PToF stick matrix!
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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).
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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!
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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
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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)
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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!!
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Complete Analysis gt 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.
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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!
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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 Ks isotope at 41 amu. Its 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.
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Complete Analysis gt 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.
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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.
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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)
Tweak Frag table
Calc Loadings
Loading waves
Frag Checks Tab
Diagnostics Plot