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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 - PowerPoint PPT Presentation
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Squirrel Tutorial
Post – Pre-Process Steps Airbeam correction
PToF DVa, DC markers Fragmentation checks
Donna SueperAerodyne, University of Colorado, Boulder
ToF AMS Training, Aerodyne, June, 2007
Tutorial Outline
Squirrel Quick-Look Flow Chart
Squirrel Complete Analysis Flow ChartCalculation discussion, Screen Shots
Airbeam correctionPToF DVa, DC markersFrag checks
Get Index
Pre-ProcessH
DF
Ind
ex T
ab
PT
oF T
abtime series,avg spectrum
image,avg size dist,size binned spectrum
_p data (DAQ sticks)
MS
Tab
Squirrel Quick-Look Flow Chart
Get Index
Pre-ProcessHD
F I
nd
ex
Ta
b
Quick-LookP
To
F T
abtime series
avgs, etc.
size dist,mass spec,image, etc.
_p data (DAQ sticks)
Complete Analysis
Pre-ProcessHD
F I
nd
ex
Ta
b
Get Index
Check m/z calibration
Co
rre
ctio
ns
Ta
b
_p data (recalc sticks)
m/z fitting params
MS
Ta
b
Check baseline
baseline fitting params
Squirrel Analysis Flow Charts
PT
oF
Ta
btime seriesavgs, etc.
size dist,mass spec,image, etc.
MS
Ta
b
Modify SI
Ion_user
Fra
g C
he
cks
Ta
bTweak
Frag table
Do Corrections
corr_fact
Calc Loadings
Airb
ea
mP
To
F
_p data (dc marker)
Loading waves DiagnosticsPlot
Complete Analysis > Corrections
There are 3 subtabs:
• Errors • 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
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.
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.
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.
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.
Complete Analysis > PToF Corrections
In the Corrections tab, press the PToF subtab.
There are 2 sections: DVaDC marker
Performing the DVa or DC marker corrections can happen at any time after pre-process.
PToF DVa Discussion
How do we convert PToF bin # to time, then size?
Mass 4
1 2 3 4 5 6 500
0.0 1.1 0.2 0.5 0.4 0.3 … 0.40.0 1.0 0.2 0.7 0.3 0.6 … 0.10.1 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
integer amu
bin
nu
mbe
r
0.001
0.01
0.1
1
10
100
PT
oF
stic
k, H
z
500400300200100m/z, amu
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).
123
90
80
60
40
20
0
76543
PToF DVa Discussion
The formula for converting PToF time to size is:
DVa = dx*((((vg - vl) / (vp - vl)) - 1) ^ (1/b)) Eqn Awhere 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.
PToF DVa Discussion
In practice, how does this work?
123
90
integer amu
bin
nu
mbe
r
1 2 3 500
0.0 1.1 0.2 … 0.40.0 1.0 0.2 … 0.10.1 0.1 1.2 … 0.3
4.0 0.1 0.5 … 0.0
0.0003270.0004870.000647
0.014567
Measurement time (sec)
PToF Size (nm)
1.04652.25534.4098
1390.4423
We don’t change the PToF stick matrix!
Eqn AEqn B
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).
PToF DVa
PToF DVa Results: 4 parameters vl, vg, dx, bOften 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!
PToF DC Markers Discussion
Mass 4
1 2 3 4 5 6 500
0.0 1.1 0.2 0.5 0.4 0.3 … 0.40.0 1.0 0.2 0.7 0.3 0.6 … 0.10.1 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
integer amu
bin
nu
mbe
r
0.001
0.01
0.1
1
10
100
PT
oF
stic
k, H
z
500400300200100m/z, amu
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).
123
90
80
60
40
20
0
76543
PToF DC Markers Discussion
Region 2
Region 1
Mass 40Define 2 regions.
(size distribution at a mass)
80
60
40
20
0
bin
num
ber
0.80.4
PToF stick, Hz
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)/2Mass Size distribution -= Avg
80
60
40
20
0
bin
nu
mb
er
0.80.40.0
PToF stick, Hz
PToF DC Markers Discussion
In practice how does this work?
80
60
40
20
0
bin
num
ber
5040
PToF stick, Hz
Mass 28
0.0 1.1 0.2 0.5 0.40.0 1.0 0.2 0.7 0.60.1 0.1 1.2 2.5 3.3
4.0 0.1 0.5 0.0 0.1
integer amu
bin
nu
mbe
r
For each run, each mass (column), find 2 averages, subtract a value from this column
This is very time consuming!!
80
60
40
20
0
76543
Mass 67
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.
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!
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.
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 listand the airbeam checkbox.
Press gold ‘Calculate…’ button.
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.
Get Index
Pre-ProcessHD
F I
nd
ex
Ta
b
Quick LookP
To
F T
abtime series
avgs, etc.
size dist,mass spec,image, etc.
_p data (DAQ sticks)
Complete Analysis
Pre-ProcessHD
F I
nd
ex
Ta
b
Get Index
Check m/z calibration
Co
rre
ctio
ns
Ta
b
_p data (recalc sticks)
m/z fitting params
MS
Ta
b
Check baseline
baseline fitting params
Squirrel Analysis Flow Charts
PT
oF
Ta
btime seriesavgs, etc.
size dist,mass spec,image, etc.
MS
Ta
b
Modify SI
Ion_user
Fra
g C
he
cks
Ta
bTweak
Frag table
Do Corrections
corr_fact
Calc Loadings
Airb
ea
mP
To
F
_p data (dc marker)
Loading waves DiagnosticsPlot
The corrections and frag checks analysis steps are often iterative with the time series and other graphs .