Squirrel Tutorial

Post – Pre-Process Steps Airbeam correction

PToF DVa, DC markers Fragmentation checks

Donna SueperAerodyne, University of Colorado, Boulder

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

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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

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Quick-LookP

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F T

abtime series

avgs, etc.

size dist,mass spec,image, etc.

_p data (DAQ sticks)

Complete Analysis

Pre-ProcessHD

F I

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Get Index

Check m/z calibration

Co

rre

ctio

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Ta

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_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

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bTweak

Frag table

Do Corrections

corr_fact

Calc Loadings

Airb

ea

mP

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_p data (dc marker)

Loading waves DiagnosticsPlot

Complete Analysis > Corrections

There are 5 subtabs:• Flow Rate • Airbeam• PToF• Errors• IE Cals

Select the Corrections tab

When the gold Do Corrections button is pressed, the actions as checked in each subtab will be performed. For example:

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

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40

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0

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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 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

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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

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PToF stick, Hz

PToF DC Markers Discussion

In practice how does this work?

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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

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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 Checks tab.

Review the species in the listand the airbeam checkbox.

Press gold ‘Calculate…’ button.

Frag Checks

Leave the Color by and Diagnostic menus as default

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 .