center for atmospheric particle studies ams data analysis training amy sage and andy grieshop march...
TRANSCRIPT
Center for Atmospheric Particle Studies
AMS Data Analysis Training
Amy Sage and Andy Grieshop
March 7, 2007
Center for Atmospheric Particle Studies
Outline
Batch and frag tables Loading data Checking diagnostics Surveying data Performing corrections MS mode TOF mode Jump mode Alice’s panel
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How mass is calculated:
• Cs = mass concentration of species s (µg m-3)• MWNO3 = molar weight of nitrate (62 g/mol)• Ces = collection efficiency (dimensionless)• RIEs = relative ionization efficiency of species s (dimensionless)• (see Jimenez et al. 2003)• IENO3 = ionization efficiency (ions detected per parent molecule) of nitrate (dimensionless)• Q = inlet flow rate (cm3s-1)• NA = Avogadro’s number (6.022 x 1023 molecules/mol)• Is,i = detected ion rate of species s at fragment i (s-1)
€
Cs =1
CE s
1012 MWNO3
RIE sIENO3QNA
Is,i
i
∑ batch
tablefragtable
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Batch table: contains the values used for CE and RIE for each species.
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Frag table: apportions the signal at each mass among contributing fragments from each species
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James’ Panel
Main GUI for the AMS Analysis software.
Software was designed and made freely available to the AMS community by James Allan at the University of Manchester
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Load Data
1) Save As…don’t overwrite your template!!!
2) Open a notebook to record experimental and analysis details
3) Load all data files from experiment in ‘Load Data’ tab
4) Find important information using the ‘List’ button after data is loaded
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diagnostics plot
notebook
command window
‘load data’ tab
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Check DiagnosticsFlowrate: changes in time due to clogs, pressure changes
Multiplier voltage & gain: set during daily single ion calibrations
Heater bias: shouldn’t change unless you tune MS
Duty cycle: CPU usage
Airbeams: reflect change in instrument, increase after start up, then decay slowly
Ionization efficiency:Set during monthlyNH4NO3 calibration
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Surveying Data:MS time series
• In the MS-Time Series tab (shown right), you can – plot the signal at any m/z as a
function of time (top) or – plot the mass concentration of
any fragment/species as a function of time (bottom)
• During data survey, make sure that the ‘Use MS correction factors’ button is NOT checked
• Note data that should be discarded and negative or unusual concentrations
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Surveying Data:MS time series
12
10
8
6
4
2
0
-2
Mass Concentration (µg m
-3)
12:00 PM3/31/06
2:00 PM 4:00 PM
Date and Time
Water Ammonium Nitrate Sulphate Organics Chloride
Respect the color scheme!
What’s with the water???
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Surveying Data:MS Average
• In the MS-Average tab (shown right) you can– make a MS for any run or
series of runs during the experiment
• During data survey, UNCHECK ‘Add errors’ and ‘Use MS correction factors’
• Look for problems with:– frag table (black sticks) – mass calibration (sticks
vs. peaks)
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Surveying Data:MS Average
10-7
10-6
10-5
10-4
10-3
10-2
10-1
100
101
Nitrate Equivalent Mass Concentration (µg m
-3)
26.025.525.024.524.023.523.022.522.0m/z
Species
Air 294Water -2.35Ammonium -0.309Nitrate 0.514Sulphate -0.0925Organics 5.34Chloride 0.00434Others 0
10-5
10-4
10-3
10-2
10-1
100
101
102
103
Nitrate Equivalent Mass Concentration (µg m
-3)
19.018.518.017.517.016.516.015.515.014.5m/z
Species
Air 294Water -2.35Ammonium -0.309Nitrate 0.514Sulphate -0.0925Organics 5.34Chloride 0.00434Others 0
Solid black peak = Negative difference signal
(background > signal)
Color over black = Apportionment problem!!!
Something’s wrong in frag table land
Need to Adjust Frag Table
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Surveying Data:MS Average
10-6
10-5
10-4
10-3
10-2
10-1
100
101
102
Nitrate Equivalent Mass Concentration (µg m
-3)
30282624222018161412108m/z
Species
Air 294Water -2.35Ammonium -0.309Nitrate 0.514Sulphate -0.0925Organics 5.34Chloride 0.00434Others 0
10-8
10-7
10-6
10-5
10-4
10-3
10-2
10-1
100
Nitrate Equivalent Mass Concentration (µg m
-3)
6462605856545250484644m/z
Species
Air 294Water -2.35Ammonium -0.309Nitrate 0.514Sulphate -0.0925Organics 5.34Chloride 0.00434Others 0
Good stick-peak alignment @ low masses
But bad stick-peak alignment @ higher masses
Need to Recalculate Sticks
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Surveying Data:TOF Size Distributions
• In the TOF-Traces tab (shown right), you can – Plot mass/signal vs
diameter/time of flight curves for your TOF masses or for species
– Make 3-D image plots of concentration vs. diameter vs. time
• During data survey, uncheck ‘Use MS correction factors’ and ‘Normalize to MS’ in the bottom (Image Plots) box
• Look for particle signal in airbeam Note recommended diameter
and smoothing settings
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Surveying Data:TOF Size Distributions
1.2x106
1.0
0.8
0.6
0.4
0.2
0.0
dS/dT (Hz)
6x10-3
543210
Time of Flight (s)
sig_p28_r15719_15752
1500
1000
500
0
dS/dT (Hz)
6x10-3
543210
Time of Flight (s)
sig_p44_r15719_15752
No particle signal apparent at m/z = 28
vs. gas and particle signal at m/z = 44
Airbeam at 28 probably OK
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Performing CorrectionsAutomatic corrections
• In the MS-Corrections tab (shown right), you can– Correct for multiplier decay
and flowrate changes– Recalibrate the MS– Do error analysis
• Choose reference period where things are relatively stable
• Suggested smoothing: – MS AB ~4 pts– TOF AB ~6 pts– Flowrate ~ 4 pts
• Outputs wave: corr_fac
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Performing Corrections:Manual corrections
€
corr _ fac = corr _ fac _ flow × corr _ fac _(AB)
The correction factor corr_fac is a product of the flow and airbeam correction factors. You can recalculate corr_fac if you need to using your own airbeam correction factor and the automatically generated flow correction. Remember that your corrections should be relative to the reference period, where the value of the correction factor is taken to be 1.
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Performing Corrections:Frag table adjustments
You may change these frags:– Frag_RH[18] = 0.1*frag_air[28]
This changes with RH, describes how much of the air is water vapor. If too much of 18 is going to air (negative water) lower this fraction.
– Frag_O16[16] = 0.353*frag_air[14]The amount of O2 that fragments to O and the amount of N2 that fragments to N is going to vary based on instrument settings. If too much of 16 is going to air (ammonium problems), lower this fraction.
– Frag_air[44] = 0.00037*1.6*1.25*frag_air[28]The amount of CO2 in air can change in some applications (i.e., diesel emissions, anyone?). You can change 0.00037 (370 ppm) accordingly.
Others, change only with caution!
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MS Mode
Now you can analyze data.
The starting points in MS mode are:
Mass spectra (top), which show mass vs m/z
Time series (bottom), which show concentration vs time
0.001
0.01
0.1
1
10
100
Nitrate Equivalent Mass Concentration (µg m
-3)
28024020016012080400m/z
Species
Air 291 ± 0.3Water 0.993 ± 0.1Ammonium 0.291 ± 0.05Nitrate 0.537 ± 0.01Sulphate -0.386 ± 0.02Organics 15.6 ± 0.04Chloride 0.0129 ± 0.003Others 0 ± 0
15
10
5
0
Mass Concentration (µg m
-3)
12:00 PM3/31/06
2:00 PM 4:00 PM
Date and Time
Water Ammonium Nitrate Sulphate Organics Chloride
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TOF mode
And in TOF mode, you can make– Image plots (top), which
show concentration and diameter vs time
– Distributions (bottom), which show concentration vs diameter
4
56
100
2
3
Vacuum Aerodynamic Diameter (nm)
12:00 PM3/31/06
2:00 PM 4:00 PM
Date and Time
30
20
10
0
dM
/dlogDva
(µg m
-3)
Organics
1.0
0.8
0.6
0.4
0.2
0.0
dM
/dlog
Dva
(µg m
-3)
102 3 4 5 6 7 8 9
1002 3 4 5 6 7 8 9
10002 3
Vacuum Aerodynamic Diameter (nm)
ug_Organics_r15719_15752
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Alice’s Panel
• Alice’s Panel runs data diagnostics that are especially helpful when you are apportioning ambient signal. You can play with it and see what you get.
• Its use is outlined in the files on the Wiki page. Let us know when you need it and we can go over it.
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AMS resources
The Wiki page, which is at:http://amsknowledge.pbwiki.com/
has useful websites and these + more data analysisfiles.
Interpretation of mass spectra by Fred W.McLafferty is a good introduction to interpretingmass spectra (and appropriately named!)
Andy, Evangelia, and I all have experience with the dataanalysis and can help as you run into problems. We can alsodirect you to which one of us might be most helpful in any givencase.
Manjula Canagaratna at Aerodyne is the official data analysisguru for the Q-AMS
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Handy Igor Keys and Commands
• Ctrl (or apple) + I: brings up markers• Ctrl (or apple) + A reverts graph to
original scale• Ctrl (or apple) + J brings command
window to front• make: Igor command to create a wave• display: Igor command to make a graph• edit: Igor command to make a table