Center for Atmospheric Particle Studies AMS Data Analysis Training Amy Sage and Andy Grieshop March 7, 2007

Center for Atmospheric Particle Studies

AMS Data Analysis Training

Amy Sage and Andy Grieshop

March 7, 2007


Outline

Batch and frag tables Loading data Checking diagnostics Surveying data Performing corrections MS mode TOF mode Jump mode Alice’s panel


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


Batch table: contains the values used for CE and RIE for each species.


Frag table: apportions the signal at each mass among contributing fragments from each species


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


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


diagnostics plot

notebook

command window

‘load data’ tab


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


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


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???


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)



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


-3)

19.018.518.017.517.016.516.015.515.014.5m/z

Species


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



10-6

10-5

10-4

10-3

10-2

10-1

100

101

102


-3)

30282624222018161412108m/z

Species


10-8

10-7

10-6

10-5

10-4

10-3

10-2

10-1

100


-3)

6462605856545250484644m/z

Species


Good stick-peak alignment @ low masses

But bad stick-peak alignment @ higher masses

Need to Recalculate Sticks


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


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


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


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.


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!


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


-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


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


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.


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


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

Documents

Center for Atmospheric Particle Studies AMS Data Analysis Training Amy Sage and Andy Grieshop March 7, 2007