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

2. 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

3. Center for Atmospheric Particle Studies How mass is calculated: C s = mass concentration of species s (µg m -3 ) MW NO3 = molar weight of nitrate (62 g/mol) Ce s = collection efficiency (dimensionless) RIE s = relative ionization efficiency of species s (dimensionless) (see Jimenez et al. 2003) IE NO3 = ionization efficiency (ions detected per parent molecule) of nitrate (dimensionless) Q = inlet flow rate (cm 3 s -1 ) N A = Avogadro’s number (6.022 x 10 23 molecules/mol) I s,i = detected ion rate of species s at fragment i (s -1 ) batch table frag table

4. Center for Atmospheric Particle Studies Batch table: contains the values used for CE and RIE for each species.

5. Center for Atmospheric Particle Studies Frag table: apportions the signal at each mass among contributing fragments from each species

6. Center for Atmospheric Particle Studies 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

7. Center for Atmospheric Particle Studies 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

8. Center for Atmospheric Particle Studies diagnostics plot notebook command window ‘load data’ tab

9. Center for Atmospheric Particle Studies Check Diagnostics Flowrate: 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 monthly NH4NO3 calibration

10. Center for Atmospheric Particle Studies 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

11. Center for Atmospheric Particle Studies Surveying Data: MS time series Respect the color scheme! What’s with the water???

12. Center for Atmospheric Particle Studies 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)

13. Center for Atmospheric Particle Studies Surveying Data: MS Average 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

14. Center for Atmospheric Particle Studies Surveying Data: MS Average Good stick-peak alignment @ low masses But bad stick- peak alignment @ higher masses Need to Recalculate Sticks

15. Center for Atmospheric Particle Studies 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

16. Center for Atmospheric Particle Studies Surveying Data: TOF Size Distributions No particle signal apparent at m/z = 28 vs. gas and particle signal at m/z = 44 Airbeam at 28 probably OK

17. Center for Atmospheric Particle Studies Performing Corrections Automatic 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

18. Center for Atmospheric Particle Studies Performing Corrections: Manual corrections 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.

19. Center for Atmospheric Particle Studies 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 O 2 that fragments to O and the amount of N 2 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 CO 2 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!

20. Center for Atmospheric Particle Studies 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

21. Center for Atmospheric Particle Studies 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

22. Center for Atmospheric Particle Studies 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.

23. Center for Atmospheric Particle Studies AMS resources The Wiki page, which is at: http://amsknowledge.pbwiki.com/ has useful websites and these + more data analysis files. Interpretation of mass spectra by Fred W. McLafferty is a good introduction to interpreting mass spectra (and appropriately named!) Andy, Evangelia, and I all have experience with the data analysis and can help as you run into problems. We can also direct you to which one of us might be most helpful in any given case. Manjula Canagaratna at Aerodyne is the official data analysis guru for the Q-AMS

24. Center for Atmospheric Particle Studies 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