FAQs AMS Data Analysis

The purpose of this page is to serve as a repository of FAQs of AMS data analysis.

The standard frag table produces unusual results, should I modify it and how?

• Typical adjustments to the frag table that need to be done for all experiments are listed in this section of the ToF-AMS Field Data Analysis Guide.

• In some cases additional adjustments are needed. Examples include changes to the frag table of SO4 and NO3 when sampling smog chamber SOA without a seed or NOx (which is known to not have those components), or biomass burning aerosol for which the SO4 and NO3 subtractions break down. If you are in this situation, keep reading.

• The AMS organic mass is calculated by applying the fragmentation matrix to the total spectrum. The fragmentation matrix is defined from the fragmentation table, as discussed in this paper (which you need to read if you want to be able to think intelligently about this topic):
  • J.D. Allan, H. Coe, K.N. Bower, M.R. Alfarra, A.E. Delia, J.L. Jimenez, A.M. Middlebrook, F. Drewnick, T.B. Onasch, M.R. Canagaratna, J.T. Jayne, and D.R. Worsnop. Technical note: Extraction of chemically resolved mass spectra from Aerodyne aerosol mass spectrometer data. Journal of Aerosol Science, 35: 909­922, 2004.

• That table was constant for field data from ~2003 and until 2008. The only one change for field data was proposed by the Aiken et al. paper below, after seeing that there was some CO+ at m/z 28 arising from ambient organics, and that the H2O+ arising from ambient organics was lower than assumed in that Allan et al. 2004 paper. We did this explicitly so that the total organic mass calculated was constant with either the "old" or the "new" frag table. (The shape of the spectrum at 16-18 and 28 does change, but the choice is obvious as soon as you see the spectrum). That paper is (see the section titled "Improved Fragmentation Table for Ambient Organics"):
  • A.C. Aiken, P.F. DeCarlo, J.H. Kroll, D.R. Worsnop, J.A. Huffman, K. Docherty, I.M. Ulbrich, C. Mohr, J.R. Kimmel, D. Sueper, Q. Zhang, Y. Sun, A. Trimborn, M. Northway, P.J. Ziemann, M.R. Canagaratna, T.B. Onasch, R. Alfarra, A.S.H. Prevot, J. Dommen, J. Duplissy, A. Metzger, U. Baltensperger, and J.L. Jimenez. O/C and OM/OC Ratios of Primary, Secondary, and Ambient Organic Aerosols with High Resolution Time-of-Flight Aerosol Mass Spectrometry Environmental Science and Technology, 42, 4478­4485, doi: 10.1021/es703009q, 2008.

So for ambient organics, there is no ambiguity (with some very infrequent exceptions which I assume are not your concern).

For lab organics one needs to modify the fragmentation table so that it is appropriate for the experiment at hand. E.g. if you know that there is no nitrate or sulfate or ammonium, you need to assign the signal at those ions to the organics, which is easily done. This is part of the "Users' Responsibility", which we have discussed at length at Users Meetings etc. I suspect this is the problem you are having, and in this case there is no ambiguity, one just has to know what the correct thing to do is (as I just described).

How do you account for variable CO2 in the sampled air during analysis ?

• The AMS samples particles 10 million times (1e7) more efficiently than gases, due to the lens and differential pumping system. E.g. N2 is about 1 kg/m3 of air, but in the AMS we measure it as 100 ug/m3 of equivalent aerosol signal, or 1e-7 of the actual concentration.

• A typical CO2 concentration is of the order of 400 ppm of air, which is of the order of 400 mg/m3, which creates to about 40 ng m-3 of equivalent aerosol signal. This average value is generally subtracted with the Squirrel frag table and the HR frag table, as discussed in this section of the ToF-AMS Field Data Analysis Guide.

• If CO2 levels in your experiment are pretty constant AND the amount subtracted is a small fraction of the aerosol CO2+ signal, that constant subtraction may be sufficient.

• If CO2 levels vary a lot in your experiment, or reach much higher values (as when sampling concentrated combustion exhaust), AND/OR if the gas-phase CO2+ subtraction is a substantial (> 10%, or whichever criterion you establish based on your desired precision and accuracy), then you need to implement a time-dependent subtraction based on a CO2 gas-phase measurement.

• If the CO2 gas-phase concentrations are very high (percent) you may be able to measure them with the AMS PToF mode, which also may allow separation of the gas vs particle phase components.