FAQs AMS Data Analysis

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

Can you explain in detail how the Frag Table works?

The Frag Table gives the mathematical formulation of the apportionment of unit resolution sticks to aerosol species. The word 'Frag' is shorthand for fragmentation. The AMS measures aerosol components that have been fragmented due to the impact and ionization processes within the instrument. This fragmentation happens in a predictable, quantifiable way, and the fragmentation table encapsulates all the information we know about this fragmentation.

As a practical matter, the AMS software code performs a mathematical multiplication of the unit resolution difference (Open beam - Closed beam) signal with coefficients determined in the frag table. The frag table itself is a group of 1 dimensional text waves in Igor that is automatically loaded and set to default values in the AMS software. The software interprets the entries in these text waves and generates numerical coefficients for the matrix multiplication. The frag table came about primarily from the work of James Allen and is detailed in the paper Allan, J.D., et al., Technical Note: Extraction of Chemically Resolved Mass Spectra from Aerodyne Aerosol Mass Spectrometer Data, Journal of Aerosol Science, 35: 909–922, 2004 and can be downloaded here. The default frag table has been optimized for common ambient atmospheric conditions; laboratory measurements, measurements of aerosol very highs loadings or of unique origins require specialized modifications.

The Syntax of the frag table

An example of a typical frag table entry is 'frag_air[14]' which has a default value of '14,-frag_nitrate[14]'. This statement should be interpreted as follows: There is a text wave, called frag_air (the wave preloaded with the AMS software) and the [14] describes the fragment, or contribution corresponding to m/z 14. The wave frag_air describes all the fragment contributions to the 'species' we call air. Air is composed primarily of N2, O2, etc. and frag_air describes all the signals we expect to see at m/z 28 (N2), m/z 32 (O2), etc. For any m/z that we do not expect a contribution, i.e. at m/z 100, the entry is blank. All frag table entries use the following syntax:

• Commas indicate addition of terms
• Integers indicate the unit resolution stick value
• Asterisk or '*' indicate a multiplicative coefficient
• Dash or '-' indicate a subtraction

Thu default value of frag_air[14] = 14,-frag_nitrate[14] means that the amount of air that we see at m/z 14 is the total amount at 14 less the amount of nitrate we see at m/z 14. At m/z 14 we expect to see most of the signal to be N+. This N+ can be due to N2 fragmenting and a very small amount of N+ can be due to aerosol nitrate, NO3, being fragmented. This default also highlights the recursive nature of frag table entries. One entry refers to another, which in turn refers to another, etc. However, the software relies on the fact that the recursion stops at some point, and the software will not give results if this condition is not met. This recursive feature also means that changes to one entry may have an impact on other values. For this reason the frag table should not be edited or changed, except for the few entries listed below unless

• The measured signal at a given m/z is designated by that m/z number. E.g. if an entry reads "48", it means that the total measured signal at m/z 48 is assigned to that element.
• Additions
• Subtractions
• Multiplications

Types of frag table corrections

• The frag table accounts for isotopes, interferences from other species, and empirically-measured fragmentation
  • Example of isotopes: frag_K[41] from frag_K[39]
  • Example of interferences: frag_CO2[44]
  • Example of fragmentation: frag_org[48] and frag_org[49]

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 so that it is appropriate for the experiment at hand. 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. Note that if you have HR data, you can measure some of these things directly and that's always better than modifying the Squirrel (UMR) frag table. This is part of the "Users' Responsibility", which we have discussed at length at Users Meetings etc.

• 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.

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.

• For other gas-phase species such as CO, N2O, CH4, at their typical ambient concentrations they produce too small of a signal to see it in the AMS. If you are sampling air with large concentrations of those gases (at least tens of ppmv), then you can apply the same principles described above for gas-phase CO2.