Frag Table Adjustments (Outdated)
Contents
Make campaign specific adjustments to fragmentation table (Outdated as of spring 2011)
In the winter of 2010/spring 2011, the guidance for modifying the default AMS frag table was simplified. Most users should adhere to the guidance outlined in the up-to-date wiki
The purpose of the fragmentation table is to apportion the ToF-AMS signal among the different chemical species present in the aerosol (ammonium, chloride, nitrate, organics, and sulfate). The following discussion assumes that the duty cycle correction has been applied to the data (this routinely occurs during data pre-processing in Squirrel unless that function has specifically been disabled by the user) and that the data has been processed to the point of calculating the air beam correction.
Background Information on the frag table:
- The fundamentals and an example (for NH4+) of the frag. table are presented in Allan et al., J. Aerosol Sci., 2004.
- An introduction to the frag table concepts and syntax is in the FAQ page for AMS Data Analysis
Below are detailed discussions and suggestions for modifying the ToF-AMS fragmentation table.
Water Fragmentation Pattern
Water typically dominates the closed spectrum so the signals at m/z's 16, 17, and 18 can be used to determine the fragmentation pattern for water.
Begin by looking at the CLOSED signals for these ions, plot m/z 16 and m/z 17 versus m/z 18, do a linear regression through zero for each plot to find the slopes, and compare those ratios with the default frag table coefficients. If significantly different from default values, the slopes of the mz16:mz18 and mz17:mz18 plots are used as user-defined coefficients at frag_RH-, frag_SO3-, frag_organic-, and frag_water[16] and [17], respectively.
NOTES:
- 1. mz17:mz18 is fairly stable over a wide range of conditions and is independent of heater temperature or pumping time (slight change may be due to varying ToF-AMS conditions);
- 2. In data where the m/z 16 signal is low due to low water in the background (long pumping times), the signal at m/z 16 is constant relative to m/z 18 and the slope becomes flat. For those cases, the current recommendation is to use the default value;
- 3. If possible, look at a high resolution spectrum at m/z's 16, 17, and 18 to ensure that there is no contribution from NH4 to these masses.
- 4. The water fragmention pattern is used in four places in the frag table and the coefficients MUST be changed at each fragment when altering the default coefficient values .
Air Fragmentation Patterns
Historically, only frag_O[16] has been modified to adjust the air fragmentation pattern. Currently, modifications to the air fragmentation patterns at m/z 29 (at frag_air[29]) and m/z 44 (at frag_co2[44]) have also been required for ToF-AMS data. As with the modification to frag_O[16], these adjustments require the user to look at the DIFFERENCE spectra during either filter periods (preferable) or otherwise periods with very low signal.
It is important to note that the frag_CO2[44] coefficient is a combination of a number of factors including:
- 1. the mixing ratio of CO2 in air (0.00037);
- 2. the RIE of CO2 from the literature (1.36);
- 3. the reciprocal of the fraction nitrogen in air (1.28), and;
- 4. a correction for mz15 fragmentation of nitrogen (1.14).
If a change is required in the frag_CO2[44] term, it is recommended that the RIE term be modified since the other terms are likely to be constant.
Modifications to the frag_O[16], frag_air[29], and frag_CO2[44] coefficients can be made in one of two ways. In the first method, the user can examine the filter period average spectrum and manually modify each respective coefficient until the contribution of the corresponding fragment or component ([NH4] in the case of frag_O[16]) in the mass spectrum is zero.
Alternatively, ratios for mz16:mz14, mz29:mz28, and mz44:mz28 can either be calculated by linear regression or by calculating the ratio for the entire set of filter periods and then calculating the average ratio across all filter periods. After calculating these ratios, the default coefficients are modified as follows:
- The measured mz16:mz14 ratio is used to modify the default coefficient at frag_O[16];
- The measured mz29:mz28 ratio is used to modify the default coefficient at frag_air[29];
- The measured mz44:mz28 ratio is used to modify the default coefficient at frag_CO2[44] (in order to modify only the RIE term of the frag_CO2[44] coefficient, multiply 1.36*(measured mz44:mz28 ratio/0.000734) and use this number to replace the default RIE value).
NOTES:
- 1. As seen in the water fragmentation pattern, water can contribute to m/z 16 if the air sampled into the instrument during filter sampling is not dry. If this is found to be the case, the water contribution should be subtracted using the water fragmentation pattern along with m/z 18.
Other Fragmentation Table Adjustments
Modifying frag_NH4_17[17] and frag_NH4[17]
The ratio of NH4_17:NH4_16 has been measured in laboratory studies using a Q-AMS to be ~1.1:1. However, different NH4 souces in the aerosol (such as amines) can have different ratios and different AMS conditions could also change the NH4 fragmentation pattern. To check this ratio plot NH4_17 vs NH4_16 and do a linear regression through zero. Under certain circumstances, these fragmentation patterns can be modified, however this is NOT recommended.
In extreme circumstances ONLY (where NH4_17 to NH4_16 ratio is very far off from 1.1:1 and is noisy) the frag_NH4_17[17] and frag_NH4[17] can modified to force a 1.1:1 ratio, but again this is NOT recommended. To force this 1.1:1 ratio, the following changes can be made (after making these changes, make sure NH4 loadings during filter periods do not change drastically):
- Change frag_NH4_17[17] to blank ("")
- Change frag_NH4[17] to "1.1*frag_NH4[16],1*frag_NH4_17[17]"
Modifying Nitrate Fragment (frag_org[30])
The current value for Frag_Org[30] is based on isotopes of Frag_Org[29]. Some non-nitrogen-containing organic material could also be present at 30, making the isotope attribution too low for Frag_Org[30]. In some cases, the ratio between NO3_30 and NO3_46 can be forced to be the same as for ammonium nitrate. This would be reasonable if there are no other types of nitrate present, such as sodium, calcium, or organic nitrate which tend to have a higher 30/46. In the absence of high resolution data, the attribution of 30 should be something for the data analysis person to decide.
Modifying Sulfate Fragments
The fragmentation pattern for sulfate is not relevant for most analyses where Frag_H2SO4 and Frag_SO3 are not examined and only the combined Frag_sulfate is used. However, there are some instrumental differences for the amount of Frag_Sulfate[18].
The diagnostics ("frag checks") plot for SO4 should be plotted. Each scatter plot between the sulfate fragments (mz64:mz48, mz80:mz48, mz81:mz48, and mz98:mz48) should have linear relationships. Although the linearity of data is important, the exact slopes of lines are unique to each instrument (these slopes can also be compared with (NH4)2SO4 calibration if required). To check for the presence of organic sulfates, the correlation of any deviation from linearity with organics can be investigated.
Modification of the sulfate fragments can be made, but are not often necessary (the possible exception being when sulfate is low and organics are high). Any adjustments can be made at frag_org[80] and [81]. If there is evidence of MSA, organo-sulfites or organo-sulfates in the aerosol, the sulfate fragments will need to be adjusted.
Time Dependent RH
Time Dependent Gas Phase CO2
The chart below presents a quick reference guide to the frag table modifications discussed above.
| Step | Ultimate Target | Adjustment required at | Spectrum to use | Diagnostic | Default coefficient | Comments |
|---|---|---|---|---|---|---|
| 1 | Water | frag_RH[16,17], | 3
1 Water frag_RH[16,17], frag_SO3[16,17], frag_org[16,17], frag_water[16,17] Closed mz16:mz18 ratio, mz17:mz18 ratio 0.04, 0.25 1. User defined coefficients are measured mz16:mz18 and mz17:mz18 ratios (if significantly different from default values). 2. When making a change to these coefficients, changes MUST be made at each of the four listed locations in the frag table. 3. HR spectrum can also be consulted to make sure there is no NH4 contributions at mz16,17. 2 NH4(I) frag_NH4[17] Difference (NH4_17:NH4_16) ratio 1*frag_NH4_17[17] 1. Changes in these fragmentation patterns is generally NOT recommended. 2. Under certain circumstances, such as when there is significant deviation from 1.1:1 ratio and if the signal is noisy, this ratio can be “forced” to 1.1:1 by: - Changing frag_NH4_17[17] to blank (""), and; - Changing frag_NH4[17] to "1.1*frag_NH4[16],1*frag_NH4_17[17]“. 3. Make sure NH4 loadings during filter periods do not change drastically. 3 NH4(II) frag_O[16] Difference from filter period [NH4] ~ 0 0.353 1. User defined coefficient should be evaluated such that [NH4] ~ 0. 2. An alternative method for calculating this coefficient is to calculate the mz16:mz14 ratio (after subtracting any water contribution using he water fragmentation pattern). 4 Organic (I) frag_air[29] Difference from filter period org_29 ~ 0 0.00736 1. User defined coefficient should be evaluated such that org_29 ~ 0. 2. An alternative method for calculating this coefficient is to calculate the mz29:mz28 ratio. 3. The default coefficient is based on isotopic ratios and needs to be changed for ToFs. 4. Purpose of this adjustment is to account for residual signal that is not captured in the baseline subtraction. 5 Organic (II) frag_CO2[44] Difference from filter period org_44 ~ 0 1.36 1. Looking at difference spectrum during filtered period, adjust this coefficient until org_44 is ~ 0. 2. An alternative method for calculating this coefficient is to calculate the mz44:mz28 ratio. 3. Value of 1.36 is RIE of CO2 from literature. 4. Also look at both diagnostics plots ("frag checks"): - Look at intercept of m/z 44 to organics plot (should go through zero); - Look at intercept of m/z 43 to m/z 44 plot (supposed to go through zero, but not as crucial as 44 vs org). 6 Nitrate frag_organic[30] All difference NO3_46:NO3_30 (ambient), NO3_46:NO3_30 (IE calibration) 0.022 1. Look at diagnostics plot ("frag checks") for NO3_46 vs NO3_30. 2. Check ambient ratio compared with ratio determined during NH4NO3 calibration. 3. If difference between ambient and cal 46 to 30 ratios, frag_organic[30] coefficient can be adjusted to match that from IE calibration. 4. However, this assumes that only NH4NO3 is present in the aerosol. 5. HR spectra can be consulted to make a better determination of this ratio. 6. In the absence of this HR data, the attribution of mz30 should be something for the data analysis person to decide based on available information. 7 Sulfate frag_organic[80], frag_organic[81] All difference SO4 “frag checks” See Comments 1. Each ratio (m/z’s 64, 80, 81, 98) should have linear relationships with m/z 48 (linearity of this data is important). 2. Exact slopes of lines are unique to each instrument. 3. Check for deviations from linearity that correlate with organics. 4. Sulfate fragments rarely need adjustment (perhaps only when organics are high and sulfate is low).</br>5. Ambient sulfate fragmentation patterns can also be compared with sulfate calibration. 5. If you have MSA, organo-sulfites or organo-sulfates, will need to adjust SO4 frags. 8 Water frag_RH[18], frag_water[18] 1. No consensus on whether or not to change frag_organic[18] (default is 1*frag_organic[44]). 2. May be better to use value < 1 for coefficient here. 3. There is no consensus yet on this. 4. SO4 frags should have informed user as to whether frag_sulfate[18] needed to be changed (most likely no). If important, can be determined with lab calibration of AS in Argon. 5. These two things very important, but need more lab work to determine these better. 6. After organic and sulfate water accounted for, rest is then attributing water vapor between gas and particle phase. 7. Can inform this decision with measurement of RH from another instrument. 8. Can use pToF to see partitioning of gas phase and particulate phase water.
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