Field Data Analysis Guide

Determine Flow Rate Calibration

 * Basic Principle: AMS flow rate is used to convert MS signal intensity to units of mass concentration. Flow rate is derived from lens pressure (analog input #3) and converted using a conversion factor.  Post-correction of flow rate MUST be performed if there is:
 * any deviation between the derived and calibrated flow rates;
 * errors in the logged flow rate value;
 * electronic noise, or;
 * drift in the zero of the baratron.
 * In the absence of errors, flow correction is made by multiplying the logged flow rate by the ratio of derived to calibrated flow rates. To correct for errors, the calibrated flow rate must be used.


 * NOTE: Save backup of flow rate wave (located in root:diagnostics) and construct new, corrected flow rate wave in Squirrel data analysis experiment. This new wave MUST be named “flow rate”.


 * Data Recording: A flow calibration MUST be performed at least once in the field using a Gilibrator.


 * How Calculated: Flow ratecorrected = flow ratederived x (flow ratecalibrated/flow ratederived)


 * How Applied: Flow rate is used in the calculation of Squirrel component mass concentrations:
 * Squirrel Code:
 * Function: SQ_MS_Concentration
 * ugfac=ug_op?((aw/Navo)*1e12/(ioneff_wave[p1]*flowrate[p1]*rie*ce)):(1)


 * Additional Resource: See Q-AMS manual for more information on correcting flow rate.

Determine Time Line of Single Ion Values

 * Basic Principle: The single ion (SI) value is used to convert MS signal intensity to units of mass conc. SI values logged by the data acquisition software may not be the true values.  Unlike threshold values, single ion values can (and in many cases must) be post-corrected by applying a new set of values prior to pre-processing the data.


 * Data recording:	It is recommended that the threshold analysis be performed daily to have adequate data for timeline of SI values.


 * How Modified: 	Single ion values should be obtained in the field using the threshold analysis window within the data acquisition software. If post-correction of the single ion values is required, this change can be made by clicking the Modify SI button in the “Optional Checks & Advanced Features” (HDF Index tab).


 * NOTE: Any change in single ion values MUST be made prior to pre-processing.


 * How Applied: SI value is applied in Squirrel to convert bit*ns to ions/s (Hz)


 * Squirrel code:
 * Function: sq_Hz(index_pos,datawav)
 * wave ion_wave=root:diagnostics:ionSingleStr_logged
 * datawav*=(1/ion_wave[series_index[index_pos[p]]]) * ToFPulserInHz[series_index[index_pos[p]]]

Process all IE/RIE_NH4 Calibrations

 * Basic Principle: The ionization efficiency (IE) calibration determines the ionization efficiency of ammonium nitrate. Quantification of all non-refractory AMS components are based on the linearity of this IE (i.e., the IE for all species can be related to the measured IE of a single species, in our case NO3).


 * Data Recording:	It is recommended that all IE calibrations be recorded periodically during samplingwith the data acquisition software running in GenAlt Mode.


 * How Derived: ToF-AMS IE calibrations are typically performed in the field using BFSP mode. Software is available to analyze these IE calibrations at the ToF-AMS Resource Page. A tutorial regarding BFSP IE calibrations is also available here.  This software should be used to determine IENO3 and RIE_NH4 values for each field IE calibration.  RIE_NH4 should be double checked using MS mode data.


 * How Applied: Calibrated ion efficiency is applied in the calculation of Squirrel component mass concentrations.


 * NOTE: Airbeam correction also influences the IE and will be discussed later (add link).


 * Additional Resource: See Q-AMS manual for more information on IE calibrations.

Evaluate SI, IE, RIE_NH4 to use, based on SI, IE, AB, flow, and IE/AB for the whole campaign

 * Basic Principle: Based on results of threshold analyses and IE calibrations performed during the campaign select single ion (SI), ionization efficiency (IE), and ammonium relative ionization efficiency (RIE_NH4) values for the entire campaign.


 * How Derived:
 * Ideally, these values are simply the averages calculated from all evaluations (i.e., threshold analyses and IE calibrations) performed during the campaign.
 * However, it is likely that the time lines of these values will need custom corrections. This is particularly true of the time series of the time line of the IE value.
 * A critical parameter used to finalize the IE time series is the (IE/AB)calibration value.           Discussion regarding the use of the (IE/AB)calibration value to correct the IE time line.


 * How Applied: After deciding on correct values:
 * SI values can be modified using the Modify SI button in the “Optional Checks & Advanced Features” (HDF Index tab)
 * IE values:
 * if no correction needed, average IE will be used during (AB correction)HL
 * When doing airbeam correction, “ioneff” is written to single constant value.
 * If autoset is not used when performing an airbeam correction, then “ioneff_logged” is never used.
 * If correction needed, see Discussion
 * for Squirrel versions earlier than 1.38, use a post-correction function
 * For Squirrel versions 1.38 and later, use “ioneff_to_AB_ratio_rel” and “user_corr_fac”.
 * RIE_NH4 value should be used to modify the batch table.


 * NOTE: When modifying SI and IE values, “*_logged” waves should never be changed as these changes will be overwritten whenever you perform a squirrel diagnostics.

IE/AB Correction

 * Basic Principle: The ToF-AMS ionization efficiency (IE) measures the sensitivity of the instrument to a measured quantity of a specific compound, typically NH4NO3, during instrument calibration. Throughout sampling, this sensitivity is reflected by changes in the instrument air beam.  In most cases, changes in sensitivity are observed in the air beam and will be accounted for when performing an AB correction.  However, there are instances where this may not the case and a custom correction is needed.  The parameter that can be used to evaluate the need for a custom correction is the (IE/AB) ratio ((IE/AB)calibration) obtained from each IE calibration.  If the (IE/AB)calibration ratio for calibrations performed throughout the sampling period do not change significantly an IE/AB correction is not needed.  If these values are not constant, a correction is required. In Squirrel versions 1.38 and greater, an IE/AB specific correction wave has been implemented to aid the user.  However, in Squirrel versions prior to 1.38, this correction must be manually constructed and implemented.

Application of IE/AB Correction

 * Basic Principle: The intended use of the “ioneff_to_ab_rel_ratio” wave is to account for circumstances where the (IE/AB)calibration changes over time. In Squirrel versions 1.38 and higher, this wave is present by default with values set to 1.  For earlier Squirrel versions, this wave will need to be created. In either case, “ioneff_to_ab_rel_ratio” MUST be modified to account for changes in (IE/AB)calibration values.


 * How Calculated: The values in the “ioneff_to_ab_rel_ratio” wave can be calculated by first establishing a correct, initial IE/AB value (IE/AB)t=0 (typically from an early IE calibration).   The value of the required correction factor at each subsequent timestep, t, is then calculated by dividing (IE/AB)t=0 by the IE/AB ratio at this time (IE/AB)t=i:


 * ioneff_to_ab_rel_ratio[t] = (IE/AB)t=0 / (IE/AB)t=i


 * A time series of (IE/AB)t=i can be constructed by interpolating linearly between the (IE/AB)calibration values from each IE calibration.


 * How Applied:
 * In Squirrel versions 1.38 and above “ioneff_to_ab_rel_ratio” is automatically applied to adjust the species mass concentrations through the SQ_MS_Concentration function.
 * In Squirrel versions prior to 1.38 a post-correction function should be used to apply a corrected IE time series (that has had the IE/AB correction factor applied), through the following convention:


 * ioneff_corr = ioneff * ioneff_to_ab_rel_ratio


 * Recommendations:

Process size calibrations

 * Basic Principle: The parameters contained in the data acquisition software to describe particle time of flight may not be correct and need to be re-evaluated using the polystyrene latex (PSL) particle size calibrations performed in the field.


 * Data Recording: It is recommended that size calibrations be performed during the field deployment using 100, 300, 500, 700, and 900 nm PSL particles. Sizes at or below 100 nm can be obtained with the classifier after it is calibrated at 100 nm.


 * How Derived: The size calibration is calculated by fitting a plot of particle size (Dva,PSL) vs. average particle velocity (Vpart, in m/s) using the following fit function:


 * Vpart = f(Dva,PSL) = Vl + (Vg - Vl) / (1 + (Dva,PSL/D*) ^ b), where
 * Dva = vacuum aerodynamic diameter;
 * Vl = lens velocity, and;
 * Vg = gas velocity


 * NOTES:
 * 1. Other fit functions can be used as long as that fit interpolates the data points.


 * 2. For conversion of time of flight to particle velocity, the typical length of particle flight chambers for ToF-AMS are:
 * 0.293 m (short chamber);
 * 0.39 m (long chamber).


 * 3. To convert nominal diameter to vacuum aerodynamic diameter:


 * Dva = (dp * p) / S, where
 * Dp = nominal diameter
 * S = Jayne shape factor (S = 1 for PSL), and
 * p = density (p = 1.05 for PSL)


 * 4. Periods with different flowrates (changes in orifice, clogging) need to have different calibrations.


 * How Applied: Parameters obtained by fit will be used to recalculate aerodynamic diameters when performing corrections in Squirrel.

Load data into Squirrel, Inspect Diagnostics
NOTE: Prior to loading data in squirrel, it is strongly recommended that the user review the General and Technical FAQs listed on the Squirrel main page as well as the several tutorials that are available on the Squirrel Help page

Squirrel requires AMS data to be saved in .HDF format. Under normal operating conditions, data is saved automatically by the data acquisition software in both .ITX and .HDF format. If .HDF files were not saved during sampling, the user can use the HieDI file converter to convert the .ITX files. To load .HDF data into Squirrel:
 * Press “Get Index” button;
 * Browse to folder containing .HDF data files.

After indexing the .HDF data, Squirrel creates a diagnostics plot that can be used to diagnose the data set.

Implement Corrected Flow Rate and Single Ion Values, if any

 * Basic Principle: As discussed previously, incorrect flow rate and single ion values must be corrected prior to Squirrel data pre-processing because these values are used to convert AMS signal intensity to mass concentration during this step.  Once data has been pre-processed, the single ion values are “set” and correcting any errors requires repeating data pre-processing.  Therefore, it is strongly suggested that the user devote significant effort to ensure that the single ion values are correct and final before moving on.  If no changes are made, pre-processing will use the flow rate and single ion values that were captured by the data acquisition software.  These values are shown in the Squirrel diagnostics plot, which can be used as a reference.


 * Data Recording: N/A


 * How Derived: N/A


 * How Applied: Recommended ways of modifying the flow rate and single ion values prior to data pre-processing were presented previously. See previous flow rate and single ion value discussions for more details.


 * Recommendations:


 * Notes:
 * Generally, it is recommended that the AMS flow calibration be expressed in terms of mass rather than volumetric flow.
 * Reported mass concentrations are dependent on the calibrated instrument flow rate. Therefore, the conditions under which the instrument flow rate was calibrated in the field should be reported in all manuscripts (e.g., at STP or ambient and, if ambient, under what conditions).

Perform m/z Calibration

 * Basic Principle: Under normal operating conditions, the user calibrates the instrument via the data acquisition software during instrument start-up.  Afterwards, the ToF-AMS data acquisition software automatically calibrates m/z during autosave operation to account for drift in the calibration over time.  Squirrel m/z calibration SHOULD be performed as a first step in ToF-AMS data analysis to ensure correct assignment of peak location in order to convert the raw data to stick format.  The m/z calibration has to be performed prior to data pre-processing in order for the Squirrel fitting parameter values to be available as an option during  pre-processing.


 * Data Recording: Initial m/z calibrations are required after restarting EITHER the instrument OR the acquisition software.


 * How Derived: N/A


 * How Applied: The m/z fitting procedure is initiated by clicking the “Check m/z calibration” button and then the “Begin mz fitting” button after the SQ_MzCalibration_Panel window appears.


 * Recommendations:
 * For most fragments, use closed spectrum for m/z fitting (exceptions are air peaks (N+, O+, and Ar) for which open spectra can be used);
 * C+, O+, and the Tungsten series have been found to be problematic for some data sets. In this case, these fragments should be removed when performing the m/z calibration;
 * It is recommended that the user have at least one peak greater than m/z 90;
 * At present, the calibration as performed cannot reliably be extrapolated to masses larger than m/z 200. This may be fixed in future Squirrel releases. As a result, if the exclusive focus of the analysis is large mass fragments, the user should remove all low mass fragments from the mass table prior to performing the mass calibration.




 * 1. Using the inset table, the user can modify the fragments used in the m/z calibration prior to beginning m/z fitting. To remove a fragment from the fitting procedure, place a zero in the corresponding cell in the SpecType column.  The table can be reset to default values by clicking the “Revert to Default” button.  Peaks from the closed spectra are typically better with the exception of the air peaks, for which open spectra can be used.


 * 2. After selecting the fragments to include in the fitting procedure, the procedure is started by clicking “Begin mz fitting”.


 * 3. The accuracy of the m/z calibration and mass calibration for each run are displayed during m/z fitting. The accuracy parameter evaluates the “goodness of fit” of the Squirrel calibration relative to that of the acquisition program.


 * 4. These plots display the results of m/z fitting from each run. The raw data (black dots) and the Squirrel fit (red line) are plotted along with the designated peak center determined from the data acquisition (black vertical line) and Squirrel (yellow vertical line) m/z calibrations.


 * 5. The overall goodness of the Squirrel m/z calibration, relative to the calibration from the data acquisition program, is reported (ratios (data acquisition/Squirrel) for intercept, slope, and power). Deviation from unity represents a “bad” fit by the Squirrel m/z calibration.


 * 6. “Bad” fits can be “filtered” after the m/z fitting procedure, if needed. The threshold criteria for filtering is the deviation of the ratios found in (4) from unity. The value of this threshold is at the discretion of the user as is the method used to fill in the bad fit value.

Perform Baseline Subtraction

 * Basic Principle: ToF-AMS mass concentrations are derived from the difference spectra.  Both raw open and closed spectra can have a significant non-zero baseline that is transferred to the raw difference spectrum as well.  The “check baseline” routine allows the user to examine and make corrections to the baseline of the difference spectrum.  This correction ensures that any baseline contribution to the stick value for each m/z fragment is removed prior to calculating the difference stick spectra.


 * Data Recording: N/A


 * How Derived: N/A


 * How Applied: The check baseline procedure is started by clicking the “Check baseline” button, which will open the SQ_Baseline_Panel.


 * Recommendations:
 * Use mass defect wave as peak center and remove additional regions from stick complement (“Advanced Options” tab).
 * Is there an objective way to say whether the baseline correction is good enough? (numerical estimate of corrected vs uncorrected)

Perform AB Correction

 * Basic Principle: As discussed above, the ionization efficiency (IE)is a fundamental quantity that needs to be known in order report AMS mass concentrations.  While it is not possible to directly measure the IE throughout the course of a sampling period, the air beam allows for an indirect measure of this property because of it's proportionality to the IE. For this reason, performing IE calibrations, The air beam correction factor (corr_fact) accounts for drift in the ToF-AMS signal over time due to changes in the instrument performance relative to a designated reference period.  Typically, chosen reference periods are around the time when an IE calibration is performed.


 * How Calculated: Corr_Fact = ABreference/ABi


 * Squirrel code:
 * Function: SQ_MS_Airbeam
 * corr_fact=(j==detector_num[p])?(airbeamCorrToFTypeValue[1][j]/airbeam[p]):(corr_fact[p])
 * Function: sq_ms_airbeamCorrNonRB??
 * corr_fact = (tempwave[p]==1) ? (airbeamCorrToFTypeValue[1][j] / airbeam_smoothed[p]): corr_fact[p]	//^ scalar/wave


 * How Applied: [component]i (units) = [component]I (units) * Corr_Fact


 * Squirrel Code:
 * Function: SQ_MS_Concentration
 * ugfac_wav_tmp*=corr_fact[p]

Correct for Flow

 * Basic Principle: The airbeam correction compensates for “all” changes in instrument sensitivity relative to a reference time period.  These changes can primarily have two components:
 * 1. “Real” changes (e.g., decrease in the performance of the MCP)
 * 2. “Artificial” changes (e.g., altered instrument flowrate).


 * Any compensation in airbeam due to these “artificial” aspects must be removed as they represent a real change in mass concentration that cannot be corrected.


 * How Calculated: Corr_fact_flow =  (Flowrate(_smoothed)i + Flowrate offset)) / (Flowratereference + Flowrate offset)


 * Squirrel Code:
 * Function: SQ_MS_Airbeam
 * If no smoothed flowrate:
 * corr_fact_flow=(flowrate+airbeam_ref_flowOffset_sv)/(airbeam_ref_flow_sv+airbeam_ref_flowOffset_sv)
 * If smoothed flowrate:
 * corr_fact_flow=(flowrate_smoothed+airbeam_ref_flowOffset_sv)/(airbeam_ref_flow_sv+airbeam_ref_flowOffset_sv)
 * Function: sq_ms_airbeamCorrNonRB??
 * If no smoothed flowrate:
 * corr_fact_flow=(flowrate+airbeam_ref_flowOffset_sv)/(airbeam_ref_flow_sv+airbeam_ref_flowOffset_sv)
 * If smoothed flowrate:
 * corr_fact_flow=(flowrate_smoothed+airbeam_ref_flowoffset_sv)/(airbeam_ref_flow_sv+airbeam_ref_flowOffset_sv)	::::://airbeam_ref_flow_sv is mode independent


 * How Applied: Corr_fact = corr_fact*corr_fact_flow

Flowrate offset

 * Basic Principle: In order to correct the airbeam correction for changes in instrument flowrate, the flowrate offset must be determined.  The flowrate offset value is that flowrate at which the airbeam is zero.


 * How Calculated:
 * 1. find region where flowrate changes over time (e.g., region where orifice is clogging)
 * 2. for only that region, make a scatterplot of flowrate vs. airbeam
 * 3. perform a linear regression from this scatterplot with a non-zero intercept (alternatively, a regression line can be drawn by eye)
 * 4. the flowrate offset is equal to the value of the y-intercept

Make campaign specific adjustments to fragmentation table
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. Details of the signal apportionment are presented in [http://cires.colorado.edu/jimenez/Papers/Allan_AMS_Part1_Published.pdf Allan, J.D., et al., J. Geophys. Res. - Atm., 108 (D3) 4090 (2003)]. 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.

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 Gas Phase CO2
The chart below presents a quick reference guide to the frag table modifications discussed above.