Analyzing data using AMS
analysis procedures
Qi Zhang
June 22, 2004
Download the Latest AMS Analysis
Template
• Latest version from James’ website:
– Analysis Toolbox version1.30
• Load data, apply corrections to the data and to generate relevant
plots
– Diagnostics version 1.1.7a
• Plot important m/z ratios for each specie of interest. These plots are
used to optimize fragmentation waves to ensure accurate mass
concentration calculations
– Delta Analysis version 5.3.7b
• Analyze the organic components of the measured mass spectra.
– Batch file 031031
• fragmentation, batch, and color waves for use with the AMS
analysis toolbox (more info see James’ website)
– ARI's preferred default values (e.g., in corrections tab).
Loading Data
• Load data without applying corrections
(uncheck “Invoke corrections”)
• Look at diagnostics plot:
– multiplier voltage/gain
– Heater Bias
– Ionization effieciency
– Duty cycle
– flow rate
– MS & TOF air beam.
Corrections (MS)
• Airbeam correction
– Set “Air beam reference runs”
– Check all 3 check boxes in the section
– Smoothing (by judgment) usually:
Smooth MS air beam (4pts), TOF air beam (6pts), and Flow rate
(4pts)
– Flowrate offset is instrument dependent and needs to be
checked per instrument. If the offset is unknown, enter 0.0
– Click “Recalculate”
– Look at the correction factors plot
Correction factor = signalt / signal0
(The correction factors for the full experiment are referenced to
the signal over the selected air beam range)
– unclick the ‘Auto-set’ checkbox under “Reference Values”
Corrections (MS)
• Generate a time series
– Under “MS” tab; Time Series” subtab
– Check and uncheck the “Use MS correction
factors” checkbox, see the difference. (When
MS correction is checked, time series plot
should shift in agreement with the ‘MS’
correction factor values).
– Closely examine the filtered air period.
• Modify frag table (e.g., frag_CO2 [mz 44],
frag_RH[m/z 18]
• Check mass spec. (org 27, org 29 …)
Corrections (MS)
• Create average MS for the entire period.
– Type in the run number interval
– Type in “Species” (Air,Water,NH4,NO3,SO4,Org,Chl)
– Check the ‘Add Discrepancies’ checkbox
• to determine if the fragmentation waves over predict signal at any given m/z
(black sticks)
• to determine the MS signal that is not assigned to a particular species via
the fragmentation waves (yellow sticks).
– Ensure that the checkbox ‘Plot new graph’ is checked
– Click ‘Calculate!’ button to generate an Average MS plot.
• Examine the Mass spec specifically for black and yellow sticks.
• Examine the Mass spec of the filtered air period.
– Choose the run number interval (can use the marquee function on the
‘MS Time Series’ plot).
– Look for problems, pay special attention to the organics
Corrections (MS)
•
Error analysis.
– The ‘sigma’ and ‘background’ (background electronic noise level) values are
instrument dependent and can be determined experimentally when sampling
through a particle filter. Typical values are Sigma factor = 1.2 and Background =
1e-5.
•
Recalculate sticks
– The default list “14,18,28,149,182,184,186” is for “open + closed”.
– You have to take out 149, 182, 184 and 186 from the list of m/z's used if you do
the stick recalculation but only apply it to the difference spectra. This is because
these peaks only feature in the background and not the sampled aerosol.
Watching the correction factors plot for large changes that may indicate mass
scale issues
– Check time series, Mass spec for changes
– (How to undo recalculate sticks without reloading the data)
•
Baseline correction:
– usually unchecked. Only use when some funny thing happened to baseline
•
Pre vs. Post corrections
– The 'pre correction' box specifically for the wire analysis. It is mainly for functions
to perform before the corrections are made, but after any data has been loaded.
– The 'post correction' box is most useful for overwriting the ioneff_ref wave in
James’ program (talk to me later for details)
Corrections (MS)
• Check for bad points
• Discard bad/unwanted points
– Find the point number(s) on the correction factors plot
(use ctrl-i).
– Read off Run Number(s) (use “List” button to bring up
a table of the Run Numbers (rn_series) and the Save
Times (t_series).
– type this Run Number into the ‘Run number(s)’ input
string
– Click the ‘Discard’ button.
– Click ‘Recalculate!’ button to update the “Correction
Factor” plots
Corrections (TOF)
• Recalculate Da
– Type in right values from your size calibration
– “t=0 offset” to correct for the situation (not often but could happen) when
the chopper starting time was not set right. The value can be measured.
• Check “Clean TOF signals” (to remove bad points)
• Check “override DC Markers” (to set the right zero level)
• E.g., those have big gas phase contribution need to be included in
“Region 2 only Channels” correction; those suffer slow evaporation need
to be included in “Region1 only Channels”
• Force DC Marker position (talk to me later for details)
Batch Table and Calibration Factors
• Batch table defines the calibration factors
(CAL_Fac, wname = CALfac_list) for species.
– IE_fac (wname = IEfac_list): ionization efficiency.
– CE_fac (wname = CEfac_list): collection efficiency
CAL_fac = 1 / (IE_fac * CE_fac)
– The mass concentration for a given species =
S(nitrate equivalent mass concentration signal for
each of its fragments) * CAL_fac.
– Read Jose’s Ambient paper and James’ JGR
Quantitative paper (I) for details
Fragmentation Table
• Fragmentation table defines the matrix that is used to
deconvolve the average ensemble mass spectra
obtained by the AMS into partial mass spectra for distinct
(and groups of) chemical species.
– Read James’ Technical note for details
– The fragmentation waves have been carefully defined based on
mass spectra taken under high and low loadings in each case.
– But there are four main parameters, defined as separate
fragmentation waves (frag_NH4_16, frag_CO2, frag_O16, and
frag_RH), that must be optimized by users to ensure accurate
mass concentrations for the water, ammonium, nitrate, SO4, and
chloride.
– The best method for checking and optimizing these parameters
is to use the Data Diagnostics panel to generate and plot the
relevant m/z ratios for each species (use Alice’s Diagnosis
routines).
Fragmentation Pattern of Species
• Water:
– The purpose of understanding H2O fragmentation patterns very well is
to establish accurate measurements for NH4.
– H2O signals in the AMS can come from four sources:
•
•
•
•
gas-phase water (RH species)
sulfate or sulfuric acid
Organics
Particle bound water
– m/z 17/18 ratio gets larger for pure water particles and is a function of
the ambient relative humidity.
– Typical values
17/18 ratio for water = 0.25
16/18 ratio for water = 0.04, and these values are defined in elements
frag_RH[17] and frag_RH[16], respectively
– If the relative humidity was monitored during an experiment, these
factors in frag_RH can be adjusted to account for the changing ambient
RH.
Fragmentation Pattern of Species
• NH4:
– NH417/16 ratio is conserved throughout an experiment (~1.1).
– 16 is the best for NH4, may have a contribution of 16(O+).
– The 16(O+) contribution is variable due to changes in the air beam
intensity and may be instrument dependent.
– The 16O+ contribution must be set using the factor in element
frag_O16[16], where the contribution is tied to the variations in the 14N
signal through frag_air[14]
– m/z 17 signal is a combination of H2O and NH4 intensities.
– Its best to use both m/z 16 and 17 to derive NH4 concentrations by
defining the element: frag_NH4[16]= frag_NH4_16[16],
0*1.1*frag_NH4[16]
– With this definition for NH4, adjust the factor in element frag_O16[16]
until the NH4[17]: NH4[16] data falls on the 1.1:1 line. This adjustment
accounts for instrument variability in air beam intensity and ensures
accurate ammonium and water signals.
– If the H2O signal is compromised by complications, its best to use
m/z16 to establish NH4 concentrations by defining the element:
frag_NH4[17]= 0*frag_NH4_16[16], 1.1 * frag_NH4[16]
Fragmentation Pattern of Species
• NO3:
– Nitrate mass concentrations is derived from 8 fragments, including nitric
acid, NO2, NO, and 14N+.
– The nitrate m/z 46/30 ratio is typically between 3 and 6.
• SO4:
– Due to different mechanisms for the evaporation and ionization of SO4
from particles (evaporation of sulfuric acid vs. SO3 from the oven), two
fragmentation waves have been defined for SO4 (frag_H2SO4 and
frag_SO3). These fragmentation waves are combined using the
frag_SO4 wave, and take into account some 25 m/z signals.
– The purpose of being so thorough on the SO4 fragmentation is to
ensure accurate organic signals at each m/z.
– Because of the different mechanisms, the m/z 48/64 ratio is not
conserved for SO4.
– Evaporated H2SO4 will fragment with 81/48 and 81/64 ~ 1.0 to 1.5,
– whereas evaporated SO3 will fragment with 81 / 48 and 81/64 ~ 0.2
Fragmentation Pattern of Species
• Chl:
– Currently, chlorides mass concentrations are derived
from the signal intensities at m/z 35, 36, 37, and 38.
The two evaporation and ionization mechanisms for
chlorine is either through evaporation of HCl from the
oven surface and the formation of HCl+ ions (m/z 36
and 38).
– This mechanism most likely occurs when the chlorine
is bound up in volatile or semi-volatile inorganic
compounds such as NH4Cl.
– Chloride ions can also be generated in the gas phase
from chlorine containing organic compounds (m/z 35
and 37).
Fragmentation Pattern of Species
• Other Metals:
– Due to unique fragmentation patterns, metal ions are usually fairly easy
to identify within a mass spectrum and thus can be accounted for by
generating a fragmentation wave for the metal.
– Although metal ions are not observed in large quantities in ambient
aerosol, there are several specific cases where they are important: (1)
variable oven temperature experiments, and (2) source characterization.
– Variable oven temperature experiments are carried out to investigate
the evaporation kinetics of semi-volatile components in ambient aerosol.
The oven consists of tungsten, and thus under high temperature
conditions, tungsten, tungsten oxides, and potential tungsten chlorides
must be account for as an experimental contamination.
– Source characterization experiments, such as incinerator emission
experiments, can potentially measure many different metal compounds,
which again can be identified and taken into account by generating
relevant fragmentation waves.
Data Analysis (MS)
• Generate Time Series
– Check “use MS correction factor”
– Simple Time Trends (note: you can plot any
mass ratio, e.g., 28/44 to plot 28m/z over
40m/z)
– Mass Calculation
• Species
• Graph option
• Diurnal plots
Data Analysis (TOF)
4 choice, x waves dsig and tsig.
Smooth along the diameter axis
Smooth along the time axis
Gives the area under the plot.
Ask me for the macro that can calculate mass
conc. in a given size range
The noise is calculated by looking at the standard
deviation of the data points within the TOF
regions while the data is in TOF space and
mapped accordingly to log(d) space (see James
JGR Quantitative paper). This noise is based on
the electronic noise and the ion counting statistics
of the background, so is really best suited to
calculating detection limits rather than absolute
uncertainties.
Delete the intermediate waves that have been
produced.