Analyzing data using AMS analysis procedures

1
Analyzing data using AMS analysis procedures

• Qi Zhang
• June 22, 2004

2
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).

3
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.

4
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

5
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_RHm/z 18
• Check mass spec. (org 27, org 29 )

6
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

7
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)

8
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

9
Corrections (TOF)

• Recalculate Da
• Type in right values from your size calibration
• t0 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)

10
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 Joses Ambient paper and James JGR
  Quantitative paper (I) for details

11
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 Alices Diagnosis routines).

12
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_RH17 and frag_RH16,
  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.

13
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_O1616, where the
  contribution is tied to the variations in the 14N
  signal through frag_air14
• 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_NH416 frag_NH4_1616, 01.1frag_NH416
• With this definition for NH4, adjust the factor
  in element frag_O1616 until the NH417
  NH416 data falls on the 1.11 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_NH417 0frag_NH4_1616, 1.1
  frag_NH416

14
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

15
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).

16
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.

17
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

18
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.