ToF-AMS Analysis with TADA Software
Manual for ToF-AMS Data Analysis with TADA Software Back
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ToF-AMS Analysis Software
- Loading Data Sets
MS Mode Data Processing
P-TOF Mode Data Processing
Information content from Silke Hings and Frank
Page last updated 03/03/2006, SSH
- When loading the data the program loads raw mass spectra for the MS mode and
stick spectra from the P-TOF mode. The raw mass spectra are converted into stick
spectra. In the first step the mass spectra are calibrated using the
(approximate) I-TOF calibration saved by the data acquisition program and the
exact masses selected in the panel. After calibration of the mass spectra the
stick spectra are calculated by integration of the peaks over a fixed width
around the exact m/z. This works fine for ambient data at relatively low m/z (up
to maybe 200). However, it probably does not work well for MS acquired with the
VUV source at high m/z. During this integration also a baseline subtraction is
- When selected, the duty cycle correction is applied to the data during the
load process. This correction corrects for extraction efficiency into the TOF-MS
as a function of m/z due to differences in flight velocity (residence time)
through the extractor.
- For calculation of species mass concentrations the full frag list from the
Q-AMS data processing program is used. However, the frag list does not exist as
a user-accessible table, but is embedded in the program code. Only three
parameters (that are in the frag list and are often adjusted) are user
accessible on the panel.
- Generally the raw MS mode spectra are not kept in memory to avoid extremely
large use of memory. However, by selecting ‘use raw spectra’ the raw MS are kept
and can be averaged and plotted.
- The program is not prepared to handle raw P-TOF data, since it would take
forever. The plan is to use a separate program that loads and integrates the raw
P-TOF data and writes new stick spectra. This program will hopefully be provided
in the near future.
- For calculation of size dependent mass spectra several corrections are made,
for example background subtraction (pretty much what is done with the DC markers
in the Q-AMS size distributions) and noise reduction. This does not work
perfectly yet and is the subject of current work. In addition, these mass
spectra can be normalized to the MS mode mass spectrum for the same run number
interval in a way that for the complete size distribution the same average mass
spectrum is achieved.
- At this time it is not possible to append data to an already existing data
set. If additional data are acquired the whole set needs to be reloaded
- Since the integration of the raw data is done during the load process and
since the raw data are erased then, it is not possible to redo the calibration
later during the processing. This seems not to be a problem with our ambient
data, however, it seems to be a problem with VUV source data that turned out to
be much trickier to convert into sticks.
- Type the load path into the panel or browse for it clicking the ‘browse’
- Select the run numbers to be loaded in the following format:
- Select the files to be loaded:
- ’Load MS files’: loads MS raw spectra and converts them into stick spectra
- ’Load P-TOF files’: loads P-TOF stick spectra, subtracts baseline
- ’Use raw spectra’: keeps MS raw spectra in memory
- ‘Apply duty cycle correction’: corrects for the m/z-dependent duty cycle of
the TOF-AMS, normalized to the chosen m/z. This should always be turned on.
- Note, that the info files (if existing) need to be in the selected data
- After pressing the 'Load' button, a panel will appear, showing the
parameters read in from the info files. Check, if all values are correct. Some
of them are needed during data processing and can not be changed later (all
values given in the 'Parameters' box can be changed
- For non-standard measurements (e.g. for VUV-source measurements) the m/z
calibration of the raw mass spectra can be influenced in various ways:
- ‘I-TOF calibration run’:
- if you want to select an individual run to be used for calibration, type in
the runnumber of that run
- if you want an automatic calibration for every MS, select ‘0’
- if you want to use your own calibration parameters, select
(IMPORTANT: the format must be: mass = (intercept + slope *
- ‘Change m/z for I-TOF calib.’:
- Select m/z that will be used for mass spectra calibration (default: N+, N2+,
Note: here the exact mass of the ions needs to be selected, not
just the integer values!
- Select how the m/z selected above will be used (row ‘use exactmass’):
- ‘1’: use MSDiff for calibration
- ‘-1’: don’t use for calibration
- ‘2’: use MSClosed for calibration
IE Calibration (only before
- Type in the values from the IE calibration. Note, that
up to version 1.21 the single ion signal needs to be given BEFORE loading
data. As of version 1.22 this is not necessary anymore.
Size Calibration (only before
- Type in the values from the P-TOF calibration (size
calibration). Note, that up to version 1.21 the P-TOF calibration parameters
need to be given BEFORE loading data. As of version 1.22 this is not
Duty Cycle Correction
- This correction is applied when loading the data. It should always be
applied (if this correction is de-selected, a warning pops up when loading).
- This correction corrects for the m/z dependence of the ion extraction into
the mass spectrometer: large ions travel slower through the extractor than small
ions, consequently the overfilling of the extractor is larger for small ions and
only a smaller fraction of all ions is extracted into the TOF-MS for smaller
- This effect is proportional to SQRT (m/z).
- It is corrected for by dividing the signal at each m/z by: SQRT (m/z(signal)
- The reference m/z is chosen on the panel.
Air Beam Correction
- Select a run-number interval for the reference airbeam or select a target
- Select the airbeam m/z to be corrected to and if you want smoothing of the
- The number of size bins generated by the TOF-AMS can be rebinned into less
- into a selected number of bins, evenly spaced in logarithmic space
- into size bins defined by an external wave (e.g. for comparison with another
instrument like an impactor)
Average Mass Spectra
- Average mass spectra will be calculated for the selected run interval or for
the whole run interval that was loaded (if ‘Averaging interval’ field is
- If ‘use raw spectra’ is checked in the ‘Load Data’ box (and if raw spectra
are available) an average raw spectrum will be calculated and displayed.
- An average stick spectrum is always calculated.
- The sticks are colored according to the species and fractions from different
species at the same m/z are stacked on top of each other according to the
- If ‘Convert to µg/m³’ is checked, the mass concentration for each species
will be calculated (according to the IE and single ion signal selected in the
‘Parameters’ box) and printed in the legend. Otherwise the signal will be
displayed in Hz.
- Time series of mass concentrations will be calculated and displayed for the
species selected in the ‘Species’ field (currently available species: NO3, SO4,
NH4, Cl, Water, PAH, Organics or individual m/z (e.g. type 'm28' for m/z
- The traces are colored in the AMS colors.
- As in the Q-AMS Toolbox diurnal patterns are calculated from the mass
concentration time series for the species selected in the ‘Time Series’ box.
- 5-95% whiskers and 0-100% whiskers can be selected.
Average Size Distributions
- Average size distributions will be calculated for the selected species (or
for individual m/z) for a user-defined run number interval or for the whole run
interval that was loaded (if ‘Averaging interval’ field is empty).
- The size distributions will be normalized to the mass concentrations for the
chosen run interval if ‘Normalize to MS’ is checked.
- Note, that the time series need to be calculated first!
- The size distributions can be smoothed by a selected amount and the size
range plotted in the average size distributions can be selected.
- Size distribution time series will be calculated and displayed as image
plots for the selected species individually.
- Generally the whole time series is used for the image plots, however, also
only a range of run numbers can be selected.
- The size range and smoothing in t- and d-direction is also selectable.
- The image plots can also be normalized to the mass spectrum mass
- In order to avoid negative numbers all negatives can be set to zero.
Size Dependent Mass Spectra
- Size dependent mass spectra will be calculated for a user-selectable run
- The size bins need to be selected in a table (after pressing the ‘Choose
size bins’ button) in the format 20-200, 200-500, ….
- If selected, the mass spectra will be normalized to the according average MS
mass spectrum (which needs to be calculated first).
- The minimum diameter for which the size-dependent mass spectra are
calculated is 20 nm even if you choose a minimum diameter smaller than 20 nm.
- For each of the size bins and for the total size distribution (> 20 nm)
the average mass spectrum is calculated individually and plotted in the same
form as in the average mass spectrum section.
- In addition, into every mass spectrum a pie chart is plotted with the
relative contribution of the different species to the individual size bins.
IE Calibration Macro
- After having performed an IE calibration in MS mode, you can process it with
help of the included IE Calibration Macro.
- Load the IE calibration runs (and only these) as usual.
- Calculate a time series for Nitrate.
- Run the 'IE Calibration' macro from the macros menu.
- Enter the values for the used DMA size and the current SI signal
- The calculated IE and the mean AB signal will be printed into the
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