ToF-AMS Analysis with TADA Software</a> <H1><FONT face=" Arial">Manual for ToF-AMS Data Analysis with TADA Software </FONT></H1><FONT face=" Arial"><A href="http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFManual/index.html">Back to Table of Contents </A><BR></FONT> <HR> <H3><FONT face=" Arial">ToF-AMS Analysis Software </FONT></H3><FONT face=" Arial"></FONT> <OL><FONT face=" Arial"> <LI><A href="#Overview">Overview </A><BR><BR> <LI><A href="#Loading">Loading Data Sets </A><BR><BR> <LI><A href="#Calibration">Calibrations </A></FONT> <UL><FONT face=" Arial"> <LI><A href="#MZcal">m/z Calibration </A> <LI><A href="#IEcal">IE Calibration </A> <LI><A href="#Sizecal">Size Calibration </A></FONT></LI></UL><FONT face=" Arial"><BR> <LI><A href="#Corrections">Corrections </A></FONT> <UL><FONT face=" Arial"> <LI><A href="#DutyCycleCorrection">Duty Cycle Correction </A> <LI><A href="#AirBeamCorrection">Air Beam Correction</A> <LI><A href="#RebinSizeDistributions">Rebin Size Distributions </A></FONT></LI></UL><FONT face=" Arial"><BR> <LI><A href="#MSmodeDataProcessing">MS Mode Data Processing </A></FONT> <UL><FONT face=" Arial"> <LI><A href="#AvgMS">Average Mass Spectra </A> <LI><A href="#TimeSeries">Time Series </A> <LI><A href="#DiurnalPlots">Diurnal Plots </A></FONT></LI></UL><FONT face=" Arial"><BR> <LI><A href="#PToFmodeDataProcessing">P-TOF Mode Data Processing </A></FONT> <UL><FONT face=" Arial"> <LI><A href="#AvgSizeDist">Average Size Distributions </A> <LI><A href="#ImagePlots">Image Plots </A> <LI><A href="#SizeDependMS">Size Dependent Mass Spectra </A></FONT></LI></UL><FONT face=" Arial"><BR> <LI><A href="#Features">Additional Features </A><BR></FONT> <UL></FONT></UL><FONT face=" Arial"><BR> <LI><A href="#Troubleshooting">Troubleshooting </A></FONT></LI></OL> <HR> <H4><FONT face=" Arial">Information content from Silke Hings and Frank Drewnick</FONT></H4> <H5><FONT face=" Arial">Page last updated 03/03/2006, SSH</FONT></H5> <H3><FONT face=" Arial"><A name=Overview>1. Overview </A></FONT></H3><FONT face=" Arial"></FONT> <UL><FONT face=" Arial"> <LI>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 performed.<BR> <LI>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. <BR> <LI>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.<BR> <LI>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.<BR> <LI>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.<BR> <LI>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.<BR> <LI>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 again.<BR> <LI>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.<BR></FONT></LI></UL><FONT face=" Arial"><BR></FONT> <H3><FONT face=" Arial"><A name=Loading>2. Loading Data Sets </A></FONT></H3><FONT face=" Arial"></FONT> <UL><FONT face=" Arial"> <LI>Type the load path into the panel or browse for it clicking the ‘browse’ button <LI>Select the run numbers to be loaded in the following format: 1-99,105,107-110 <LI>Select the files to be loaded: </FONT> <UL><FONT face=" Arial"> <LI>’Load MS files’: loads MS raw spectra and converts them into stick spectra <LI>’Load P-TOF files’: loads P-TOF stick spectra, subtracts baseline <LI>’Use raw spectra’: keeps MS raw spectra in memory <LI>‘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. </FONT></LI></UL><FONT face=" Arial"> <LI>Note, that the info files (if existing) need to be in the selected data folder. <FONT face=" Arial"> <LI>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 later).</FONT></LI></UL><FONT face=" Arial"><BR></FONT> <H3><FONT face=" Arial"><A name=Calibration>3. Calibrations </A></FONT></H3><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=MZcal>m/z Calibration </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>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: </FONT> <UL><FONT face=" Arial"> <LI>‘I-TOF calibration run’: <UL> <LI>if you want to select an individual run to be used for calibration, type in the runnumber of that run <LI>if you want an automatic calibration for every MS, select ‘0’ <LI>if you want to use your own calibration parameters, select ‘-1’<BR><B>(IMPORTANT: the format must be: mass = (intercept + slope * pointnumber)˛)</B> </LI></UL> <LI>‘Change m/z for I-TOF calib.’: <UL> <LI>Select m/z that will be used for mass spectra calibration (default: N+, N2+, O2+, Ar+)<BR>Note: here the exact mass of the ions needs to be selected, not just the integer values! <LI>Select how the m/z selected above will be used (row ‘use exactmass’): <UL> <LI>‘1’: use MSDiff for calibration <LI>‘-1’: don’t use for calibration <LI>‘2’: use MSClosed for calibration </LI></UL></LI></UL></FONT></LI></UL><FONT face=" Arial"></FONT></LI></UL><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=IEcal>IE Calibration (only before v1.24)</A></B><BR></FONT></P> <UL> <LI><FONT face=" Arial">Type in the values from the IE calibration. Note, that up to version 1.21 the single ion signal needs to be given <B>BEFORE </B>loading data. As of version 1.22 this is not necessary anymore.</FONT></LI></UL><FONT face=" Arial"></FONT> <P></P><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=Sizecal>Size Calibration (only before v1.24)</A> </B><BR></FONT></P> <UL> <LI><FONT face=" Arial">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 <B>BEFORE </B>loading data. As of version 1.22 this is not necessary anymore. </FONT><FONT face=" Arial"></FONT></LI></UL> <P></P><FONT face=" Arial"><BR></FONT> <H3><FONT face=" Arial"><A name=Corrections>4. Corrections </A></FONT></H3><FONT face=" Arial"><A name=Corrections></A></FONT> <P><FONT face=" Arial"><A name=Corrections><B></B></A><B><A name=DutyCycleCorrection>Duty Cycle Correction </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>This correction is applied when loading the data. <B>It should always be applied</B> (if this correction is de-selected, a warning pops up when loading). <LI>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 ions. <LI>This effect is proportional to SQRT (m/z). <LI>It is corrected for by dividing the signal at each m/z by: SQRT (m/z(signal) / m/z(reference)). <LI>The reference m/z is chosen on the panel. </FONT></LI></UL> <P></P><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=AirBeamCorrection>Air Beam Correction </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>Select a run-number interval for the reference airbeam or select a target airbeam manually. <LI>Select the airbeam m/z to be corrected to and if you want smoothing of the airbeam. </FONT></LI></UL> <P></P><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=RebinSizeDistributions>Rebin Size Distributions </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>The number of size bins generated by the TOF-AMS can be rebinned into less size bins: <UL> <LI>into a selected number of bins, evenly spaced in logarithmic space <LI>into size bins defined by an external wave (e.g. for comparison with another instrument like an impactor) </LI></UL></FONT></LI></UL> <P></P><FONT face=" Arial"><BR></FONT> <H3><FONT face=" Arial"><A name=MSmodeDataProcessing>5. MS Mode Data Processing </A></FONT></H3><FONT face=" Arial"><A name=MSmodeDataProcessing></A></FONT> <P><FONT face=" Arial"><A name=MSmodeDataProcessing><B></B></A><B><A name=AvgMS>Average Mass Spectra </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>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 empty).<BR> <LI>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. <BR> <LI>An average stick spectrum is always calculated.<BR> <LI>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 fraglist.<BR> <LI>If ‘Convert to µg/mł’ 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. </FONT></LI></UL> <P></P><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=TimeSeries>Time Series </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>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 28)).<BR> <LI>The traces are colored in the AMS colors. </FONT></LI></UL> <P></P><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=DiurnalPlots>Diurnal Plots </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>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. <BR> <LI>5-95% whiskers and 0-100% whiskers can be selected. </FONT></LI></UL> <P></P><FONT face=" Arial"><BR></FONT> <H3><FONT face=" Arial"><A name=PToFmodeDataProcessing>6. P-TOF Mode Data Processing </A></FONT></H3><FONT face=" Arial"><A name=PToFmodeDataProcessing></A></FONT> <P><FONT face=" Arial"><A name=PToFmodeDataProcessing><B></B></A><B><A name=AvgSizeDist>Average Size Distributions </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>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).<BR> <LI>The size distributions will be normalized to the mass concentrations for the chosen run interval if ‘Normalize to MS’ is checked.<BR> <LI><B>Note, that the time series need to be calculated first!</B> <BR> <LI>The size distributions can be smoothed by a selected amount and the size range plotted in the average size distributions can be selected. </FONT></LI></UL> <P></P><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=ImagePlots>Image Plots </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>Size distribution time series will be calculated and displayed as image plots for the selected species individually. <BR> <LI>Generally the whole time series is used for the image plots, however, also only a range of run numbers can be selected. <BR> <LI>The size range and smoothing in t- and d-direction is also selectable. <BR> <LI>The image plots can also be normalized to the mass spectrum mass concentrations. <BR> <LI>In order to avoid negative numbers all negatives can be set to zero. </FONT></LI></UL> <P></P><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=SizeDependMS>Size Dependent Mass Spectra </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>Size dependent mass spectra will be calculated for a user-selectable run number interval.<BR> <LI>The size bins need to be selected in a table (after pressing the ‘Choose size bins’ button) in the format 20-200, 200-500, …. <BR> <LI>If selected, the mass spectra will be normalized to the according average MS mass spectrum (which needs to be calculated first). <BR> <LI>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. <LI>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. <BR> <LI>In addition, into every mass spectrum a pie chart is plotted with the relative contribution of the different species to the individual size bins. </FONT></LI></UL> <P></P><FONT face=" Arial"><BR> <H3><FONT face=" Arial"><A name=Features>7. Additional Features (v1.28)</A></FONT></H3><FONT face=" Arial"><A name=Features></A></FONT><FONT face=" Arial"></FONT> <P><FONT face=" Arial"><B><A name=IEMacro>IE Calibration Macro </A></B><BR></FONT></P> <UL><FONT face=" Arial"> <LI>After having performed an IE calibration in MS mode, you can process it with help of the included IE Calibration Macro.<BR> <LI>Load the IE calibration runs (and only these) as usual.<BR> <LI>Calculate a time series for Nitrate.<BR> <LI>Run the 'IE Calibration' macro from the macros menu.<BR> <LI>Enter the values for the used DMA size and the current SI signal intensity.<BR> <LI>The calculated IE and the mean AB signal will be printed into the history.<BR></A></FONT></LI></UL><FONT face=" Arial"><BR> <H3><FONT face=" Arial"><A name=Troubleshooting>8. Troubleshooting </A></FONT></H3><FONT face=" Arial"><A name=Troubleshooting></A></FONT> <UL><FONT face=" Arial"><A name=Troubleshooting> <LI>Size distribtuions are not displayed correctly (i.e. they are negatives or somehow shifted)<BR>Very likely you need to change the DC markers: <UL> <LI>Go to the function called 'Get_Parameters' and search for 'dc_front_1 = '<BR> <LI>Choose your DC markers according to the number of TOF spectra acquired (type 'print nbr_tof_spectra' to the command line to see what this number is).<BR> <LI>Example: If you have 260 TOF spectra (i.e. 260 size bins in the size distribution), usually dc_front_1 = 20, dc_front_2 = 50, dc_back_1_in = -20, dc_back_in_2 = -5 will work.</LI></UL></A></FONT></LI></UL> <HR> <FONT face=" Arial"><A href="http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFManual/index.html">Back to Table of Contents </A></FONT></FONT></FONT></FONT></DIV> <script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> </script> <script type="text/javascript"> _uacct = "UA-251251-1"; urchinTracker(); </script>