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1. GLITTER User s manual On line Interactive Data Reduction for the LA ICPMS Microprobe Esm van Achterbergh Chris G Ryan William L Griffin CONTENTS 1 INTRODUCTION 2 OVERVIEW 2 1 Terminology 2 2 Structure 2 3 Data Selection The Review window 2 4 U Pb dating 2 5 GLITTER Simple On Line Analysis 3 GETTING READY 3 1 Installing GLITTER Step 1 Close all open applications Step 2 Install IDL Step 3 Licensing IDL Step 4 Install GLITTER Step 5 Create a GLITTER shortcut on the desktop Step 6 Run GLITTER 3 2 Creating Readable Datafiles Perkin Elmer ELAN 5100 Perkin Elmer ELAN 6000 Perkin Elmer ELAN 6100 ThermoFinnigan Element and Element 2 Hewlett Packard HP 4500 Agilent 7500 Micromass VG PQII The Generic Spreadsheet Format 3 3 Adding Data for Additional Standard Reference Materials Step 1 Create a new text file Step 2 Edit the Alias txt File 4 GETTING STARTED 4 1 Example 1 Element concentrations Mode Step 1 Creating the right output file step 2 Run GLITTER Step 3 Set the analytical mode Step 4 Select the ICP MS device Step 5 Load the data Step 6 Identify and enter the internal standard values Step 7 Select integration intervals Step 8 Save the data Step 9 Update the dataset 4 2 Example 2 Isotope ratio mode 11 11 13 13 13 13 13 14 I5 15 16 16 16 17 18 20 20 21 23 23 24 24 25 28 28 28 29 29 29 29 29 31 31 32 33
2. Next button IDL now needs to be licensed the details for this are in the paperwork that accompanies GLITTER Click Yes to license IDL now Step 3 Licensing IDL If you have already exited the installation program and licensing wizard click the Windows Start button and select All Programs RSI IDL 6 1 License Product Licensing Enter evaluation licenses for j Research systems products Request a permanent Node locked or Floating license enter a license of this type or view and modify an existing license Help Exit Display the Product Licensing dialog Click Permanent and then License from the Permanent Licensing dialog Permanent Licensing Gather machine and user information hecessary to request a permanent license Send a request to obtain a license Enter or modify permanent licensing Information Help Exil Follow the instructions to complete licensing using the key obtained from RSI by following the instructions of MRL sales glitter gemoc com Step 4 Install GLITTER Copy the Glitter directory from the GLITTER CD to the hard drive An example l location is C Glitter Table 1 contains a list of files required to run GLITTER that e are supplied in the Glitter directory on the CD If any of these are missing except eesk the device dependent files marked in Table 1 contact technicalsupport gglitter gemoc com Tab
3. Plot window GLITTER runs in a different analytical mode when calculating ages from zircons this mode is activated by clicking the Isotope ratios button on the GLITTER splash page introduction window see Section 5 1 No internal standard values are required and special signal selection options are provided For example Jackson et al 2004 showed that significant U Pb fractionation necessitates the selection the same part of the signal relative to the rise time of the signal for standard analyses and unknowns This can be done in GLITTER by selecting the option via a droplist in the Options window Data are displayed as single isotopes or as isotope ratios in the Review window and isotope ratios age estimates and one sigma uncertainty estimates ratios and ages can be displayed in the table and exported to a ASCII text file The position of the analyses on the Concordia diagram can be shown in the Plot window 2 5 GLITTER Simple On Line Analysis On line analysis requires an initial Load Data step to identify the active file after which each analysis 1s reduced as soon as data acquisition is completed by clicking the Update button in the main GLITTER window The first results will be calculated as soon as one standard and one sample have been loaded With each additional standard analysis the data are instantaneously adjusted to take account of changes in the analytical conditions Wi
4. button in the FILE menu to save data tables to an ASCII text file any filename is acceptable The default export option is a comma delimited file with the extension csv but space tab and double quotes can also be selected as delimiters in which case the file is automatically saved with the extension txt Step 9 Update the dataset During on line analysis data are dynamically updated as soon as the each analysis 1s completed by clicking the Update button The latest analysis is added to the dataset Simply enter the appropriate internal standard value if required as Step 6 above select the correct integration intervals as Step 7 above and save the new data as Step 8 above to update the gli file as well The Review and Plot windows can remain open during the repetition of these steps 36 5 REFERENCE THE WINDOWS ONE BY ONE 5 1 The Splash page The GLITTER splash page appears on the screen as a visual introduction to GLITTER However it also serves an important purpose in setting the analytical mode in which GLITTER will operate Two buttons allow the user to chose between the calculation of simple element concentrations or the determination of isotopic ratios A click on either of the buttons will dismiss the splash page and activate the main GLITTER window 5 2 The GLITTER window This is the main window and the majority of the operations are carried out from the menus that appear at
5. 18 881 BE 4 499 20 0020142 0283 20 86081406881 PB BHHO9284545 7692 18 HAT HAAG 007 5 249 28 882814520283 15 BBHBB 875 0885 38 0030673180637364 60 0 5 999 28 8828145280283 38 808880031588833 548 0854505651132 8 18 80818036 6 7549 28 882814520283 28 8080801580888801 280 002015420283 28 8028152 8283 F499 28 86201420283 35 HBH0D542875053 78 0807172235795 106 0010036 BE 8 240 3B8 883831886365 28 80081400081 40 66485641192 18 8818836087 8 0990 18 881883588711 38 686888315 00033 F0 88363918 66964 60 28 88281 9 7499 68 6806126625528 18 0006003500061 60 0 0 10 499 10 061003736 00711 1060 00000375 88881 38 80803831886365 18 8818036 11 249 20 0020142 0283 30 000603150003733 0 00 12 6 625528 106 00610076E 11 999 20 86201426283 15 0006007875064 16 8818836 88711 8 18 BBTHE 12 7459 480 00405641132 306 0000631500033 7 0 007172234795 0 0 13 499 40 00405641132 30 0000631500033 HA 00405641132 0 0 14 249 60 15 000007875004 40 66465641192 106 0016036 00711 6 4 Figure 9 A simple spreadsheet style format for importation of time resolved data in GLITTER as viewed in the text editor Notepad Note the two lines of important header information and the comma used as a delimiter 3 3 Adding Data for Additional Standard Reference Materials GLITTER s data library contains information regarding the values of the standard reference materials that are used routinely during analysis
6. Standards window Enter the dwelltime in units of milli seconds ms and press Enter or select Multiple dwells if necessary and proceed to the dwelltimes popup window The Standards window can be called at any time during the session if changes are required to the internal standard by clicking the selecting Standards from the WINDOW menu Step 7 Select integration intervals GLITTER initially calculates the results using a set of default integration intervals which are derived using a simple algorithm These should by no means be viewed as the final or best selections Users are urged to initiate the Review window from the WINDOW menu and to re select the integration intervals for background and signal for each analysis Two displays appear in Review Fig 2 containing the time resolved laser ablation signals on an analysis by analysis basis The analysis to be displayed in the draw area is selected by a mouse click in the list on the left of the window or by clicking the Next or Previous buttons at the bottom of the Review window The top display is a pixelmap of all isotopes or isotopic ratios analysed with intensity shown as colour brightness black to blue means little or no counts yellow to white means high counts The bottom display shows one isotope or ratio at a time selectable by the horizontal green marker on the pixelmap or from the left hand droplist below th
7. window without providing or changing the internal standard identity or values No calculation or re calculation is carried out when this button 1s clicked When in isotope ratio mode When GLITTER operates in isotope ratio mode internal standards are not required and therefore the IS droplists do not appear and no values need to be entered in the table Instead details of the rise time laser on are given in the table in units of replicates and seconds Analyses of standard reference materials if recognised by GLITTER will be marked with an asterisk 1n the table If a standard analysis 1s not recognised by GLITTER click on the row label that contains that analysis to activate it as a standard another click on the row will de activate 1t The calibration values reference material that were used appear in the droplist in the window and can be changed if required by making another selection in the droplist The main purpose of this window when in isotope ratio mode is to set the dwelltime for those ICP MS devices where the dwelltime is not written to the datafile It must 48 be entered manually by the user in units of milli seconds in the text box popup table that appears in the Standards window The rise time replicate not rise time second can be edited in the Standards window if it appears that GLITTER has not detected the correct rise time e g if a strong inclusion peak is encountered 49 5
8. Button The Close button appears below the primary droplist A mouse click on the Close button will close the Plot window causing it to disappear from the display 63 5 6 The Options Window The Options window allows the selection of customised calculation options It appears when Options is selected from the WINDOW menu Some elements of the Options window depend on the mode in which GLITTER is operating as indicated in each section below The Yield Interpolation droplist This droplist applies both to element concentration and 1sotope ratio mode The type of interpolation that is used to derive the yield ratios for the unknown elements in the sample analyses 1s selected here The results of the selection of a yield interpolation can be viewed in the Plot window Run Quality Control must be selected in the primary droplist and Std Yield Ratios must be selected in the secondary droplist see section 5 5 The Standard Yield Ratio for isotope i at standard analysis n 1s given by Yieldi Yieldis where Yield Yield for the internal standard at n The yield ratio interpolation options as determined by the selection in this droplist include An average yield across all standard analyses To choose this option at least one standard or one group of standards has to be analysed This is the default setting at the start of on line data reduction when only a few stan
9. Chondrite elemental abundances nist 18 old txt 618b HIST6 18b nist 16b HIST 616b nist 18b HBS616b HBS 610b nbs 16b nbs 616b HIST 618 S88 ppm glass Norman et al 1996 nist 11 txt 611 HIST 11 nist 11 HIST 611 nist 611 NBS611 NBS 611 nbs 11 nbs 611 HIST 611 500 ppm glass dmm wafer Figure 10 The appearance of the alias txt file Lines and text that appear in red do not occur in the file but have been added here to describe the elements of the file To add information for a new standard the following lines have to be typed at the bottom of the file starting at line 14 Line 14 The name of the txt file created in Step 1 above for example my new standard file txt no spaces allowed Line 15 All aliases by which this new standard will be known for example mystandard MYSTANDARD myfile MYFILE newstandard NEWSTANDARD Note that there are NO spaces between the characters for each alias and that different aliases are separated by a space It is a good idea to enter all the aliases in upper and lower case since GLITTER s search for these strings is case sensitive These alias strings are used as the standard analysis ID s in the acquisition software for example the analysis ID std 1 mystandard will use the new standard as the standard reference material For more detail how this 1s used see sections 4 1 and 4 2 Line 16 A label string by which the standard will be identified in the Stan
10. Currently values for the NIST610 glass after Norman et al 1996 and Pearce et al 1997 and the NIST61 1 and NIST612 glasses after Pearce et al 1997 are available and can be viewed and changed by opening the relevant txt file see Table 1 above in a simple text editor such as Notepad However it is more than likely that this database is insufficient for many users and additional standard reference materials will be needed To add this data two important steps have to be followed Step 1 Create a new text file Create a new txt file that contains the values of the reference material The existing files e g NIST610 txt can be used as a template The new file has to comply with the following guidelines 24 It must have the extension txt It must NOT contain any header information It must consist of two columns the first contains the element pneumonic case sensitive and the second contains the corresponding concentration of the particular element as a floating point number 1 e there MUST be a decimal place or a dot e after the number For example 455 and 455 0 are correct 455 is incorrect The columns have to be separated by a tab or space or both It must NOT contain any compound molecules e g Al Os is incorrect Al is correct All values have to be in units of ppm including major elements The order in which the elements are listed in the file 1s unimportant Step 2 Edit the Alias txt Fi
11. GLITTER will use the values of Norman et al 1996 28 Step 2 Run GLITTER Double click the GLITTER icon on the desktop or if no shortcut appears on the desktop double click the glitter sav file in the appropriate directory using the Windows Explorer Step 3 Set the analytical mode The GLITTER splash page appears on the screen with two buttons below the picture If you want to do simple determination of element concentrations click the Element concentrations Mode button This will activate the appropriate plots and calculation procedures for the data analysis To change the mode during a session you will have to exit GLITTER and start again Step 4 Select the ICP MS device DEVICE A droplist appears below the table in the main GLITTER window which allows you to select the ICP MS device that you are running on The default is the Agilent 7500 but other options include the Perkin Elmer ELAN 5100 ELAN 6000 ELAN 6100 Finnegan Element and Element II Micromass VG PQ2 and a generic spreadsheet format Step 5 Load the data In the GLITTER window click the Load data button upon which a file requestor will appear Datafiles with the appropriate extension e g prn for ELAN 5100 output rep for ELAN 6000 output etc will appear in the requestor Click on the desired datafile and then click the Open button If data are arranged in directories e g HP4500 VG POIL double click on th
12. Step 1 Creating the right output file DEVICE The first and most important step in using GLITTER both for off line and on line data reduction is to create a readable file format This has to be done as outlined in section 3 2 and the procedure is different for each ICP MS platform currently supported by GLITTER Standard analyses can be identified with the string std and name of standard e g 610 Take care that the string std does not appear anywhere in the sample ID of the unknowns The string can appear either in upper STD or lower std case Standard analyses that are not labeled as such can be toggled on as a standard at any time during the session by selecting EDIT Toggle Standard ON The name of the reference material can be labeled in any one of the following ways std 1 610 STD6101 std NIST610 1 std 610 analysis number 1 etc except in the case of the HP4500 where sample names are limited to eight characters e g astd6 10 This labeling system allows GLITTER to detect which analyses were standards and which standard concentration values should be used in the calculation of trace element concentrations reference material values are stored in GLITTER s data library In this version of GLITTER the above notations will use the values for the NIST610 glass as published by Pearce et al 1997 If the character b is added to the labels above e g std 1 610b
13. Step 1 Creating the right output file Step 2 Run GLITTER Step 3 Set the analytical mode Step 4 Select the ICP MS device Step 5 Load the data Step 6 Set the dwelltime Step 7 Select integration intervals Step 8 Save the data Step 9 Update the dataset 5 REFERENCE THE WINDOWS ONE BY ONE 5 1 The Splash page 5 2 The GLITTER window The FILE menu The EDIT menu The DISPLAY menu The WINDOW menu The HELP menu The Table of Results The Device Droplist The Display Droplist The PPM Weight Option Buttons The Update Button Context Sensitive Help 5 3 The Standards Window The Reference Materials Droplist The Internal Standards Droplists element concentrations mode only The Dwelltime Text Box The Table of Internal Standard Values element concentrations mode only The Accept Button The Save Settings Button The Load Settings Button The Help Button The Cancel Button When in isotope ratio mode 54 The Review Window The Sample List The Draw Windows The Isotope Droplist The Ratios Droplist The Linear Log Square root Droplist When in isotopic ratio mode The P Button The F Button The Set Marks Button The Save Button The Undo Button The Previous Button The Next Button The Help Button The Close Button Context Sensitive Help 5 5 The Plot Window The Draw Area 33 34 3
14. at least one standard or one group of standards has to be analysed This is the default setting at the start of on line data reduction when only a few standards have been analysed A linear fit across all standard analyses To choose this option at least two standards or two groups of standards have to be analysed If fewer than two standards standard sets have been analysed GLITTER alerts the user to this fact and reverts to using the average yield across the standards This is the recommended setting for all data analysis except where special circumstances indicate atypical drift has taken place A quadratic fit across all standard analyses To choose this option at least three standards or three groups of standards have to be analysed If fewer than three standards standard sets have been analysed GLITTER alerts the user to this fact and reverts to using a lower order polynomial It 1s strongly recommended that this setting be only used where special circumstances indicate atypical drift has taken place A cubic fit across all standard analyses To choose this option at least four standards or four groups of standards have to be analysed If fewer than four standards standard sets have been analysed GLITTER alerts the user to this fact and reverts to using a lower order polynomial It 1s strongly recommended that this 60 setting be only used where special circumstances indicate atypical drift has taken place The selection o
15. the user 1s alerted to this fact by a pop up message when the dataset is loaded This 5 cut off level can be edited in the Options window by either entering the desired value in the white text entry field provided or by using the slider to obtain the desired number Note however that the fractionation test is only carried out once when a dataset is loaded If the cut off level is changed during a session the data have to be loaded again to check for fractionation outside the new cut off The Close OPTIONS window Button A mouse click on the Close OPTIONS window button will close the Options window 68 6 THE THEORY BEHIND THE CALCULATIONS 6 1 Trace Element Concentrations Trace element concentrations are calculated using the following equations conc CPSnij abundance yieldni 1 where conc the concentration of element i in analysis n CPSnij the mean count rate background subtracted of isotope j of 1 in analysis n abundance natural abundance of isotope J yield cps per ppm of element i in analysis n The yield of element 1 in analysis n is determined by yield yieldns Int yieldn yiel das IN where yields cps per ppm of the internal standard s in analysis n std Int yield yields the ratio of the yield of element i in analysis n to the yield of the internal standard s in analysis n interpolated over the standard analyses 6 2 One Sigma Error The
16. Output button Select the output options as shown in Fig 3 and take care to give the output file the extension rep For off line analysis select the range of analyses of interest within the ELAN workspace and click the Reprocess button For on line analysis each analysis will automatically be written to the rep file as it reaches to completion unless the analysis is interrupted before all required readings have been registered by the ICP MS In this case you must select that particular analysis in the sample list and click Reprocess otherwise the data will not be written to file Runs that have not gone to completion are easy to recognize in the datasheet of the ELAN software as they appear in red font in the sample list Analyses that have run to completion and have already been written to file appear in black font Do not reprocess these latter analyses as it will cause duplication of data in the output file Report To File Send to File Send to Serial Port Port Report Options Template Report Filename c public my file rep Report Format File Write Option Include Titles Append _ Use Delimiter O Overwrite Use Separator O New Per Sample Figure 3 The appearance of the report options dialogue box to create the correct file format for GLITTER when using the ELAN 6000 Perkin Elmer ELAN 6100 Analyses obtained using the ELAN6100 are stored in separate files one per anal
17. Review window and how the calculations are performed The first selection allows the independent movement of all the markers which is the default way in which GLITTER operates in element concentration mode However when analysing isotope ratios in particular the U Pb system used for dating some isotopes may fractionate significantly with time within a single analysis It 1s therefore important to select the same part of the signal relative to the rise time 1 e when the laser was turned on for the unknown and the standards Two options within the Marker Mode droplist allow this Firstly the marker positions for the unknowns can be moved independently of each other but the marker positions for the standard analyses are tied to these offset by rise time differences In other words each unknown analysis dictates which part of the signal in all the standard analyses will be used for the calculation of the yield ratios for that unknown Secondly all the signal markers can be moved together Thus if one marker is moved within an analysis of an unknown all the other markers for unknowns and standards will be moved to reflect this change offset to account for the different rise times The Background Interpolation Droplist This droplist allows the use of an interpolated background across all analyses and applies to both analytical modes By default GLITTER subtracts the integrated background at the beginning of a particular analysis fr
18. a little tedious at this stage To activate a cell select the cell with the mouse a correctly selected cell appears blue bordered by a dotted yellow line press Enter type the value and press Enter again Move to the next cell by using the arrow keys or the mouse and repeat the process Take care to enter the values correctly and delete any extra periods that may appear in the active cell while typing Upon entering the last value be sure to press Enter before clicking the Accept button The values of the internal standard s for all analyses 1f known can be supplied to GLITTER 1n advance at the beginning of an on line session to streamline the on line data reduction process This is done by simply typing ahead in the appropriate column even though no sample ID s will appear in the row title bars Once a particular sample has been analysed the value in the corresponding row will be used as internal standard and the sample ID will appear in the row title bar Upon clicking the Save button GLITTER does NOT write the internal standard values to file if 46 the corresponding sample has not yet been analysed i e if the row title bar is empty The Accept Button The Accept button appears in the bottom left of the window Click the Accept button once the internal standard s has have been identified using the droplists and all the values have been entered in the appropriate column i
19. contact Prof William L Griffin GEMOC National Key Centre Macquarie University NSW 2109 Australia International Tel 61 2 9850 8954 International Fax 61 2 9850 8943 Email technicalsupport glitter gemoc com 71 8 REFERENCES Fryer B J Jackson S E and Longerich H P 1995 The Design Operation and Role of the Laser Ablation Microprobe Coupled with an Inductively Coupled Plasma Mass Spectrometer LAM ICP MS in the Earth Sciences Canadian Mineralogist 33 303 312 Jackson S E Pearson N J Belousova E and Griffin W L 2004 The application of laser ablation inductively coupled plasma mass spectrometry LA ICP MS to in situ U Pb geochronology Chemical Geology 211 47 69 Longerich H P Jackson S E and Gunther D 1996 Laser Ablation Inductively Coupled Plasma Mass Spectrometric Transient Signal Data Acquisition and Analyte Concentration Calculation Journal of Analytical Atomic Spectrometry 11 899 904 Norman M D Pearson N J Sharma A L and Griffin W L 1996 Quantitative Analysis Of Trace Elements In Geological Materials By Laser Ablation ICPMS Instrumental Operating Conditions And Calibration Values Of NIST Glasses Geostandards Newsletter 20 p247 261 Pearce N J G Perkins W T Westgate J A Gorton M P Jackson S E Neal C R and Chenery S P 1997 A Compilation Of New And Published Major And Trace Element Data For NIST SRM 610 And NIST SRM 612 Glass Reference Materials
20. for a single isotope or isotopic ratio selected using the horizontal green marker in the top pixelmap display or the left hand droplist below the displays On the Y axis two numbers appear in the bottom left corner the minimum value of the axis 1s shown in the top left corner the maximum value of the axis 1s shown Note that the values represent the minimum and maximum values of the Y axis NOT the minimum and maximum values of the data The values will change by clicking the Log Lin Square root droplist or by selecting another isotope to display in the window On the X axis a single number appears in the bottom right corner the maximum number of readings replicates that were measured for that particular analysis 50 The calculation of trace element concentrations requires the selection of a background and a signal area for integration Four vertical green markers appear on the displays to allow this From left to right the markers indicate the lower background limit the upper background limit the lower signal limit and the upper signal limit respectively The quality of the results depends on the accurate selection of these areas and it is the single most important step in successful data reduction of laser ablation ICP MS data The markers are moved by clicking on or near the required marker and with the left mouse button depressed dragging the marker to the required position Upon release of the mouse button GLITT
21. list of reference materials appear in the secondary droplist and are read directly from the alias txt and alias ratio txt files see section 3 3 as created by the user This option has the advantage of checking the quality of the data on line with the analysis of secondary standards e g BCR 1 etc Select the analysis of the secondary standard in the main GLITTER window and its values from the secondary droplist on the Plot window Active standard analysis are not plotted until they are toggled off and being treated as unknowns in the main GLITTER window select the relevant standard analysis and then select EDIT Toggle Standard OFF The y axis is scaled dynamically to the currently selected analysis Best results should scatter around 1 and GLITTER 62 draws a heavy dashed line at 1 to help guide the eye Any values that fall outside 20 variation drawn either side of 1 by GLITTER in faint dotted lines indicates some serious problems with the instrument or the data that will need your attention The Print Button The Print button appears below the primary droplist This allows the data plotted in the drawing area to be printed directly to the default printer The Help Button The Help button appears below the primary droplist The Online Help window is called from this button and multiple copies of the Help window may be opened while reducing the data The Close
22. one sigma error estimates use VN counting statistics on the signal and background counts propagated through the equations An assumed 1 uncertainty relative on the elemental concentrations of the reference material and a 3 uncertainty relative on the values of the internal standard 1s propagated throughout the calculations These values can be changed or turned off completely by the user via the Options window 69 6 3 The Minimum Detection Limit The detection limit MDL at the 99 confidence level is determined by Poisson counting statistics MDL 2 3 2B where B is the total counts in the background interval 6 4 U Pb Age Estimates The age estimates are calculated from each of the isotope ratio pairs as follows assumes no initial common Pb age LN ratiot 1 X where ratio the 1sotope ratio of interest e g 20 pp U lambda the decay rate of the parent isotope in ratio Age from the 207Pb 9pb ratio is calculated by solving for t time in the equation 207Pp ppb 1 137 88 e D e t 1 where i the decay rate of SS Ay the decay rate of U 70 7 CONTACT INFORMATION For general inquiries please contact Dr John Roy Vice President New Wave Research Merchantek Products 47613 Warm Springs Blvd Fremont CA 94539 International Tel 1 510 771 3845 International Fax 1 510 249 1551 Email jroy new wave com For technical and software inquiries please
23. ro 4 Lu I i T i 5 I i Tr EY i e LL Jd ex a qd I 10 Analysis Run iuality Control E Print Help Close Figure 12 The Plot window showing the variation with time of the average background counts for each isotope solid lines and a linear interpolation selected from the Options window across all analyses for each isotope dashed lines Note for example that at the current analysis at the vertical grey line the interpolated background that will be used for Ni fourth set of lines from the top coloured green is lower than the measured background at that analysis 66 The Timed Save Droplist By default GLITTER saves the parameters of the current session 1 e the internal standard values marker positions etc to file with the extension gli every sixty seconds This is a safeguard against the loss of data during a computer crash However there may be some cases where this is undesirable and the timed save feature can be turned off using this droplist Setting the Uncertainty for the Standard Reference Material When calculating the l sigma uncertainty for each analysis GLITTER takes into account the uncertainty that is associated with the standard reference material used during analysis By default this 1s set to 1 relative error but can be changed to any desired value or set to 0 in one of two ways Enter the desired value in the white text entry field p
24. supplied the Standards window will appear requesting this information Context Sensitive Help In the lower part of the GLITTER window a framed text area appears which provides context sensitive on line help This means that information about some of the functions within the GLITTER window are displayed here by simply moving the cursor over the component for which help is sought When the cursor is not positioned over a particular component GLITTER displays the name of the currently loaded datafile in this frame 43 5 3 The Standards Window When GLITTER is operating in element concentrations mode the Standards window is an important step in data reduction However in isotopic ratio mode it purpose is more to give information and detailed user input is often not required Thus most elements of the window excluding the dwelltime text box and the buttons only apply to element concentrations mode A paragraph is added at the end of this section to described the function of the Standards window when in isotope ratio mode Note that the Standards window is modal which means that the rest of GLITTER cannot be operated while the Standards window 1s open The window is called at any time during a session by selecting WINDOW Standards The elements of the Standards window are The Reference Materials Droplist The Reference Materials droplist at the top of the window re
25. the main GLITTER window this rep file is required ThermoFinnigan Element and Element 2 Compatibility between the output from the ThermoFinnigan ICP MS systems and GLITTER is managed by the ELEMENT software suite Version gt 2 1 Contact ThermoFinnigan MAT in Bremen directly for more information A typical ThermoFinnigan LAM session consisting for example of 20 analyses is summarised in a header file with the raw data stored in separate datafiles one per analysis All files are simple comma delimited ASCII text the header file has the extension fin and the datafiles the extension fin2 If Finnigan ME is selected as the default device from the device droplist on the main GLITTER window GLITTER will search for this file The header file describes all the conditions common to a particular run and a list of filenames that point to the individual datafiles In an on line data reduction session the header file is dynamically updated as the run progresses The list of filenames does not include the path in order to allow the whole set to be moved freely between directories and computers GLITTER will simply assume that the header file and the raw datafiles are stored together Fig 5 below 1s an example of a header file and Fig 6 of a typical datafile El GlitterTest FIN Notepad File Edit Search Help Finnigan HAT ELEMENT Wednesday Hay 18 2000 14 1718 59 6168 nyi SequenceName Commenti Header Comment Commenta C
26. the top of the window Some controls are also located beneath the table These and the menus are discussed below The FILE menu DEVICE Standard file operations are carried out from the FILE menu Load Data This is the first important step in reducing data on line and off line Clicking on this button pops up a dialogue window asking for the filename of the raw data to be imported Depending on the current ICP MS platform files with the appropriate extension e g prn for ELAN 5000 rep for ELAN 6000 etc are displayed in the list Once a selection has been made click Open Note to users of the HP 4500 Agilent7500 and VG PQII In the case of the HP 4500 Agilent7500 and VG PQII as well as the generic spreadsheet format an entire directory 1s loaded and it 1s this directory that has to be selected Note that due to a bug in Windows you must select the directory with a double click and then a click on Open A single click simply won t work If new data are loaded the Standards window appears automatically section 5 3 requesting information regarding the internal standards element concentrations 37 mode only otherwise the details of a previously saved dataset are restored from a previously saved gli file and the user is returned to the main window When loading a previously analysed dataset it 1s not necessary to load the gli file manually as GLITTER will find it automatically
27. when GLITTER 1s running in isotope ratio mode When the marker positions for the standard analyses are tied to the marker positions for the individual unknown analyses see section 5 6 the Options window an entire matrix of marker positions exists for each standard analysis Thus to view the marker positions relating to a specific analysis but still viewing the signal for the standard analysis in the window select the analysis from the right most droplist below the draw areas Moving any markers while viewing the signal for a standard analysis will not modify the values for the selected analysis in the droplist Note that if an unknown analysis 1s the currently selected analysis this droplist is irrelevant and disappears The P Button The time resolved signals for the currently selected analysis are printed to the default printer by clicking the P The signals for each isotope are displayed separately and are arranged in two columns paper in portrait orientation with the pixelmap display repeated at the top of each column The current marker positions and plotting mode e g linear or log are retained in the print out and up to ten isotopes are printed per page The F Button A click on the F button will apply a sliding median filter 3 channels at a time to the selected isotope of the current analysis This has the advantage of filtering unwanted single channel spikes and allows the selection of smoother sig
28. 4 34 34 34 35 36 36 37 37 37 37 39 40 4 4 41 42 42 42 42 43 44 44 44 45 45 47 47 47 48 48 48 50 50 50 5 5 5 52 52 52 53 53 53 54 54 54 54 54 55 55 The Primary and Secondary Droplists The Print Button The Help Button The Close Button 5 6 The Options Window The Yield Interpolation droplist The Marker Mode Droplist The Background Interpolation Droplist The Timed Save Droplist Setting the Uncertainty for the Standard Reference Material Setting the Uncertainty for the Internal Standard Setting the Fractionation Test Cut Off The Close OPTIONS window Button 6 THE THEORY BEHIND THE CALCULATIONS 6 1 Trace Element Concentrations 6 2 One Sigma Error 6 3 The Minimum Detection Limit 6 4 U Pb Age Estimates 7 CONTACT INFORMATION 8 REFERENCES 55 63 63 64 64 65 65 67 67 67 68 68 69 69 69 70 70 T1 72 1 INTRODUCTION The laser ablation ICPMS microprobe LAM ICPMS was introduced in the early 1990s largely through the work of geologists especially the group at Memorial University Newfoundland and is now becoming an important technology The capability for rapid sensitive spatially resolved in situ trace element analysis will have the same impact on the geosciences and material sciences as the spread of the electron microprobe EMP did in the 1970s Today the EMP is found in nearly every significa
29. 4 The Review Window selecting the correct background and signal intervals for use in the calculation of results 1s a vital step in successful analysis of the time resolved laser ablation signals The elements of the Review window are The Sample List The sample list appears on the left of the Review window It contains a list of the samples in the currently loaded dataset in the order in which they were written to the datafile directory by the acquisition software The analysis that 1s currently displayed in the draw windows is highlighted in the sample list The current selection can be changed by clicking on any analysis with the mouse or clicking on the Next or Previous buttons at the bottom of the window An analysis with asterisk 1ndicates a standard analysis and a question mark indicates that the analysis 1s hidden in all plots that appear in the Plot window see the EDIT menu on the main GLITTER window The Draw Windows The time resolved laser ablation signals are viewed in two ways in the main display area of the Review window Fig 2 The top display consists of rows of pixels each representing the variation of the signal with time for a single isotope or isotopic ratio with intensity shown by colour brightness This gives direct visual indication of any spikes in the data or heterogeneity in the samples for one or more isotopes The bottom spectral display shows the time resolved signal
30. 8888 11811 0HAHHA 49544 B 8 9548808 6886 8888808 55808 AAL 11811 000000 49544 6606 1 888888 11813 888888 55808 BE Raw counts data 55HBB8 d0888888 2752 2 608 1 286888 6886 888888 16511 888888 15511 HAHAHA EL 88 00A0HAHH 38533 BH 1 331888 9511 8888808 55808 888888 11811 888888 55 88 888888 6 0555 006g 1 457888 9818 888888 11811 8888808 22022 000000 5500 000000 27522 BOE 1 58388H8 75808 8888808 22022 B8808888 38533 088888 5588 006000 77077 BH 1 708888 11813 8880880888 11811 888088088 228022 88080008 55 88 000000 15055 B Er Figure 6 An example of a fin2 file created by the ThermoFinnigan Element Element 2 acquisition software It contains the raw counts data for the first analysis called standardl fin2 Explanatory comments have been added in red they do not form part of this file The detector mode for each isotope is not read by GLITTER but has been added to the file for the user s information where 0 Pulse mode 1 Analog mode and 2 both 19 Hewlett Packard HP 4500 Readable data formats using the HP4500 are created using the tabchart macro which must be obtained directly from Agilent The macro will run automatically after each analysis if the command is added to deuser mac file deuser mac must be edited separately for each method file that is used It resides in the Hpchem methods directory Open the deuser mac file and between the lines NAME CustomAnalysis and
31. ER detects that a new selection has been made and the data are automatically updated in the results table and in all plots displayed on the screen at the time to reflect this change The current position in units of replicates of the marker being moved is shown in a label to the left of the isotope droplist The Isotope Droplist The left hand droplist below the draw windows shows the identity of the isotope or isotope ratio currently displayed in the window The current isotope can be selected from this droplist or by moving the horizontal green marker up and down in the upper pixelmap display The Ratios Droplist The spectral display in the lower draw window can appear as raw counts or as counts relative to the internal standard IS by selecting an option from this droplist Ratios can also be displayed corrected for relative isotope abundance where the abbreviation AN means abundance normalised Ideally time resolved spectra displayed relative to the internal standard should be perfectly flat This display option is therefore a useful tool in assessing the quality of the data for a specific isotope and whether or not the signal is fractionated relative to the internal standard The Linear Log Square root Droplist The scale on the Y axis can be displayed in linear logarithmic or square root units by selecting an option from this droplist 5 When in isotopic ratio mode An additional droplist appears
32. Geostandards Newsletter 21 p115 144 12
33. REMOVE CustomAnalysis type tabchart Data for each analysis is stored within directories rather than within a single file and the name of the directory will be same as the sample name file name given at the start of the run Within each of these directories there will be two files called tabchart csv and qcdetail txt The former contains the time resolved data and the latter the time of creation used by GLITTER to order the analyses If GLITTER cannot find qedetail txt in any of the analyses for a particular run this may happen if a run is stopped before reaching the required number of replicates and a tabchart csv file is created manually the analyses will be ordered alphabetically It is very important that analyses are loaded into GLITTER in the order in which they were analysed otherwise GLITTER cannot accurately correct for instrumental drift It is therefore up to the user to name files alphabetically or numerically if there is any chance that the qcdetail txt files will not be created Data that belong to a common run are grouped together in a higher directory and the gli file created by GLITTER will have the same name as this directory If problems arise with the naming sequence of files the directory ies can be renamed in Windows Explorer provided that the first line within each relevant tabchart csv file s opened in Notepad is renamed as well Agilent 7500 Readable data formats using the A
34. Simply load a datafile directory as usual When data are being processed on line use FILE Load Data only once i e at the start of the session The filename selected at that time is stored in memory and new data are loaded on an analysis by analysis basis by clicking the Update button in GLITTER Save Details regarding the current GLITTER session are saved to a file with the extension gli using this option A dialog window appears prompting for the filename and it is recommended that the data be saved using the same filename as the current datafile the default For example if the datafile jn26b rep is currently being analysed save the details of the session to jn26b gli This will allow GLITTER to correctly restore the parameters of jn26b e g internal standard values marker positions etc if loaded again at a later session This option is analogous to the Save buttons in Standards and Review All three Save buttons in the GLITTER Review and Standards windows save ALL the details of a session marker positions IS isotope s and IS values not isolated or selected parameters It 1s therefore important to be aware that if this button is clicked in Review to save marker settings the latest internal standard values in Standards are written to disk as well and vice versa Export Select FILE Export to save the data to an ASCII text fil
35. alues should be entered in the appropriate column see section 5 2 for more details For some ICP MS instruments the dwelltime 1s not written to the datafile and it must be entered manually by the user in the text box that appears in the Standards window Enter the dwelltime in units of milli seconds ms and press Enter or select Multiple dwells 1f necessary and proceed to the dwelltimes popup window Typing the IS values in the table provided is unfortunately a little tedious at this stage an IDL and Microsoft Windows problem To activate a cell select the cell press Enter type the value and press Enter again Move to the next cell by using the arrow keys or the mouse and repeat the process Once all the values have been entered excluding the values for the standards GLITTER enters these automatically click the Accept button The Standards window disappears the results are calculated and the data appear in the results table Click any of the Save Settings Save buttons in the GLITTER Review or Standards windows to write the values of the internal standard s and the current marker settings to a file with the same name as the datafile but with the extension gh Step 8 below 30 The Standards window can be called at any time during the session if changes are required to the internal standard by clicking the selecting Standards from th
36. analyses are 1dentified by an asterisk appearing next to the sample name in the row heading These can be toggled off and on by first selecting the row in which the analysis of interest appears and then selecting on of the toggle options under the EDIT menu A question mark next to a sample name indicates that particular analysis 1s hidden from the display in the Plot window also set using the EDIT menu The data in the table are dynamically linked to the Review and Plot windows This means that 4 a If marker positions are changed in the Review window the table of results is automatically updated to reflect these changes If the marker positions of a standard analysis are changed all other analyses are affected If the marker positions on a sample are changed only the results of that analysis are affected b The selected highlighted analysis number in GLITTER is also the selected analysis number in Review and Plot and vice versa The Device Droplist DEVICE The Device droplist selects the current ICP MS system in use and it is a first and important step in using GLITTER The default is the Agilent 7500 but other options include the Perkin Elmer ELAN 5100 ELAN 6000 ELAN 6100 Finnegan Element and Element II Micromass VG PQ2 and a generic spreadsheet format The Display Droplist The Display droplist is used to select the type of data that appears in the tab
37. ard reference materials can be turned off by selecting the standard analysis in the results table click on the row which contains the analysis and then selecting EDIT Toggle Standard OFF The standard analysis will then be ignored in the calculation of the interpolated yield and will simply be treated as an analysis of an unknown Hide current analysis and Reveal current analysis The currently selected analysis can be hidden from the graphics display in the Plot window by selecting EDIT Hide current analysis A hidden analysis is identified by a question mark next to the sample name in the table and this can be a useful feature when a particular analysis is distorting the X and Y axes of a chosen plot Note that the analysis cannot be deleted from the datafile and it will be exported along with the rest of the data To view the analysis again select EDIT ee Reveal current analysis The DISPLAY menu The DISPLAY menu is used to select the type of data that appears in the table of results e g concentrations error estimates etc The list of options that appears under DISPLAY are self explanatory and details on how these values are calculated other than the raw data are given in Section 6 Note that the DISPLAY menu is linked to the Display droplist below the table and whichever datatype is selected under the menu will also be selected and displayed in the droplist 40 The WINDOW men
38. ars in bright green The Plot window is linked to the main GLITTER and Review windows and the selected highlighted analysis 1n the latter windows therefore appears as the selected highlighted analysis in the Plot window C Backgrounds The magnitude of the background signals 1s displayed in the draw window when this option is selected An average background for each isotope is displayed on the Y axis in units of counts and the analysis number is shown on the X axis Therefore each coloured line on the plot represents the variation in the background signal with time through the run for a particular isotope The currently selected analysis appears as a vertical grey line and because the Plot window is linked to the other windows this analysis 1s also the currently selected analysis in the Review and GLITTER windows D Ablation rates A relative measure of the amount of ablated material for each analysis 1s shown when this option 1s selected The yield cps per ppm for the internal standard across all analyses 1s shown on the Y axis The currently selected analysis appears as a vertical grey line and because the Plot window is linked to the other windows this analysis 1s also the currently selected analysis 1n the Review and GLITTER windows E Concentrations The concentration values in units of ppm are displayed in the draw area when this option 1s selected All analysis in
39. cluding the values for the standard analyses are shown Concentrations are plotted on the Y axis and elements are plotted on the X axis This plot allows the user to view the concentration of all elements since the chondrite normalised diagrams sometimes omit elements that do not appear in any of the currently available display lists All data are plotted in light grey with the exception of the currently selected analysis which appears in bright green The Plot window is linked to the main GLITTER and the Review windows and 59 the selected highlighted analysis in the latter windows appears as the selected highlighted analysis 1n the Plot window F Std Yield Ratios The variation of yield cps per ppm for each element with time 1s displayed in the draw area when this option is selected The Standard Yield Ratio the Y axis for isotope i at standard analysis n 1s given by Yield Yieldis where n is plotted on the X axis and Yield Yield for the internal standard at n For each isotope two lines are drawn A solid line simply connects the points for each standard analysis obtained by the above expression and a dotted line shows the interpolation that is used to calculate the yield ratios for the unknown elements in the sample analyses GLITTER allows various fitting options selected from the Options window Section 5 6 An average yield across all standard analyses To choose this option
40. d by GLITTER are covered in this manual operations that apply only to specific platforms are identified with a Device icon in the margin 2 2 Structure The structure of GLITTER is shown in Fig 1 GLITTER consists of five main interactive user interfaces windows 1 The GLITTER window containing the main menu options and the table of results 2 The Standards window calling for the user to input the identity and values of the internal standard 3 The Review window s where the time resolved laser signals are viewed and integration intervals are selected by the user 4 The Options window which selects customised calculation options e g the type of yield interpolation cps ppm across the standard analyses the background fitting procedures and the magnitude of the error associated with the internal standard values 5 The Plot window s where data are visualised in various ways There is also a sixth window the Help window s It is not interactive but provides on line help with the organization and use of GLITTER One or more copies of the Help window can be open at a time to provide simultaneous help on different topics The GLITTER and Review windows and one or more versions of the Plot window typically remain on the screen during a session whereas the Standards Options and Help windows only appear when needed or when called by t
41. d for most of the samples and Al27 is used for the remainder of the samples When this option is selected three minor droplists appear where these isotopes are identified Note that the selected isotopes in the minor droplists also appear as the column headings in the internal standards table see below and in the current version of GLITTER the values are translated to weight oxide as most internal standards are derived from electron microprobe analysis of major elements The Dwelltime Text Box DEVICE some ICP MS devices do not output the dwelltime in the datafile e g ELANS5100 HP4500 If this is the case GLITTER detects if dwelltimes are missing from the datafiles an extra option will appear below the internal standards droplists where the dwelltime s can be entered in units of milli seconds ms If all isotopes were analysed using a single dwelltime select the radio button next to the words Equal dwells and enter the dwelltime in the text box provided In the case of different dwell times for different isotopes select Multiple dwells and then click the Set dwell times button A pop up window will appear where the dwell times for each isotope can be entered separately To facilitate the process select any blocks of data which have the same dwelltime and click Fill Down The selected part of the table will be filled with the value which appears in the first cell of the selection The Table o
42. dards window see the Reference Materials droplist in section 5 3 This string may contain spaces between characters for example This Standard is for illustration purposes only As an example this information was added to the alias txt file as shown in Fig 11 26 The header the number of standards incremented by one B alias txt Aotepad File Exft Search Help 5 nist 1lB txt 618 HIST618 nist616 HIST 618 nist 616 HBS5618 HBS 618 nbs616 nbs 616 HIST 610 58 ppm glass Pearce et al 1997 chondrit txt Chondrite C1 Chondrite elemental abundances nist lB old txt 618b NIST616b nist l b NIST 616b nist 616b NBS616b HBS 618b nbs l8b nbs 1t b HIST 618 S68 ppm glass Norman et al 1996 nist611 txt 611 HIST 11 nist 11 HIST 611 nist 611 NBS611 HBS 611 nbs 11 nbs 611 HIST 611 S66 ppm glass dmm wafer my new standard file txt y l The new standard mystandard HYSTAHDARD myfile HYFILE newstandard HEUSTRHDRRD i information This standard is for illustration purposes only Figure 11 The appearance of the aliastxt file after the information for my new standard file has been added 3 lines of new information at the bottom of the file and the first line modified to reflect the addition Lines and text that appear in red do not occur in the file but have been added here to describe the elements of the file 27 4 GETTING STARTED 4 1 Example 1 Element concentrations Mode
43. dards have been analysed A linear fit across all standard analyses To choose this option at least two standards or two groups of standards have to be analysed If fewer than two standards standard sets have been analysed GLITTER alerts the user to this fact and reverts to using the average yield across the standards This is the recommended setting for all data analysis except where special circumstances indicate atypical drift has taken place A quadratic fit across all standard analyses To choose this option at least three standards or three groups of standards have to be analysed If fewer than three standards standard sets have been analysed GLITTER alerts the user to this fact and reverts to using a lower order polynomial It 1s strongly recommended that this setting be only used where special circumstances indicate that atypical drift has taken place 64 A cubic fit across all standard analyses To choose this option at least four standards or four groups of standards have to be analysed If fewer than four standards standard sets have been analysed GLITTER alerts the user to this fact and reverts to using a lower order polynomial It 1s strongly recommended that this setting be only used where special circumstances indicate that atypical drift has taken place The Marker Mode Droplist This droplist only appears when GLITTER is running is isotope ratios mode and selects the way in which markers are controlled in the
44. e WINDOW menu The Standards window will not appear if the dataset that 1s being loaded has been processed previously by GLITTER and the settings were saved to a gli file In this case the IS values and marker settings are automatically read from the gli file Step 7 Select integration intervals GLITTER initially calculates the results using a set of default integration intervals which are calculated using a simple algorithm These should by no means be viewed as the final or best selections Users are urged to initiate the Review window from the WINDOW menu and to re select the integration intervals for background and signal for each analysis Two displays appear in Review Fig 2 containing the time resolved laser ablation signals on an analysis by analysis basis The analysis to be displayed in the draw area is selected by a mouse click in the list on the left of the window or by clicking the Next or Previous buttons at the bottom of the Review window The top display is a pixelmap of all isotopes analysed with intensity shown as colour brightness black to blue means little or no counts yellow to white means high counts The bottom display shows one isotope at a time selectable by the horizontal green marker on the pixelmap or from the left hand droplist below the displays Other display options include the Raw Data Ratio to IS droplist and a Linear Log droplist More details of these options a
45. e any filename is acceptable The Export window appears and allows the user to choose which data should be written to the output file and how the data should be delimited The selection s is are made from the list of options a small tickmark inside the 38 white box circle next to the name of the option means that it is selected The default export option is a comma delimited file with the extension csv_ but space tab and double quotes can also be selected as delimiters in which case the file is automatically save with the extension txt A click on the Export button will write the data to the output file via another file requestor Any filename with the extension xt is suitable because this file will not be accessed by GLITTER again When opening the csv file for further off line data analysis a simple double click on the file is usually all that 1s required to open the file in the default spreadsheet program However if one of the other delimiters have been selected extension txt the file has to be opened via the spreadsheet program s import dialogue box Make sure to select the correct delimiter and in the case of the Space Tab option in GLITTER make sure to select both space AND tab as delimiters as well as the option to treat multiple delimiters as one Print Table Select FILE Print to print the results directly to the default printer The output will appear automatically in
46. e directory name and then click Open On line data reduction requires this step only once at the beginning of the run 1 e as soon as one standard and one sample have been analysed From here it will always load this file when data are updated Step 6 Identify and enter the internal standard values The Standards window appears automatically prompting the user to identify the internal standard s using the droplist s and enter the values in the table provided in weight oxide or ppm as indicated in the column heading 29 Analyses of standard reference materials if recognised by GLITTER will be marked with an asterisk in the table If a standard analysis is not recognised by GLITTER click on the row label that contains that analysis to activate it as a standard another click on the row will de activate 1t The standard reference material used appears in the first upper droplist in the window and can be changed if required by making another selection in the droplist The use of up to three isotopes as internal standards IS is allowed The number of internal standards to be used is selected from the second lower droplist in the Standards window and the identities of the internal standards are selected from the minor droplists below it The selected IS 1sotopes appear as column headings in the table and the IS values for the standard analyses e g NIST 610 ALWAYS appear in the first column Other v
47. e displays The display options such as choosing whether to display individual isotopes or isotopic ratios e g 29bb bb are selectable from the droplist below the table More details of these options are given in section 5 3 35 Integration intervals are selected by a simple click and drag action of the four vertical green markers As the markers are moved the data are dynamically recalculated and updated in the results table in the GLITTER window When in isotopic ratio mode the markers for the standard analyses should be tied to the interval chosen for each analysis This is selectable via the Options window section 5 6 In this mode only set the markers for the unknown analysis GLITTER will automatically use the same settings for the standards The final positions of the markers for each analysis should be saved as described in Step 9 below to a file by clicking the Save button before proceeding to Step 6 Clicking the Update button will overwrite selected marker positions if they were not saved Step 8 Save the data Click any of the Save settings Save buttons in the GLITTER Review or Standards window to save all GLITTER parameters marker settings etc to a file with the extension gli Remember that the gli file must have the same name as the datafile or data directory This 1s selected by default when the file requestor appears Click the Export
48. eet programs b Details of the GLITTER session the internal standard values and the marker positions are saved via any of the Save buttons that appear in the GLITTER Standards or Review windows An automatic timed save feature is also available selected in the Options window 3 GETTING READY 3 1 Installing GLITTER GLITTER is written in the IDL programming language Therefore IDL has to be installed on the computer for GLITTER to run IDL Version 6 requires Windows XP or 2000 Step 1 Close all open applications It is prudent to close all open applications before any software installation 1s initiated Step 2 Install IDL The following instructions are based on the IDL 6 documentation Place the IDL CD ROM in the CD ROM drive The IDL installer should start automatically If not select Start Run In the Run dialog type x DEMO where x is the name of your CD ROM drive and click OK Start the installation process by clicking the Install IDL button and then Next to start the installation wizard Accept the license agreement click OK review the release notes and click Next Complete the Customer Information Form click Next to continue then select to install the full application NOT the IDL Virtual Machine Choose the destination location the default is OK under most circumstances No special features are required and the installation can be started using the
49. er than the internal standard at any analysis other than the standard analysis is an unknown quantity and the values used here are interpolated between the standard analyses More details of this yield interpolation are given below in paragraph F Standard Yield Ratios as well as in section 5 6 The Options window The drift for isotope 1 is then defined as the variation of the above expression around 1 and the minimum and maximum values measured for the entire run are shown at the bottom of the display Ideally these values should be as close as possible to 1 57 and these numbers allow the user to assess whether or not the overall drift was significant The drift is plotted using a temperature colourscale highest values are white to yellow then to red to blue to black the minimum and the full colour range is normalised to fill the measured minimum and maximum values The colour variation for a particular isotope row allows for a highly visible indication of the direction of the drift a variation from lighter colours e g white to yellow to darker colours e g blue to black indicates that the yield for that particular isotope decreased with time relative to the yield for the internal standard Similarly a variation from darker colours e g blue to black to lighter colours e g white to yellow indicates that the yield for that particular isotope increased with time relative to the yield for the in
50. f Internal Standard Values element concentrations mode only An interactive and scrollable table occurs on the right of the Standards window The values of the internal standard in weight 9o oxide are entered in this table If the analyses of standard reference materials have been labeled correctly the values 45 will automatically already appear in the table and any user input in these cells will simply be ignored by GLITTER If GLITTER recognises an analysis as a standard analysis through the use of the string std see section 4 1 it is identified by an asterisk If not it can be toggled on as a standard by simply clicking on the row label sample name By analogy a standard can be toggled off by another click on the row label and will thus be analysed as an unknown and no asterisk will appear next to the name Depending upon the mode selected in the major droplist one two or three isotopes as internal standard one two or three columns are activated for user input The column headings correspond to the isotope identities selected in the minor droplists as described above If any internal standard values are omitted the user will be informed via a pop up error message upon attempting to click Accept and calculation will not proceed until each analysis has been assigned an internal standard value Due to a known IDL related bug typing the internal standard values in the table is unfortunately
51. f a different yield interpolation effects all the data and the concentration values the mass dependent drift etc are immediately updated to reflect the changes Here and elsewhere in GLITTER standard analyses that occur together sequentially are treated as a unit to avoid exaggerated distortions in the yield interpolation G Fractionation Elemental fractionation is a well documented problem in laser ablation ICP MS analysis GLITTER uses a simple scheme to indicate the possibility that significant fractionation has occurred and this scheme is shown graphically in the drawing area when this option is selected Fractionation as defined here is calculated by dividing the user selected integration interval across the time resolved signal into two equal parts The trace element concentrations are calculated for each part independently conc and conc and the difference is compared with the results obtained by using the entire signal conc totai Fractionation 96 conc conc conc totai 100 This simple equation does not attempt to encompass the complexity of elemental fractionation It is merely a tool to alert the user that certain elements show variability in their time resolved signals relative to the signal for the internal standard The plot in the drawing area shows the fractionation in units of on the Y axis and the list of elements on the X axis All data are plotted in light grey with
52. ference material values are stored in GLITTER s data library In this version of GLITTER the above notations will use the values for the NIST610 glass as published by Pearce et al 1997 If the character b is added to the labels above e g std 1 610b GLITTER will use the values of Norman et al 1996 As soon as at least one standard and one unknown have been analysed on line data reduction can be initiated 33 Step 2 Run GLITTER Double click the GLITTER icon on the desktop or if no shortcut appears on the desktop double click the glitter sav file in the appropriate directory using the Windows Explorer Step 3 Set the analytical mode The GLITTER splash page appears on the screen with two buttons below the picture For data analysis involving isotopic ratios click the Zsotope ratios Mode button This will activate the appropriate plots and calculation procedures for the data analysis To change the mode during a session you will have to exit GLITTER and start again Step 4 Select the ICP MS device DEVICE A droplist appears below the table in the main GLITTER window which allows you to select the ICP MS device that you are running on The default is the Agilent 7500 but other options include the Perkin Elmer ELAN 5100 ELAN 6000 ELAN 6100 Finnegan Element and Element II Micromass VG PQ2 and a generic spreadsheet format Step 5 Load the data In the GLITTER windo
53. fide standard Calibration values of zircon standard 02123 Griffin unpubl Text file with information about GLITTER for on line help Text file with help on the display menu for on line help Text file with help on the edit menu for on line help Text file with help on the Standards window for on line help Text file with help on the file menu for on line help Text file with help on the help menu for on line help Text file with help on the Plot window for on line help Text file with help on the Review window for on line help Text file with help on getting started for on line help Text file with help on the window menu for on line help Step 5 Create a GLITTER shortcut on the desktop This optional step allows easy access to GLITTER Within Windows Explorer select the glitter sav file in the IDL directory by clicking on it once From the FILE menu select Create Shortcut Move the file called Shortcut to glitter sav onto the desktop and rename the file GLITTER if required If the computer was not rebooted in Step 3 reboot it now step 6 Run GLITTER Double click the GLITTER 1con on the desktop or if no shortcut was created open Windows Explorer Navigate to the Glitter directory and double click the glitter sav file The GLITTER splash screen will then appear and the software is ready to be used 15 3 2 Creating Readable Datafiles Perkin Elmer ELAN 5100 On line analysis is
54. file is given below in Figure 8 B 260100N612 4 TXT Notepad File Edit Search Help Retention Time 6 042 42 0000 15236 42 9500 1304 132 9100 136 9888 138 9100 139 9100 140 9100 142 9100 146 9188 150 9200 156 9268 158 9300 162 9300 oo Se m om om om om oo Eogh GGG G m E Mw S Zh e cs Ch m 2 Retention Time 6 668 h2 888H 12146 Figure 7 An example of a datafile file created by the Micromass acquisition software It contains the data for a single analysis and has the extension txt B 260100SAMPLELIST LIST Notepad File Edit Search Help 2661 66H612 4 Figure 8 An example of a samplelist file created manually by the user of the Micromass ICP MS in a text editor such as Notepad It lists 22 VG POT the filenames of all the analyses in a particular run in the order in which they were created Note that this particular run only contained 3 analyses and that this file with the extension ist has to reside in the same directory as the raw datafiles Time resolved output from the VG PQII instrument are stored in single files one per analysis and analyses common to a single run are stored together and exclusively in a directory The files are comma delimited text files with the extension slk File naming is not critical as GLITTER uses the time of creation given in the header to order the analyses To open a directory with a group of slk files double click the directory name in t
55. ghlight One Concordia Isochrons XY Scatter This option only applies to data reduction in element concentration mode The data are plotted normalised to chondritic values All data are plotted in light grey with the exception of the currently selected analysis which appears in bright green The Plot window is linked to the main GLITTER and the Review windows and the selected highlighted analysis in the latter windows therefore appears as the selected highlighted analysis in the Plot window The standard analyses those tagged with the label std are not shown The secondary droplist that appears with this selection 1n the framed area to the right of the window allows a choice of the order in which the elements are listed from left to right on the X axis This option only applies to data reduction in isotope ratio mode U Pb isotope ratios are plotted on a concordia diagram X 0 Pb U Y Pb U Time steps are plotted as purple stars along the concordia and are labeled in white font in units of billions of years Ga Data are plotted as green crosses with the currently selected analysis appearing in orange This option only applies to data reduction in isotope ratio mode and has not yet been implemented The data are plotted as simple X Y scatter plots and the standard analyses those tagged with the label std are not shown Two secondary droplists appear in the framed area to the right of t
56. gilent are created using the tabchart macro which must be obtained directly from Agilent The macro will run automatically after each analysis if the command is added to deuser mac file deuser mac must be edited separately for each method file that is used It resides in the Hpchem M methods directory Open the deuser mac file and between the lines NAME CustomAnalysis and REMOVE CustomAnalysis type tabchart 20 Data for each analysis is stored within directories rather than within a single file and the name of the directory will be same as the sample name file name given at the start of the run Within each of these directories there will be two files one called qedetail txt and a second with the extension csv and the same name as the analysis name e g std610 csv The latter contains the time resolved data and the qcdetail txt or qcdtlO1 txt file NB filename depends on Chemstation version contains the time of creation used by GLITTER to order the analyses If GLITTER cannot find qedetail txt or qcdtl01 txt in any of the analyses for a particular run this may happen if a run is stopped before reaching the required number of replicates and the datafile is created manually the analyses will be ordered alphabetically It is very important that analyses are loaded into GLITTER in the order in which they were analysed otherwise GLITTER cannot accurately correct for instrumental drif
57. he user The main window GLITTER automatically appears on the screen when the program is opened When the dataset is loaded using the Load Data button FILE menu the Standards window appears automatically and prompts the user to identify the internal standard and enter the values in the table provided Internal standards can be changed at any time during the session Up to three isotopes can be used as internal standards and are chosen from droplists Compositions of reference materials are held in GLITTER s data library Standard analyses should contain the string std and the name of the reference material e g NIST 610 when they are first run At a click of the Accept button GLITTER calculates the trace element concentrations and the results appear in the table in the GLITTER window GLITTER uses a simple algorithm to select a default set of integration intervals for the background and signal counts these should be checked and re set interactively by the user in the Review window see below Other important information such as the 1 sigma error estimates minimum detection limits fractionation trends chondrite normalised values etc also are calculated and can be displayed in the table The Options window selects the type of yield interpolation cps ppm across the standard analyses the average yield of all the standard analyses or a linear quadratic or cubic fit acro
58. he file requestor before clicking Open The Generic Spreadsheet Format If all else fails GLITTER allows the importation of a simple spreadsheet format for data reduction Each analysis should be stored in a comma delimited text file with 6 the extension xl The text files should be named alphabetically numerically to ensure that they are loaded in the correct order and contain the time resolved data with isotopes as columns and timestamps as rows Two lines of header information is required where line 1 should indicate whether the data are in units of Raw Counts or Counts Per Second The second line are the column headings e g Time Ca44 T146 etc To open a directory with a group of xl files double click the directory name in the file requestor before clicking Open An example of the first few lines of such a file 1s given in Fig 9 Zo Ap fb 0 xl Notepad File Edt Search Help Intensity Us Time Counts Per Second Time in Seconds Pb 286 Pb287 Pb288 Th232 U238 8 48 66465641192 5 GHBHBHBBS 75 BBB2 88 H882254855515 B8 18 06100376 BE H 75 B8 15 BBBBB7875885 58 085056541132 18 8818836808711 8 1 5 28 88281520283 38 B8888315808833 88 8082248545515 8 H 2 2549 28 882814520283 38 B0880880315 88833 38 00306318 06364 1060 0601863668 2 999 5 858055541132 548 8880568B88878 58 88505651132 0 0 3 49 3B8 883831886365 18 8088855 00081 O HB 8802855457692 B
59. he window enabling the user to select the elements to be plotted on the X and Y axes respectively 56 Histograms The data are plotted as simple histograms and the standard analyses those tagged with the label std are not shown The secondary droplist that appears in the framed area to the right of the window is used to select the element to be plotted as a histogram or the isotope ratio or age estimate when GLITTER is running is isotope ratios mode Run Quality Control The run quality control plotting options provide tools by which the quality of each run can be assessed When this option is selected in the primary droplist the secondary droplist that appears in the framed area to the right contains different options for viewing the quality control data The types of plots that can be displayed are A Mass Dependent Drift The mass dependent drift is visualised by a pixelmap display with isotopes plotted as rows and analysis numbers plotted as columns The yield for each element relative to the yield of the internal standard for each analysis is plotted relative to the same ratio for the first standard analysis Therefore if yield is defined as the number of cps measured for each ppm of concentration then the pixel for isotope 1 at analysis number n in the display is equal to Yield Yieldis n Yield Y teldis 1 sta where Yield yield for the internal standard Note that the yield for any isotope oth
60. landscape orientation for element concentrations and in portrait orientation for isotope ratios Print options cannot be formatted manually and it is recommended that the data are exported see Export above to your favourite spreadsheet and formatted and printed from there Currently the print buffer will not permit printing tables which exceed 78 analyses and 36 isotopes Exit Select FILE Exit to exit GLITTER Marker positions and IS values should be saved before quitting using any of the Save buttons Other windows open at the time of quitting e g Review will disappear with the main GLITTER window The EDIT menu The EDIT menu is used to view and edit the structure of the current datafile Toggle Standard ON 39 GLITTER automatically recognises analyses of external standards also called standard reference materials when they are labeled with the string std and marks them in the table of results with an asterisk However if for some reason GLITTER doesn t recognise the analysis as a standard analysis no asterisk you can overcome this by selecting the standard analysis in the results table click on the row which contains the analysis and then selecting EDIT Toggle Standard ON Toggle Standard OFF Sometimes it is necessary to exclude a bad standard analysis from a dataset because it distorts the yield interpolation beyond reasonable estimates of the drift Analyses of stand
61. lays the name of the reference material used during the run e g NIST610 or NIST612 This 1s mostly detected automatically by GLITTER 1f the analyses of the reference materials are labeled correctly but they can also be set changed during a session by making a selection from this droplist The Internal Standards Droplists element concentrations mode only The Internal Standards droplist second from the top allows the use of anywhere from one to three isotopes as internal standard s Depending on the choice made in this droplist one to three minor droplists appear requesting the identity of these internal standards In more detail the choices are a One isotope as internal standard recommended This 1s the default choice and a single minor droplist appears where the 1sotope to be used as internal standard 1s selected b One isotope for standards another for samples Two isotopes of the same element e g Mg24 and Mg25 are used as internal standard When this option is selected two minor droplists appear where these isotopes are selected Be aware that 44 the use of two isotopes of the same element as internal standards assumes that there is no fractionation between these isotopes c One isotope for standards two others for samples This is a variant of b above with the addition of another isotope to be used as internal standard for the samples For example Mg24 is used for the standards Mg25 is use
62. le GLITTER has to be aware of the new data that have been added It uses the alias txt file alias ratio txt when in isotope ratio mode to search for the values of standard reference materials The alias txt file in this example consists of one line of header information and information for 4 standard files the chondrite values are read as a standard in this context Each of the standard files contains three lines of information thus there are 12 lines 1 line header 13 lines of information in this file GLITTER reads the information line by line Therefore it is very important that the program finds the information it seeks in the line where it looks for it Fig 10 shows the current appearance of the alias txt file The header is a number equivalent to the number of standards in the file Currently the file contains the information for four standards and the header l therefore has the value of 4 Increment this number for each standard that is added For example if data for one standard are added change the number to 5 if two standards are added change the number to 6 etc If this header is not altered as described GLITTER will simply ignore any additions The header 25 B alias_txt Notepad File Edit Search Help m nist lB8 txt l 618 HIST 18 nist 16 HIST 618 nist 610 NBS616 HBS 618 nbs lB nbs 18 HIST 618 S88 ppm glass Pearce et al 1997 3 lines of information for each standard
63. le 1 The files that are required to run GLITTER successfully Filename glitter sav glitter2 sav Description Runtime GLITTER module 1 Runtime GLITTER module 2 glitter rop The report options template to be used by the ELAN software to create the correct output format ELAN 6000 only Kum tabchart Macro to created readable datafiles for HP4500 only DEVICE alias txt Reference material aliases label strings and the name of the text files to alias ratio txt Chondrit txt element txt isotope txt mass txt nist610 txt nist610 old txt nist611 txt nist612 txt nist612 marc txt PGE A txt Zircon 02123 txt help about txt help display txt help edit txt help emp txt help file txt help help txt help plot txt help review txt help start txt help window txt consult for the values of the reference materials As alias txt but used when operating GLITTER in isotope ratio mode Values of C1 chondrite for the elements from P to U A list of chemical elements A list of isotopes and their abundances in A list of chemical elements and their atomic mass numbers The values of the NIST610 glass from Li to U Pearce et al 1997 The values of the NIST610 glass from Li to U Norman et al 1996 The values of the NIST611 glass from Li to U Pearce et al 1997 The values of the NIST612 glass from Li to U Pearce et al 1997 The values of the NIST612 glass from Li to U Norman et al 1996 Calibration values Alard unpubl for PGE sul
64. le of results e g concentrations error estimates etc The list of options that appears in the droplist is self explanatory and details on how these values are calculated other than the raw data are given in Section 6 Note that the function of the Display droplist is analogous to the function of the DISPLAY menu The PPM Weight Option Buttons Two radio buttons appear below the table of results only when GLITTER 1s running in element concentration mode In isotope ratio mode a label appears here that identifies the current isotopic system e g U Pb These radio buttons allow the user to view the values of the internal standard in units of parts per million ppm or weight percent oxide The selection toggles between the two concentration units When the weight button is selected concentration values error estimates and minimum detection limits for the internal standard are displayed in units of weight oxide They will also be exported in weight 9o oxide to the txt file The Update Button The Update button appears below the table of results in the bottom right corner of the window This button is used exclusively for on line data reduction Once the active dataset has been identified FILE Load Data the Update button is 42 clicked to load and analyse the data dynamically on an analysis by analysis basis If the identity and values of the internal standard s have not been
65. n the table If all values have been entered correctly the Standards window will disappear upon this click and the results will be calculated and displayed updated in the results table within the main GLITTER window If any internal standard values are omitted the user will be informed via a pop up error message and calculation will not proceed until each analysis has been assigned an internal standard value The Save Settings Button The Save Settings button appears at the bottom of the window Details regarding the current GLITTER session are saved to a file with the extension gli using this button A dialog window appears prompting for the filename and it must have the same filename as the current datafile For example if the datafile jn26b rep is currently being analysed save the details of the session to jn26b gh This will allow GLITTER to correctly restore the parameters of jn26b e g internal standard values marker positions etc if loaded again at a later session This button is analogous to the Save buttons in the main GLITTER window via the FILE menu and in the Review window All three Save buttons save ALL the details of a session not isolated or selected parameters It is therefore important to be aware that if this button is clicked in Standards to save internal standard values settings the latest marker positions in Review are written to disk as
66. nal areas for integration However use this option with discretion as it can severely alter the results of low statistics isotopes and there is currently no simple Undo option e available It should only be used to filter spikes that are clearly outside the analytical uncertainty If the last spike filtering operations have not been saved to a gli file either manually or automatically every 60 seconds via the Timed Saves option spike filtering can be undone by simply reloading the data However if the data have been saved to the gli file after spike filtering the gli file must be deleted to undo unwanted spike filters and the data reduction process has to be started anew 52 The Set Marks Button The Set Marks button is designed to assist the user in the selection of background and signal integration intervals Clicking this button will re set the marker positions to the default values calculated by a set of mathematical algorithms that avoid obvious irregularities in the data However it 1s strongly recommended that the user check the integration intervals set in this way as no algorithm can adequately account for the complexities of many geological specimens It is important to note that clicking the Set Marks button will re set the marker positions only in the currently selected analysis not in all the analyses in the dataset The Save Button Details regarding the current GLITTER ses
67. not possible with the Perkin Elmer ELAN 5100 Off line analysis of complete datasets is done by creating an output file containing all analyses for a particular run with the extension prn To ensure that the file is exported in the correct format select UTILITIES from the main ELAN5000 window Within the Utilities window select Configuration Windows Reports Check that the String Quoting Character is set to double quotes and the delimiter is set to Space To create the datafile select Applications Graphics from the main ELANS5000 window The list of analyses appear select Reports Computer Format To File To File Enter the filename with the extension prn in the box provided and click OK Select the first analysis to be written to file and then select Analyze Analyze To End Perkin Elmer ELAN 6000 GLITTER reads the data from the Perkin Elmer ELAN 6000 as a simple text file line by line The ELAN 6000 software allows the user to set up a template for the output file and this 1s saved as a Report Options file with the extension rop The Report Options template for GLITTER is supplied on Disk 1 called glitter rop and should be copied to the appropriate directory where the ELAN 6000 software 1s stored for example C ELANDATA ReportOptions allowing the ELAN software to access it Click the Method button in the ELAN workspace and then the Report
68. nt geoscience laboratory in the world academic government industry commercial laboratories The development of on line real time data reduction was a major factor in the rapid spread of EMP laboratories in the 1970s It enabled the user to view the results of an analysis within seconds of data acquisition and to use that input to guide further analytical strategy Compared to the off line data reduction available previously this meant a great increase in productivity flexibility and applicability This interactive analytical environment is now taken for granted in EMP work A similar interactive environment has not been available for the LAM ICPMS To meet this need GEMOC has developed GLITTER the GEMOC Laser ICPMS Total Trace Element Reduction software package GLITTER gives users of the laser ablation microprobe a unique analytical environment based on the interactive selection of background and sample intervals from the time resolved signal provided by the ICPMS pioneered by Longerich et al 1996 and Fryer et al 1995 in the off line LAMTRACE software It provides real time on line data reduction for the LAM ICPMS and features linked graphics and analysis tables greatly improving both productivity and the flexibility of analysis GLITTER is written in the IDL programming language and provides cross platform support for a number of environments including Windows XP and 2000 This manual is written for the Microsoft Window
69. om the signal for that analysis This is what is meant by Use local backgrounds the first item in the droplist However if there 1s evidence for abnormal variability or systematic variation with time in the background signals for one or more isotopes an interpolated background over all analyses can be switched on by selecting the second item in the droplist Background interpolation ON The interpolation fits a line through the average 65 background counts for each analysis and the interpolation appears as a dotted line in the Plot window as shown in Fig 12 in the Plot window select Run Quality Control in the primary droplist and Backgrounds in the secondary droplist In the Options window a second droplist appears when Background interpolation ON is selected and it requires the user to select the type of interpolation to use across the run The choices are a an average of all backgrounds b a linear fit c a quadratic fit and d a cubic fit to the backgrounds The choice should be made by viewing the variation in the background signals in the Plot window and obtaining the best fit using one of these choices Fig 12 GLITTER vetoes high order fits if there are not sufficient analyses in the run to use it Note that the background interpolation 1s either ON or OFF for all isotopes in all analyses it cannot be turned on selectively for some isotopes B Plot Results qd Lu i L
70. omment4 Pig aaa Total no of isotopes Hg282 T1283 T1285 Pb285 Pb286 Pb2807 Pb288 Th232 U235 U238 18 18 18 18 18 18 18 18 18 18 S wells ms PE standardi FIMN2 io Isotope Y List of P analyses standard FIN in this run information Figure 5 An example of a fin file created by the ThermoFinnigan Element Element 2 acquisition software It lists the conditions common to a particular run and a list of the raw datafiles in the run in this run there were 5 analyses standardl acql acq2 acq3 and standard2 each with the extension fin2 To use the Finnigan ME import option from the main GLITTER window this fin file is required Explanatory comments have been added in red they do not form part of this file B standard1_FIN Notepad File Edit Search Help Finnigan HAT ELEMENT Raw Data Wednesday Hay 18 2000 14 1718 59 61608 Header standard1 FIN information 756 n 1 1 1 1 1 1 2 1 Detector mode for each isotope Timne Hg282 T1283 T1285 Pb2805 Pb286 Pb287 Pb288 Th232 U0235 U238 u 28888B8 75808 888888 16511 BHBBBB 4905454 HAHAHA B 000006 57055 0000H u 32680808 7887 888888 22022 8808888 15511 088888 11811 BBBBHB 55 B55 B u 45 2888 18811 888888 16511 0888888 11811 888888 11811 BBHBOHBB 38533 H u 5778008 5586 888888 55 08 6000606 55055 BHO 55 88 BHO 33833 6608 8 783000 7508 6600006 16511 8HB8B888 22022 88888 55 88 dB8B8B88B8 27522 BB u 8298808 7887 888888 11811 888888 15511 08
71. ppear in Review containing the time resolved signals of the current analysis Fig 2 The top display consists of rows of pixels each representing the variation of the signal with time for a single isotope with intensity shown by colour brightness This gives an immediate and highly visible indication of any spikes in the data or heterogeneity in the sample for one or more isotopes The bottom display shows the time resolved signal for a single isotope selected using a horizontal marker in the pixelmap display the identity of the selected isotope appears in the information field below the displays Other display options include a Linear Log Cubic droplist and a Raw Data Ratio to IS droplist The latter option which can be corrected for relative isotope abundances plots time resolved data for each isotope normalised to the signal for the internal standard this display allows the user to assess the amount of fractionation for a particular isotope relative to the internal standard Si Review Signal Selection Analysis Ma 4 98CGO02e 008 et MAAC Ar i DT GUCCI zn 54 Countsisec Log Pl F zet Marks Save Undo Previous Mest Help Close Move pointer slowly inta an object to view context sensitive help far it including a description af the abject and tips on its use Figure 2 The Review window Analysis labels are displayed on the left and the time resolved laser ablation signal
72. re given in section 5 3 Integration intervals are selected by a simple click and drag action of the four vertical green markers As the markers are moved the data are dynamically recalculated and updated in the results table in the GLITTER window The final positions of the markers should be saved periodically during the session Step 8 below to a file by clicking the Save button Step 8 Save the data Click any of the Save settings Save buttons in the GLITTER Review or Standards window to save all GLITTER parameters marker settings IS isotopes 31 and IS values to a file with the extension gli Remember that the gli file must have the same name as the datafile or data directory for HP 4500 and VG PQII This 1s selected by default when the file requestor appears Click the Export button in the FILE menu to save data tables to an ASCII text file any filename is acceptable The default export option is a comma delimited file with the extension csv but space tab and double quotes can also be selected as delimiters in which case the file is automatically saved with the extension txt Step 9 Update the dataset During on line analysis data are dynamically updated as soon as each analysis 1s completed by clicking the Update button The latest analysis 1s added to the dataset Simply enter the appropriate internal standard value 1f required as Step 6 above select
73. rovided by clicking in the field with the mouse and then typing the number Use the slider to obtain the desired number by clicking on the slider button with the mouse and while holding the mouse button down moving the slider until the desired value 1s obtained Release the mouse button setting the Uncertainty for the Internal Standard When calculating the l sigma uncertainty for each analysis GLITTER takes into account the uncertainty that 1s associated with the internal standard used during analysis By default this is set to 3 relative error but can be changed to any desired value or set to 096 in one of two ways Enter the desired value in the white text entry field provided by clicking in the field with the mouse and then typing the number Use the slider to obtain the desired number by clicking on the slider button with the mouse and while holding the mouse button down moving the slider until the desired value 1s obtained Release the mouse button This selection does NOT appear when GLITTER 1s operating in isotope ratios mode because internal standards are not used 67 Setting the Fractionation Test Cut Off When two or more isotopes of the same element e g Mg24 and Mg25 are analysed GLITTER checks the raw counts to detect whether or not these isotope are fractionated relative to each other By default if a difference of more than 5 relative in the yield between the isotopes within an analysis is detected
74. s XP environment 2 OVERVIEW 2 1 Terminology Throughout this manual the internal standard refers to the value for the abundance of a single element or oxide which is known for each analysis for example CaO from electron microprobe analysis and it 1s often abbreviated to IS The user is required to provide GLITTER with these values Standard analysis refers to the analysis of a standard reference material such as the NIST 610 glass normally at the beginning and the end of a run It 1s often abbreviated to std Current analysis or selected analysis refers to a specific analysis within the run that is selected highlighted from either the main GLITTER window the Standards window or the Review window by clicking on the analysis number ID in the tables or lists Dynamic updates and the highlighted analysis in the Plot window relates to this analysis Current isotope or selected isotope refers to the isotope plotted as a time resolved signal in the lower part of the Review window and is selected by either dragging the horizontal marker or selecting the isotope from the isotope droplist in the Review window Throughout this manual hints are identified with a small oval in the margin and the word TIP inside it Important procedures for the successful use of GLITTER are highlighted by an exclamation mark in the margin All ICP_MS platforms that are currently supporte
75. s immediately following the currently displayed analysis If the current analysis is the last analysis of the run no action will be taken The Help Button The Online Help window is called by a click on this button Multiple copies of the Help window can be opened while reducing the data The Close Button A mouse click on the Close button will close the Review window Context Sensitive Help In the lower part of the Review window a framed text area appears which provides context sensitive on line help This means that cryptic information about some of the functions within the Review window is displayed here by simply moving the cursor over the component for which help is sought 54 5 5 The Plot Window The Plot window is designed to provide an interactive environment for viewing the results in various ways from simple X Y scatter plots to detailed run quality control Clicking on the Plof button from the WINDOW menu opens the window The elements of the Plot window are The Draw Area The main feature of the plot window 1s the drawing area All plots are displayed here and the type of plot is selected from the droplists below the drawing area These options are discussed below in more detail The Primary and Secondary Droplists The primary droplist appears below the drawing area and to the left of the window The selection that 1s made in this droplis
76. s on the right The top pixelmap display shows all isotopes for the selected analysis with colour brightness representing signal intensity The bottom display shows the signal for a particular isotope in this case Zn selected using the horizontal green marker in the pixelmap display Integration intervals are selected by dragging the four vertical markers Note that context sensitive help is given in the HELPFRAME at the bottom of the window GLITTER initially calculates the results using a set of default integration intervals chosen using a simple algorithm It sets the markers to avoid obvious heterogeneity and large spikes in the signal However users can re select the integration intervals for each analysis by simply dragging any of the four vertical markers in the Review window As the markers are moved the data are dynamically recalculated and updated in the results table and Plot window s Review can be called from the WINDOW menu for any analysis at any time during the session See the reference section Section 5 for more details 2 4 U Pb dating Jackson et al 2004 developed an analytical protocol for the dating of single zircons using the U Pb isotopic system analysing py pp Spb Th and U and assuming no initial common Pb analysed in situ with the laser ablation ICP MS GLITTER allows the rapid reduction of these data calculating age estimates from isotopic ratios and plotting a concordia diagram in the
77. sion are saved to a file with the extension gli using this button A dialog window appears prompting for the filename and it should have the same filename as the current datafile For example if the datafile jn26b rep is currently being analysed save the details of the session to jn26b gh This will allow GLITTER to correctly restore the parameters of jn26b e g internal standard values marker positions etc if loaded again at a later session This button is analogous to the Save buttons in GLITTER and Standards All three Save buttons save ALL the details of a session not isolated or selected parameters It 1s therefore important to be aware that 1f this button 1s clicked in Review to save marker settings the latest internal standard values in Standards are written to disk as well and vice versa The Undo Button A click on the Undo button will undo individual marker moves and reset them to the preceding positions Ten levels of undo are currently supported and note that 1f the choice to undo follows a click on the Set Marks button the Undo must be clicked four times because four markers were moved 53 The Previous Button Click on this button to move to the analysis immediately preceding the currently displayed analysis If the current analysis is the first analysis of the run no action will be taken The Next Button Click on this button to move to the analysi
78. ss the standard analyses are selectable from this window Other options include control over the background fitting procedures and the magnitude of the error associated with the internal standard values File Edit Display Window Help Help Window s Table of results Review Signal Selection wj TY O lsinppm iSinw Update On line help frame contextfsensitive Standards Review Signal Selection Plot Results Plot Results Options Figure 1 A schematic representation of the structure of GLITTER All the main operations are carried out in the GLITTER window shown in the top left part of the diagram The identity and values of the internal standard s are entered in the Standards window The selection of integration intervals is done in Review Signal Selection and results are displayed graphically in one or more Plot Results window s The Options window allows the selection of advanced calculation options and on line help is available in the context sensitive help frame in the lower part of the GLITTER window For more detailed help one or more Help windows can be consulted On line data reduction uses the Update button 2 3 Data Selection The Review window Selection of background and signal intervals from the time resolved signal is the key to rapid and accurate on line analysis this is done in GLITTER s unique Review window Fig 2 Two displays a
79. t It is therefore up to the user to name files alphabetically or numerically if there is any chance that the qcdetail txt files will not be created Data that belong to a common run are grouped together in a higher directory e g runl and the gli file created by GLITTER will have the same name as this directory If problems arise with the naming sequence of files the directory ies can be renamed in Windows Explorer provided that the first line within each relevant datafile opened in Notepad is renamed as well Micromass Analyses obtained using the Micromass ICP MS are stored in separate files one per analysis and all analyses for a particular run are stored together in the same directory Each datafile has the extension txt and the first few lines of a typical Micromass datafile is shown in Figure 7 To ensure that the analyses are loaded in the order they were analysed you have to create another text file listing all the analyses for a particular run in the correct order Note that the Micromass acquisition software does not create this file it must be created manually by copy paste action from the samplelist window in the Micromass workspace to a text editor such as Notepad The samplelist file must then be saved with the extension list this 2 is the file GLITTER will look for when the Micromass option is selected under the device droplist on the main GLITTER window An example of such a samplelist
80. t determines which secondary droplist appears in the framed area to the right of the primary droplist It contains five options where the first two options depend on the mode element concentrations or isotope ratios in which GLITTER 1s running Chondrite Normalised All or Concordia Chondrite Normalised Highlight One or Isochrons XY Scatter Histograms Run Quality Control Ratio to standard These options are discussed individually in the following sections The functions of the secondary droplist s associated with each of these options are also discussed The properties of the plots e g the axes ranges tickmarks plotting symbols etc are not editable by the user Chondrite Normalised All This option only applies to data reduction in element concentration mode This is the default option when the Plot window is first opened The data are plotted normalised to chondritic values for each element Each analysis 1s plotted using a different colour and standard analyses those tagged with the label std are 55 not shown The secondary droplist that appears with this selection in the framed area to the right of the window allows a choice of the order in which the elements are listed from left to right on the X axis These plotting orders are pre defined in the GLITTER code and are not accessible to the user User defined plotting orders will be added to the next version of GLITTER Chondrite Normalised Hi
81. ternal standard The isotope ID for each row is listed on the left of the display At the start of on line analysis insufficient standard analyses are available to calculate the interpolated yield and the concentrations are calculated using an average yield from the standard data No drift can be measured until more standards are analysed and no data will appear in the drawing area only a large white square This is simply an indication that the data needed to calculate the mass dependent drift are not yet available As soon as another standard or group of standards is analysed and the appropriate standard yield interpolation is selected from the droplist in the Options window the display will automatically be updated to reflect these additions Here and elsewhere in GLITTER standard analyses that occur together sequentially are treated as a unit to avoid exaggerated distortions in the yield interpolation B Sensitivity The calculated minimum detection limits for each element are displayed when this option is selected The method for calculating the detection limits is discussed in section 6 The Calculation of Trace Element Concentrations Theory The detection limits in units of ppm are plotted on the Y axis against each element as shown on the X axis All analyses including standard analyses are shown 58 All data are plotted in light grey with the exception of the currently selected analysis which appe
82. th the last Update click all data are re calculated and no off line reprocessing is required Results can be viewed graphically in the Plot window s which are called from the WINDOW menu on the main window As with Review Plot can be called at any time during a session and several Plot windows can be opened at a time The data can be displayed in several ways Chondrite normalised with a choice of trace element order Concordia plot for U Pb dating X Y scatter plots Histograms Run quality control data drift ablation rates detection limits backgrounds etc The size of datasets is unrestricted Movement within a dataset also is unrestricted and all windows are dynamically linked This means that a If marker positions are changed in the Review window the table of results and all data plots on the screen at the time are automatically updated to reflect these changes b The selected highlighted analysis number in GLITTER is also the selected analysis number in Review and Plot and vice versa At the end of the session or at any time during the session data can be written to disk in two ways a The tables of results data chondrite normalised data minimum detection limits etc are written to a space tab delimited ASCII text file extension txt using the Export button FILE menu in the GLITTER window This format is suitable for importation into spreadsh
83. the exception of the currently selected analysis which appears in bright green The Plot window is linked to the main GLITTER and the Review windows and 61 the selected highlighted analysis in the latter windows therefore appears as the selected highlighted analysis 1n the Plot window H Fractionation Error The decision to reject data on the basis of significant fractionation as defined above must be made within the context of the inherent error associated with the calculation of the trace element concentrations Select this option to view the fractionation relative to the error The plot in the drawing area shows the fractionation divided by the 1 sigma error estimate on the Y axis and the list of elements on the X axis This 1s a more realistic way to view the magnitude of the fractionation Assuming that no significant fractionation occurred for a run 99 of the data will plot below 3 3 sigma Values that scatter above 3 indicate possible fractionation or other errors and the time resolved signals for those elements should be investigated more carefully As previously indicated all data are plotted in light grey with the exception of the currently selected analysis which appears in bright green Ratio to standard This option is used to plot the current analysis relative to any of the standard reference material values currently held in GLITTER s reference library The
84. the correct integration intervals as Step 7 above and save the new data as Step 8 above to update the gli file as well The Review and Plot windows can remain open during the repetition of these steps 32 4 2 Example 2 Isotope ratio mode Step 1 Creating the right output file DEVICE The first and most important step in using GLITTER both for off line and on line data reduction is to create a readable file format This has to be done as outlined in section 3 2 and the procedure is different for each ICP MS platform currently supported by GLITTER Standard analyses can be identified with the string std and name of standard e g 610 Take care that the string std does not appear anywhere in the sample ID of the unknowns The string can appear either in upper STD or lower std case Standard analyses that are not labeled as such can be toggled on as a standard at any time during the session by selecting EDIT Toggle Standard ON The name of the reference material can be labeled in any one of the following ways std 1 610 STD6101 std NIST610 1 std 610 analysis number 1 etc except in the case of the HP4500 where sample names are limited to eight characters e g astd610 This labeling system allows GLITTER to detect which analyses were standards and which standard concentration values should be used in the calculation of trace element concentrations re
85. u The WINDOW menu is used to call the other interactive windows Standards Review Signal Selection Plot Results and Options that are used by GLITTER for data reduction and display Each of these windows are described separately below 5 3 5 6 The HELP menu The HELP menu provides on line help with the structure and use of GLITTER The help information is displayed in a Help window and every time help is sought a new window is opened This allows the user to simultaneously view help about different subjects while reducing data The Help window s are dismissed by a click on the Close HELP window button s Three options are selectable under the HELP menu Getting Started Quick step by step information on how to get started Help on menus Compact descriptions of the GLITTER menus About GLITTER Details about GLITTER e g authors version number etc The Table of Results The table of results is the main feature of the GLITTER window Data are tabulated with isotopes or isotope ratios as columns and analysis numbers as rows and the order in which the isotopes appear follows the order exported from the ICP MS software The table is non interactive which means that the user cannot type in any of the cells or add delete any columns or rows To allow plotting of the data in the Plot window the results are retained as floating point numbers and are not detection limit filtered Standard
86. w click the Load data button upon which a file requestor will appear Datafiles with the appropriate extension e g prn for ELAN 5100 output rep for ELAN 6000 output etc will appear in the requestor Click on the desired datafile and then click the Open button If data are arranged in directories e g HP4500 and VG PQID double click on the directory name and then click Open On line data reduction requires this step only once at the beginning of the run 1 e as soon as one standard and one sample have been analysed From here it will always load this file when data are updated Step 6 Set the dwelltime The Standards window appears automatically and details of the rise time laser on are given in the table in units of replicates and seconds Analyses of standard reference materials if recognised by GLITTER will be marked with an asterisk in the table If a standard analysis 1s not recognised by GLITTER click on the row 34 label that contains that analysis to activate it as a standard another click on the row will de activate it The calibration values used appear in the droplist in the window and can be changed if required by making another selection in the droplist The main purpose of this window when in isotope ratio mode is to set the dwelltime for those ICP MS devices where the dwelltime 1s not written to the datafile It must be entered manually by the user in the text box that appears in the
87. well and vice versa The Load Settings Button The Load Settings button appears at the bottom of the window This button allows the user to independently load a gli file the values of the internal standards and previously selected marker settings It is particularly useful if for some reason the gli file does not have the same name as the current rep file and thus not recognised 47 by GLITTER or if there is any doubt as to whether GLITTER loaded the gli file successfully Clicking the Load Settings button will open a dialog window which prompts for the name of the file to be loaded Select the gli file and then click Open The identity and values of the internal standard s are then loaded into the Standards window Note that doing this also will load previously selected marker positions and any current marker settings will be overwritten The Help Button The Help button appears at the bottom of the window and the Online Help is called from this button Note that because the Standards window is modal 1 e the rest of GLITTER cannot be operated while the Standards window is open the Help window called from this button is modal as well an IDL Windows limitation It has to be dismissed before continuing with the session The Cancel Button The Cancel button appears at the bottom right of the window Click this button to close the Standards
88. ysis and all analyses for a particular run are stored together in the same directory Each comma delimited datafile has the extension xl and looks identical to the spreadsheet format data already described below see Fig 7 Thus users of the ELAN6100 can also use the spreadsheet option for importing data However the ELAN6100 acquisition software allows the creation of a file with the extension rep which is a summary of all files in a particular run and the order in which they were analysed If the ELAN6100 option is selected from the device droplist on the main window GLITTER will search for and load this rep file Provided the rep file is in the same directory as the xl datafiles all analyses listed in the rep file will automatically be loaded into GLITTER in the order in which they appear in the file Fig 4 below 1s an example of such a rep file El Glitter rep Notepad File Edit Search Help 61211 C XelandataXReport utput s6121H 651212 C XelandataXReport utput 61232 Puta Cc XelandataMXReport utput seuft 6a puf 6b C XelandataXReport utput seuft h 61215 C XelandataXReport utput 6 1214 61215 C XelandataXReport utput s61215 Figure 4 An example of a rep file created by the ELAN6100 acquisition software It lists the names and filenames of all the analyses in a particular run and the order in which they were created To use the ELAN6100 import option from

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