Clarity ClarityStarted Getting Getting Started ENG Code/Rev.: M006/26A – 15 February 2008 Phone: +420 - 251 013 400 Fax: +420 - 251 013 401 clarity@dataapex.com www.dataapex.com © DataApex Ltd.
® Clarity®, DataApex® and are trademarks of DataApex Ltd. ® TM Microsoft and Windows are trademarks of Microsoft Corporation. DataApex reserves the right to make changes to manuals without prior notice. Updated manuals can be downloaded from www.dataapex.com.
Clarity - Getting Started Contents 1 Brief Description............................................................6 1.1 Hardware and software requirements....................6 2 Installation ....................................................................8 2.1 Software Installation.............................................8 2.1.1 Windows Vista instalation ...........................9 2.2 Hardware Installation ...........................................9 2.2.1 Hardware key (dongle) installation.....
Clarity - Getting Started Contents 5.4.1 Sample description ................................... 33 5.4.2 Signal monitoring ..................................... 34 5.4.3 Analysis run ............................................. 35 5.4.4 Analysis monitoring .................................. 35 5.4.5 Analysis stop ............................................ 36 5.5 Chromatogram evaluation .................................. 37 5.5.1 Display chromatogram .............................. 37 5.5.
Clarity - Getting Started Contents 7.4.2 Rockey LPT dongle (re)installation ............. 58 7.4.3 Sentinel dongle installation ....................... 58 7.5 System Files (systeminfo.txt file) ......................... 59 7.6 Sleep Mode ......................................................... 60 7.7 Switching Users in Windows OS .........................
Clarity - Getting Started Brief Description 1 Brief Description Clarity chromatography station is an effective tool for the acquisition, processing and evaluation of data from any gas or liquid chromatograph with analog output and from selected chromatographs with digital output. In the maximum configuration, it is possible to measure on up to four chromatographs simultaneously, from which, each may be equipped with up to 12 detectors.
Clarity - Getting Started Brief Description PC Configurations: Minimal Recommended MS Windows Vista the same like MS Vista system requirements MS Windows 2000/XP PC Pentium III/700 PC Pentium 4/2 GHz, MHz, 256 MB RAM 512 MB RAM MS Windows NT/(98/Me*) PC Pentium/200 MHz, PC Pentium/450 32 MB RAM 128 MB RAM Monitor Resolution 1024x768, 64K (16 bit High color) MHz, Resolution 1280x1024, 64K (16 bit High color) CD ROM drive, free slot for A/D converer (ISA/ PCI/USB), USB or LPT for a dongle * Sup
Clarity - Getting Started Installation 2 Installation Verify that the package is complete (packing list). Caution! 2.1 Install the Clarity before inserting any devices (INT7, U-PAD, etc.). Software Installation Installation of the program requires 50 to 210 MB of free hard disk space depending on the number of components you want to install. Caution! Ensure you have Administrator access rights in your system before you proceed with the installation.
Clarity - Getting Started 2.1.1 Installation Windows Vista installation When installing the Clarity software, Windows Vista may create a large number of warning screens (depending on the security levels set). These should be ignored for Clarity to function correctly. Note: Caution! 2.2 It is highly recommended not to install the Clarity software into the PROGRAM FILES directory. Also, the User Account Control (UAC) in Windows Vista should better be disabled when working in the Clarity.
Clarity - Getting Started 2.2.1 Installation Hardware key (dongle) installation The hardware key needs to be installed and present in the PC when using the Clarity Chromatography Station. The drivers will automatically be installed during Clarity software installation. If the installation did not proceed automatically (older versions of MS Windows), refer to the chapter 7.4 - Hardware key on pg. 57. Caution! Install Clarity software from the CD ROM first and only then insert the key into the PC.
Clarity - Getting Started Installation in order to prevent the reassignment of INT7 acquisition channels between Clarity Instruments. 2.2.3 Installation of the U-PAD Converter Note: In Windows 2000/XP/Vista the drivers will be installed automatically during the installation of the Clarity software. Install the software before attaching the device to USB slot. • Install Clarity software from the CDROM. • Connect the U-PAD with a cable to a USB port on the computer.
Clarity - Getting Started 2.3.1 Installation Standard cable for Clarity station • Signal cables Labelled “DET1” to “DET4” (according to the number of channels), the cables are supplied as standard without connectors with only stripped, tinned endings – red (+), white (-) and shielding (analogue ground). • Starting (marker) cables Labelled “IN1” to “IN4” (according to the number of channels), ended with CINCH connector.
Clarity - Getting Started Installation Digital output (Relay) Starting cable Red Shielding Signal cable Red White START (REMOTE, …) 1V (100mV, Hi, +, …) 0 (COM, AGND, …) Shielding NONSYMMETRICAL CONNECTION Digital output (Relay) Starting cable Red Shielding Red Signal cable White Shielding SYMMETRICAL CONNECTION Fig. 1.
Clarity - Getting Started Installation For easier changing of the wiring we supply SV8 Terminal board with screw contacts for INT7 and U-PAD A/D Converters. Connection of starting cables: Starting input reacts to a change of the TTL logical level (5V) or to a connection by any contact (button, contact of relay). Input implicitly reacts to a change from HIGH to LOW (or closing of a contact). The input function may be changed by switching the Down item of Ext.
Clarity - Getting Started Installation Fig. 2. System Configuration dialog • Set the number of instruments in the Number of Instruments field . Note: A larger number of instruments can be set than the amount you have purchased. You will not be able to measure on the surplus instruments (indicated by a blue symbol of the curve on the tab), but you may use them e.g. for “offline” preparation of methods. • Set the corresponding type of chromatograph (GC/LC/EA/GPC...
Clarity - Getting Started Installation • The configuration dialog of the corresponding card or equipment is displayed with a doubleclick on its icon or using the Setup button: Fig. 3. Dialog for setting the converter INT7 • Check that the correct number of channels is displayed, and, if necessary, perform further settings (e.g. set the names of the detectors). Note: You can change signal units using this dialog. More accurate description can be found in the manual of your A/D converter.
Clarity - Getting Started Qualification procedures 3 Qualification procedures The quality of analytical data is an issue that has been gaining increased attention in many laboratories these days. One of the requirements for ensuring the reliability of generated results is the validation of all instrumentation and procedures that are used to acquire data. For chromatography data stations usually three levels of validation (qualification) are relevant: 3.
Clarity - Getting Started Qualification procedures • If the Installation Qualification fails, it is recommended to uninstall and then re-install Clarity. If it fails again contact DataApex user support. Note: The most common reason for obtaining a "Failed" result of the qualification is due to the installation of the station upgrade over an existing full version of Clarity.
Clarity - Getting Started Program structure and control 4 Program structure and control The Clarity software has a hierarchic structure. After start-up the main Clarity window will be displayed with the symbols of the configured instruments. After clicking on the chromatograph picture and entering the User Name (more information on User Names can be found in the Reference Guide) the Instrument window will be displayed. This window is used for acquisition and data processing on the connected chromatograph.
Clarity - Getting Started Program structure and control or System – By setting access rights ( User Accounts command) you will allocate each user a name and password and you will determine the extent of authority for individual operation types (e.g. access to files, possible modification of calibration, integration parameters, etc.). Each user can set his/her own station appearance. For help on how to set a User Account, see Clarity Reference Manual. 4.
Clarity - Getting Started Program structure and control diagram. Windows are distinguished by line color in the analysis-processing diagram and Instrument name in the header. Windows enabling performance of required actions on a given Instrument can be displayed by clicking on individual icons in the diagram or on commands from the menu. Caution! 4.3 Certain Clarity windows (e.g. File Open or parameter setting dialogs) are modal.
Clarity - Getting Started Program structure and control Acquisition – section of parameters for signal measurement – voltage range, sampling rate, … Integration – section with an integration table Calculation – section with parameters for setting the type of calibration calculations LC/GC– optional section matograph control for direct chro- Advanced – section with advanced parameters for chromatogram calculations Note: 4.4 Individual instruments may add their own tabs into the method setup window.
Clarity - Getting Started Program structure and control Selection of displayed Switch to instrument or chromatogram calibration window Chromatogram Result table Other table tabs modifications Fig. 8. Work with several detectors/chromatograms Splitters Custom label Setting type of res ult calculation Chromatogram window The Result Table for a selected chromatogram can be found on Results tab.
Clarity - Getting Started 4.4.1 Program structure and control Multi-detector chromatograms In the case of multi-detector measurement, all signals are saved in one chromatogram. Individual signals from detectors are displayed as independent curves. To work with individual signals, it is necessary to select the required signal from the Chromatogram menu or by using the coloured symbol in the Overlay toolbar.
Clarity - Getting Started Program structure and control Note: Special add on module SST (p/n: A22) is available for statistical processing of results and monitoring of selected parameters. Multiple chromatograms can be opened simultaneously in the Overlay Mode. To switch it on/off use the File – Overlay Mode menu command or icon. 4.5 Calibration window The window for creating, modifying and displaying calibration curves is displayed by clicking on the icon.
Clarity - Getting Started Program structure and control Fig. 10. Note: 4.6 Individual compound tab The procedure for creating a simple calibration and its use is included in Chapter 5.6 on pg. 40. Single Analysis dialog The dialog for defining individual analysis contains fields for sample description, sample naming wizard and buttons for controlling the analysis. Fig. 11.
Clarity - Getting Started 4.7 Program structure and control Sequence window The window for defining sequential measurement of several samples is displayed using the icon in the Instrument window. Measuring is performed by rows in the table. Each row can define measuring of a greater number of samples by the same method or multiple measurements of one sample. Fig. 12. Sequence window ACTIVE or PASSIVE operation is possible.
Clarity - Getting Started 4.8 Program structure and control Program exit Shut down the program using the System Exit command from the main Clarity window. Before exiting you will always be informed of all running measurements and unsaved files. 4.9 Data update and consistency The Clarity station automatically keeps all data updated and consistent. For example, modification of the baseline is automatically manifested in the Result table.
Clarity - Getting Started First “Analysis” 5 First “Analysis” Description of an exemplary analysis will demonstrate basic practical work procedures with the Clarity station. Naturally, this description does not exhaust all of the station’s capabilities. • • • • • • • • 5.1 The First Analysis will guide you through the following steps: Program Start Project assignement Method development (data acquisition parameters, integration parameters, etc.
Clarity - Getting Started First “Analysis” • Click on the picture of the gas or liquid chromatograph. 5.2 Create new project Comments The default projects WORK1 - 4 are predefined for each Instrument. It is recommended to create your own new project to store your data. The Project serves as a base unit to organize corresponding methods, sequences, chromatograms and calibration files. Note: There are several DEMO projects that contain example data for selected separation techniqes.
Clarity - Getting Started First “Analysis” Fig. 13. Creating new project All template method (*.MET) and sequence (*.SEQ) files will be stored in the MYPROJECT folder. Calibration files (*.CAL) and calibration standards (*.PRM) will be implicitly stored in CALIB and Chromatograms (*.PRM) in DATA subfolders. folder contains files shared The COMMON among projects (e.g. report styles). 5.
Clarity - Getting Started First “Analysis” The calibration file (*.CAL) used for identifiing and quantitating the peaks is linked by its name in the template method and consequently in the chromatogram method. In the next step we will prepare template method for new chromatograms with general acquisition parameters. Later, after measuring the chromatogram, we will modify further parameters (e.g. integration table) in the chromatogram method.
Clarity - Getting Started First “Analysis” Note: range settings will increase the resolution at the baseline. The 10 Hz (10 points per second) Sample Rate is appropriate for most packed column separations in GC or HPLC, for capillary GC or CE with peak widths below 2 sec the 25 or 50 Hz should be used. • On the Integration tab, the Global Peak Width and Global Threshold can be set according to the expected peaks. Note: 5.3.2 Default settings can be used in most cases.
Clarity - Getting Started First “Analysis” It is advisable to include all information that may be used for searching for the measured chromatogram later on. Proceed • Click on the icon and fill in the header of the measured analysis (Sample ID, Amount, etc.). Fig. 14. Single Analysis dialog • Write the name of the chromatogram in the Chromatogram File Name field (you can use the wizard Note: 5.4.2 icon to add variables).
Clarity - Getting Started First “Analysis” • Finally, close the window using the the File - Exit command. 5.4.3 icon or Analysis run Comments Acquisition can be started externaly from the autosampler or by pressing the Run button. While running, the current measurement time and RUNNING inscription will be displayed in the Instrument window in the Status line under the diagram. Proceed • Run the analysis using the external start or the Run command in the Single Analysis dialog. 5.4.
Clarity - Getting Started First “Analysis” Fig. 15. Data Acquisition window The measured chromatogram can be compared to an already completed chromatogram, e.g. solvent, calibration standard, etc. Two types of chromatograms can be displayed in the background: • Simply by using the File – Set Background Chromatogram command select which chromatogram is to be displayed in the background.
Clarity - Getting Started 5.5 5.5.1 First “Analysis” Chromatogram evaluation Display chromatogram Comments The completed analysis is automatically displayed in the Chromatogram window. Automatic analysis display can be prevented by switching the symbol next to the icon to the symbol. The Chromatogram window can also be displayed icon. manually by clicking directly on the The required chromatogram can be selected icon.
Clarity - Getting Started 5.5.2 First “Analysis” Chromatogram processing Comments After stopping an analysis it is advisable to check and optimize the integration parameters. The key parameters are Peak Width and Threshold. Their simplified definition is: • The Peak Width parameter determines that all distinctly narrow peaks, compared to the defined value, will not be integrated.
Clarity - Getting Started First “Analysis” to suggest the initial values based on the narrowest peak of interest (peak width) and baseline part with no peaks of interest (threshold). Proceed • Switch to the Integration tab in the Chromatogram window to see the amendments to the chromatogram method integration table. • Use the Global Peak Width and Global Threshold interactive commands to optimize the integration of peaks.
Clarity - Getting Started 5.5.4 First “Analysis” Saving of a template method The changes made to the Integration table affect only the current chromatogram. To use those parameters for new chromatograms or reprocess, the current chromatogram method has to be saved as a template method using the command Method - Save as Template. Note: 5.
Clarity - Getting Started 5.6.1 First “Analysis” Opening a calibration file • • • • Note: When a calibration file was specified in the template method used for acquiring the chromatogram, you can open it from the Chromatogram window. Use the View button in the Chromatogram Results window. Use the File - Open Standard (yellow icon) command to open an integrated chromatogram representing a calibration standard.
Clarity - Getting Started First “Analysis” It can be also attached to a template method file to be applied to new chromatograms (or to reprocess existing ones) in the Method Setup – Calculation dialog. 5.6.3 Calibration curve use • • • • • The simplest way of verifying the correctness of the calibration is to link it to the chromatogram from which it was created. Move to the Chromatogram window (e.g. by icon). clicking on icon to display the dialog for Here, use the chromatogram selection.
Clarity - Getting Started First “Analysis” the retention time, the quantity will be zero. If the calibration compound is found and allocated, but no calibration curve exists, the Peak Type column will display the word Error. Caution! 5.7 The chromatogram typically uses calibration curves from the calibration file whose name is shown in the right-hand section of Results tab of the Chromatogram window. Therefore, this is calibration by reference.
Clarity - Getting Started Connecting Autosamplers you have invoked the printing commands. The content relevant in the current window is printed. You can easily customize the report styles according to your preference. Proceed • Click on icon in the Chromatogram window. • Using the Printer command on the right-hand side of the Report Setup dialog select and set the printer. • Modify current report style by selecting options on the individual tabs.
Clarity - Getting Started Connecting Autosamplers time. The sampler is thus synchronized with the GC by a signal wire (READY), alowing next injection only after the GC gets to the READY state. The Autosampler performs the injection and starts the GC using another signal wire (START). Any autosampler that is used in the Clarity Active Sequence without an AS Control module must be synchronized by cable with the Clarity station as well as with a chromatograph.
Clarity - Getting Started Connecting Autosamplers Wiring of the autosampler, that will be started by closing the contact at the READY input. AUTOSAMPLER READY INJECTION PC INT 7 (U-PAD, INT 5) OUTPUT CHROMATOGRAPH Digital output - OUTnR READY START INPUT EXT. START/STOP Fig. 17. Starting cable - INn START OUTPUT Wiring of the autosampler – variant A The injection will start only after both serially connected contacts (Clarity and the GC) are closed.
Clarity - Getting Started Connecting Autosamplers Variant B - started by opening the contacts In the second scheme there is autosampler wiring that conversely waits for output contacts to be opened. This requires different connection (marked by circle). The OUTPUT and READY contacts are connected parallel to each other and the autosampler will start its operation after both contacts are opened.
Clarity - Getting Started Connecting Autosamplers Any autosampler that is used in the Clarity Active Sequence without an AS Control module must be synchronized with the Clarity station by cables. The INn starting cable should be plugged into the synchronization output (INJECTION) of an autosampler and the OUTnR cable plugged into the synchronization input (READY) of an autosampler. Note: Further information about Active Sequence is available in the Clarity User Guide.
Clarity - Getting Started Connecting Autosamplers utilize the OUTnR digital output cable. All timings are governed by the chromatograph; Clarity only performs one analysis for each start signal received. All synchronization only includes external start up of data acquisition in Clarity using the INn starting cable. Fig. 20. Wiring of an autosampler in Passive Sequence A Passive Sequence has to be used e.g. in the sets with Headspace autosamplers (without AS Control module). Caution! Note: 6.1.
Clarity - Getting Started Connecting Autosamplers Autosampler wiring in Active Sequence with AS Control module. PC COM RS 232 INT 7 (U-PAD, INT 5) AUTOSAMPLER READY INJECTION OUTPUT Starting cable - INn Fig. 21. 6.1.5 Wiring of an autosampler with AS Control module + A/D converter AS – Active Sequence + AS Control + digital acquisition When using optional AS Control module in combination with digital acquisition detectors (e.g.
Clarity - Getting Started Troubleshooting 7 Troubleshooting If you will not find your answers here, use the www.dataapex.com website where the Support menu will navigate you to frequently asked questions (FAQ), Clarity email conference archive or contact to DataApex helpdesk. 7.
Clarity - Getting Started Troubleshooting Note: You may find other Error Messages and solutions for problems connected to particular hardware in its respective manuals. 7.2 Problems at station start 7.2.1 DEMO – missing HW Keylock The Rockey (or Sentinel) protective key (dongle) must be plugged in either a parallel or USB port and its driver must be properly installed. Several problems may cause this error message: 1. Solution: 2. Solution: Your protective key may not be properly installed.
Clarity - Getting Started Troubleshooting 3. Solution: Your protective key may not be correctly connected. a) For a dongle connected to a parallel port: • Try to print on the connected printer. • Ensure that the printing cable is not too long (>3m). • Disconnect the printer cable and connect the dongle directly to the port of the computer. b) For a USB dongle, check the following: • A USB dongle may not be used in Win NT • See whether the USB port is working (e.g. try to connect a different device, etc.
Clarity - Getting Started 7.2.4 Troubleshooting DEMO - Trial Expired Solution: 7.2.5 DEMO (in the window header) Solution: 7.3 7.3.1 Grey icon File CLARITY.SNO is missing from the CLARITY directory or is empty. It is missing or empty erroneously or your Clarity station just ended its trial period. Copy the file CLARITY.SNO to the main (CLARITY) folder from the installation CD (it can be found in the DEMO subdirectory).
Clarity - Getting Started Troubleshooting If your A/D card is not in the left-hand list Setup Control Modules, add it using the Add button and repeat the previous step. Note: See chapter 2.4 - Clarity configuration on pg. 14 for detailed description.
Clarity - Getting Started Troubleshooting From the list of equipment allocated to the instrument, take the Detector x from DEMO driver field and draw the correct detector of the A/D card you are using from the list on the left. If you only have Demo detectors in the lefthand Setup Control Modules list and your A/D card is missing, open the Available Control Modules dialog and using the Add button add it to the configuration of the station. Then repeat the previous step. 7.3.
Clarity - Getting Started 7.4 Troubleshooting Hardware key 7.4.1 Rockey USB dongle (re)installation • Install Clarity software from the CD ROM. Caution! Be sure to have suitable drivers at hand before inserting the USB token into the PC slot for the first time! • Connect the USB dongle to a USB port of the computer. INSTDRV.EXE file from • Use the C:\CLARITY\HW_DRIVERS\ROCKEY\ folder to (re)install the Rockey drivers.
Clarity - Getting Started 7.4.2 Troubleshooting Rockey LPT dongle (re)installation • • • • • • • • 7.4.3 If you encounter problems with printer port Rockey hardware key, then: Verify that the key is properly inserted in the printer port. In filemanager (e.g. Windows Explorer) navigate to C:\CLARITY\HW_DRIVERS\ROCKEY\ Run the INSTDRV.EXE file to invoke the Setup Wizard. Select Repair in the first dialog and click Next. In the second dialog check the "Install parallel driver" checkbox.
Clarity - Getting Started 7.5 Troubleshooting System Files (systeminfo.txt file) The C:\CLARITY\SYSTEMINFO.TXT file contains valuable diagnostic information. Its contents can also be displayed in the Clarity Help – About – System Files dialog. Fig. 23. Help – About – System Files The file contains following information (these are examples of what the listings could look like. The information in the program section are visible in the Fig. 23): System: Microsoft Windows 2000 version 5.
Clarity - Getting Started Troubleshooting the build, serial number of the station, number of instruments allowed, extensions available, purchased control modules, type and serial number of the hardware key and list of A/D converters/detectors connected to the computer and configured in the station. Solution: 7.6 The registered files entries should match the installed files in version and location. When there are some discrepancies, it may (but need not) cause some problems.
