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1. 81 YL Clarity User Guide 11 2 Files 11 2 1 Chromatograms PRM Each chromatogram contains the following e A header that specifies the date and time of an analysis name of the analyst and the parameters of the sample e Original raw data of the whole analysis from up to four detectors e Chromatograms from up to four detectors with the originally detected baseline e Method describing the progress of a measurement its modifications and evaluation e A link to the name of the calibration file being used e Storage of all methods including the calibration files from all the states in which they were ever saved printed or exported e Descriptive labels and lines only those attached to the signals yi Full version e A record of all chromatogram changes Chromatogram Audit Trail e An electronic signature 11 2 2 Template Method Files MET Each template method file specifies the conditions under which the chromatogram will be measured and evaluated The content of the template method file is copied to each chromatogram at the moment an analysis is terminated The Template Method File contains the following e Indicative information the column and mobile phase used the type of detector employed and its settings etc e Parameters of the input converter detector selection and a table for controlling the control outputs according to defined events for up to four detectors e An integration table for up to
2. YL Clanty User Guide ENG Tel 82 31 428 8700 Fax 82 31 428 8779 Email export younglin com www younglin com 2008 Young Lin Instrument Co Ltd 899 6 Young Lin Bldg Hogye dong Anyang Gyeonggi do The Republic of Korea YOUNG LIN INSTRUMENT Using this document The User s Manual offers users of the YL Clarity chromatographic station a detailed description of controls a procedure for processing the first analysis detailed guidance concerning the fundamental types of analyses and calibrations as well as copious additional information about the options and variants relevant for working with the station Chapters 1 2 and 3 are earmarked for beginners who will quickly find the required information there Once the user has become acquainted with the fundamental procedures of the station turn to Chapter 10 Troubleshooting for a list of the most common problems encountered when working with the YL Clarity station The Reference Guide contains summary information regarding all commands and error messages The User s Manual presupposes that the user is coming to the station with some prior knowledge of the fundamental concepts such as file directory path etc of Windows operating systems The following fonts are used in the manual to highlight parts of the text Open Commands and items bold Instrument Window titles Sans Serif bold WORK Filenames and directories uppercase lettering Key des
3. Abort Help Fig 30 The Recalibrate Peak Dialog The window offers a selection of the recalibrated level and contains the compound name the total amount of recalibrations already effected and the recalibration table The first calibration of the compound is included in the number of recalibrations and is reset to 1 each time recalibration of the Replace type has been undertaken The Cancel command will skip the recalibration of the currently displayed compound and the Abort button will terminate the recalibration of all compounds The recalibration table contains the previous and current values of the two responses the amount including the units and the absolute and relative deviations A differing amount if any will be recalibrated in the same manner as the responses The Default Injected Amount item offers a more suitable method for correcting differences in the injected amount see Chapter 6 12 The Over message will appear in the Departure column each time a permitted deviation set in the Search Criteria field has been exceeded 6 10 Multidetector calibration Calibration and recalibration for multidetector measurement is performed in the same way as the single detector described in the previous chapters When the multi detector calibration standard has been loaded and the calibration of the first signal has been calibrated another signal may be selected using the Calibration Set Signal or using corresponding colour symb
4. Among other things a user may be restricted in their authorisation to change fundamental station settings access certain instruments inspect or change the data of other users etc Active chromatogram The chromatogram name that is displayed in the header of the Chromatogram window All data being displayed and operations performed will only relate to this active chromatogram The name of the active chromatogram is highlighted in the key by bold letters Active chromatogram signal When performing a multi detector measurement each chromatogram file may contain a record from up to four detectors this is what we call signals The active signal in the chromatogram is the signal whose name is being displayed behind the name of the chromatogram in the window header and header of the tables divided by a hyphen The name of the active signal together with the name of the chromatogram will be highlighted by bold letters in the legend of the graph Active calibration signal When performing a multi detector measurement each calibration file may contain calibration curves for up to four signals The active signal i e its table or curve of the calibration will be highlighted in the header of the calibration table or curve by its name At the same time all values that are signal specific will be displayed in the same colour as the active signal Active detector A detector whose measurement and calculation parameters are displayed in the Ac
5. Check the template method using the Method button Having injected the sample run the analysis using the Run button The control of an analysis through an external signal is described in chapter 4 3 1 1 External Control of Analysis Run on page 22 Note Measurement can also be run by using the Analysis Run Single command or using the 6 icon from the Data Acquisition window 19 YL Clarity User Guide Monitoring the analysis By default the range of the signals from detectors will not be automatically identified during analysis The fixed range defined in the Time to and Voltage to fields will always be displayed When the preset values are exceeded the window will not be automatically redrawn Note The values entered in the Time and Voltage fields do not in any way limit the scope of the acquired data The maximum voltage range is defined by the Range items from the Method Setup Acquisition dialog The duration of an analysis may only be restricted by checking the Enable Autostop checkbox and setting the Run Time field from the Method Setup Measurement dialog Background chromatogram You can also compare the analysis that is in progress to a completed chromatogram by invoking the File Set Background Chromatogram command and selecting the chromatogram that is to be displayed in grey in the background of the Data Acquisition window The chromatogram in the background will only appear after the current analysis has
6. Presentation 22 Retention Time correction 64 updating 59 65 Run command 19 25 26 Run Program 25 Sequence 29 RUNNING 15 25 Sample ID 28 Sample Rate 16 Save 10 Save As command 10 dialog 10 Scale 38 Scheme of data processing 3 Search Criteria 61 Select all 8 Separation 47 Sequence 25 Active 26 problem solving 76 run 29 Sequence Table 27 window 27 Setup Columns 8 49 Shortcuts 5 Single Analysis 19 Slices 78 Snapshot 22 Solvent Peak 46 Start 44 Start Restart 22 Start Stop 22 Station configuration 99 Statistical Moments 50 Status Table 99 Std 28 User Guide Stop command 21 22 State 15 25 SV 27 System files 99 Tables Changing values 7 Configuring 7 Entering new values 6 Local menus 7 Tail Tangent 43 Tangential separation 42 Template method 99 Text Label 35 Threshold 20 40 77 Time 19 Time to 20 Title Font 35 Together 42 Toolbars 3 Units Font 35 Unprotected mode 100 Unzoom 56 Up 22 Update Retention Time 65 User Accounts 99 Validity Interval 41 Valley 41 Value Font 35 68 Voltage 19 Voltage to 20 WAITING 15 25 Window Calibration 13 Chromatogram 13 Clarity 13 Instrument 13 Sequence 13 Zooming 33
7. ccccccccccccccccceeesseeeseeeeeeeeseeseeeeeeeeessnaaeeees 22 4 3 1 2 Continuous Preliminary Measurement Processing cccccsseeeeeeeeseeeeeeeeaeees 22 YL Clarity Contents 4 3 1 3 Control of External Devices 0 0 eee eccccccecccseeseeeeeeeeeeeeeeeeeeeeeeesaeeeseeeeeeeessaaaaaaess 22 4 3 1 4 Automatic Functions after Analysis Termination ccccssscccssseeeeeeseeeeseeeeeeens 24 4 3 2 Batch Measurement of Analyses SEQUENCE ccceeeeeeeeeeeeeeeeeeeeeeeeeeeeaaaeseeeeeees 25 rss a FAS WE EOU ee eee ee 25 4 3 2 2 Active Sequence without Control ccccccceesceeccceeeeeeeeseeceeeeeeeeesseeeeeeeeseaeaseees 26 4 3 2 3 Active Sequence with Control Marty ec ccccccccsseseeeceeeeeeseeeeseeeeeeesseeaeeees 27 4 3 2 4 Sequence Table and lts Creation ccccccccceccceeeeceeeseseceeeeeeeaeeeeeeeeeeessuaaeeess 27 4 3 2 5 Procedure of Sequence Measurements cccccccceesseeseeeeeeeeeeeeeeeeeeeeesesuaeseees 29 4 3 3 Batch Processing of Analyses CMa i iecccccssseeeceeseeecceeseeeseeeecsseeessaaeees 30 4 4 DDE synchronization with other Programs cccccccseeeceeeeeeeeeeeeeeeeeeeeeseeeeeesenseneeeees 31 5 CHROMA TOGRAM accesses eee 33 5 1 WISHIAVING SB ChromatograiTi cscs cerstseacnestesenc cacieentanneticectaontiaacadetsdaninac aceonbertenstesonedoanivania 33 52 Display Characteristics sacccacccccnscconcenpancamuadeazaonosiceaccdaevinsundassaaradneanennaceabouapanaagondeaataueeans 33 5 2 1 Chromat
8. in other words you cannot add new compounds in this manner Identifying a calibration using the Add Group command will only proceed according to the group identifier 7 Updating retention times of compounds The retention time of any compound can be changed manually in the Retention Time column at anytime The retention time is also automatically updated during each new calibration or recalibration of the compound in question The updated retention time is taken as the arithmetic mean of all values established using existing re calibrations of that compound The automatic update can be switched off by unchecking the Update Retention Time item in the Calibration Options dialog 6 7 Manual Calibration If you wish to acquire full control over the calibration process reset the Automatic parameter to Manual in the toolbar Calibrate Peak 14 29 First Free Level 9 Amount Current Level 1 0 9 g kg Compound Name Area 2197 06952 Peak 14 29 Height 608 43061 Compound Type Left Win Right Win Ordinary v 0 2 0 2 Skip Abort Help Fig 27 The Calibrate Peak Dialog After using certain of the Add All Add Existing Add Peak Add Group commands in the manual regime the Calibrate Peak Group dialog will be displayed for each compound in which you may immediately amend and enter all data on the calibrated compound For the Add All command you can then skip the calibration of the currently displayed compound using the S
9. specifies the overall amount of components in calculation of percentages in Chromatogram Results window These parameters can also be modified later in the right part of the Chromatogram Results window If the Amount field is left blank 0 the total amount Total row value of Amount column in the Results table will be computed as the sum of calibrated amounts of all compounds also including unidentified compounds if Response Factor from Unidentified Peaks field is non Zero If the Amount field is provided non Zero its value will be substituted for the Total row value of Amount column in the Results table The Amount column values will be then calculated with itas a base The Dilution field multiplies the values in the Amount column Result Table ESTD 2506multi UV SSS Rainy Rd A Lid gn N 3 eee etree al A All ld 3 ified Peak Response Base Area 4563 3 613 A 0 053 0 2 Ordnr oxalic cee enti led reaks s 5 203 253 325 A 3 217 10 7 Ordnr citric All Peaks in Calibration 5417 561 713 A 4743 158 Ordnr tartaric E Response Factor 6 300 217 455 A 2 362 7 9 Ordnr malic E 8160 176 947 A 2250 7 5 Ordnr succinic Scale Amount g l ISTD Amount EM 8 550 193 934 A 3 941 13 1 Ordnr lactic M Use Scale Factor 10 347 152602 A 2 623 8 7 Ordnr acetic Tota C a T cale Factor ai hialueaaleall Dilution Non zero Amount is used as Total in the Amount column thus being a base for calculating the figures in Amount column Re
10. table already contains compounds then only these compounds will be calibrated Add Existing AddPeak Only the selected peak will be calibrated Only the group containing the peak selected using the amp Add Group ee oe a cursor will be calibrated 5 Supplying known amounts and other data items Enter all known amounts for all compounds in the Amount column below the calibration level Level 1 Update the compound name in the Compound Name column 6 How to display and check the calibration curve Click the tab with the name of compound whose calibration curve you want to see the calibration table the calibration curve and parameters of that compound will be displayed 7 How to redisplay the main calibration table and the standard Click the General tab 8 Saving the calibration file To save the calibration file invoke the File Save command 57 YL Clarity User Guide 9 How to use the calibration file Open the Chromatogram window using the Window Chromatogram command or the icon Open the chromatogram to be evaluated using the calibration that has just been created Set the created calibration file using the Set command in the right hand side of the Results tab Do not forget to set the appropriate type of calibration calculation in the Calculation item If all went well the Amount column of the result table should now contain the amounts for all calibrated and identified peaks 6 6 Creatin
11. trailing edge of the external pulse The Start Only item specifies that the external signal will only start analyses subsequently manually terminated either by the Stop command or by checking the Enable Autostop checkbox V External Start Stop C Start Only Start Restart C Start Stop Up Down Fig 5 External Start Stop section of the Measurement tab The Start Restart item decides on whether the external signal will stop the currently running analysis and immediately start the next one continuous series of analyses The Start Stop item specifies that the external signal will only terminate the currently running analysis and the start of the next analysis will wait for an additional external signal 4 3 1 2 Continuous Preliminary Measurement Processing While an analysis is running the already acquired part can be evaluated while the analysis continues using the Snapshot command from the Single Analysis or Data Acquisition windows This command is almost identical to the Stop command but does not stop the analysis The Snapshot is suitable e g for a preliminary evaluation of a prolonged analyses The Snapshot does not increment the counter of the analyses n and a warning message regarding an eventual overwrite of the existing chromatogram will be displayed only when the Snapshot command has been used in the analysis for the first time Any changes will then be overwritten by next use of the Snapshot command or a
12. z Note It follows from the above that separation parameters will not be applied e g to manually added peaks and their effect might be suppressed e g by using the Together and Valley commands specified in the integration table Major commands and global parameters are explained and their effect illustrated in the following chapters General modification procedure Click the corresponding icon on the Baseline and Peak toolbars or from the Chromatogram Baseline Peak menu to initiate the manual chromatogram modification procedure The mouse cursor will be displayed at approximately the centre of the active chromatogram as a vertical line with an arrow pointing to the signal level Point the mouse cursor to the location where you wish to effect the requested operation and left click the mouse button If an interval operation is involved a second vertical line will appear and the second point can be similarly selected The user can cancel the operation anytime using the right mouse button or the key Repeated usage of selected operation If you want to use a certain operation several times it is advantageous to hold button before After selecting the operation and releasing the button you will be able to repeat selected operation until you chose another function or press the button 5 4 1 Baseline Modifications The Baseline submenu and the corresponding toolbar contain the commands used for modifying the baseline operations and elimi
13. A list of all files of the given type from the current directory is displayed on the left the path is shown in the title bar Information about the file If you click any file and have the panel with a detailed view of the file open by i icon the items below indicate a detailed description of the file the name of the author the version potentially a preview of the data Opening a file Use the OK button or double click on the filename to display a file If the station is operating in the password protected mode and you do not possess the necessary authorisation to access the file an error message will appear Changing the directory If you wish to open a file from another directory click the Look In combo box pull down menu to inspect and change the current path The following icons are displayed in the top right portion of the window They allow the user to directly return to the current directory F Current project storing the template methods The common project COMMON storing the report styles Data subdirectory of the current project storing chromatograms fc Calibration subdirectory of the current project storing calibration files and standards Ordering files Files are ordered alphabetically by default To order files either by date time size or when last saved set a detailed view using the T icon and sort the files by double clicking the heading of the corresponding column Double clicking agai
14. Active Chromatogram 36 Automated reporting 25 Automatic Functions after Analysis Processing 24 Axes Fixed rendition 35 Back Horizontal 42 Baseline drift and noise 19 Modifications 40 toolbar 41 Batch command 24 dialog 30 Between 68 Bipolar 19 Both 45 Calculation description 49 ESTD 52 ISTD 52 non calibrated 52 percentages 51 unidentified peaks 51 Calibrate Calibrate Group 59 Calibrate Peak 59 Calibrated group 96 Calibration artificial 62 calibration curve 55 Compound tables 54 description 49 How to create one 57 level 58 Manual 59 Standard 96 Table 53 54 units 62 Calibration File 20 description 53 modification 61 Calibration Options Defaults 62 window 60 Cancel 5 Chromatogram 33 3D View 39 Colour 37 Descriptive labels 35 displaying 33 Modifications 39 window 18 Clamp Neg 43 CLARITY EXE 98 Clear 3D 39 Clipboard 8 97 Color 35 Compound Calibration Table window 55 Compute with Origin 56 Concentration Levels 58 Control of External Devices 22 Copy From 48 From Model 48 Copy from Model 98 Correlation equation 56 YL Clarity Factor 56 Create Label 35 CSW32 Evaluation 97 Curve fit equation 56 Curve Passes Through Origin 56 Cut Neg 43 Data processing string 97 Data Acquisition disabled 75 no signal 75 premature termination 75 sampling rate 16 Data evaluation 22 Default Injected Amount 61 Default Injected Volume 63 De
15. Compound Name Reten Time Rae aya o eee Peak Type RB 0 0000 6 6144 0 101 0 0153 0 0000 30 0980 0 210 0 0070 0 0000 102 9247 0 441 0 0043 0 0000 121 1866 0 600 0 0050 0 0000 180 1218 4 003 0 0056 0 0000 180 9175 0 600 0 0033 0 0000 37 1333 0 239 0 0064 0 0000 58 8496 0 600 0 0102 0 0000 216 8337 1 223 0 0056 oxalic 0 200 Ordnr citric 0 200 Ordnr tartaric 0 200 Ordnr glucose 0 200 Ordnr malic 0 200 Ordnr fructose 0 200 Ordnr succinic 0 200 Ordnr lactic 0 200 Ordnr 0 200 Ordnr rPrPPrPPrPrPPrPPrP rr 2506MULTI RI 2506MULTI UVvIS amp 6 100 glucose 3 6 623 fructose 5 8220 succinic 6 6 547 glycerol 3 a acetic 9 7 8 Retention Time Compounds A oxalic A citric A tartaric glucose A malic fructose A succinic A lactic A glycerol A acetic methanol ethanol For Help press F1 Chromatogram 2506MULTI Fig 24 The Main Calibration Table The table can be displayed above or below the calibration standard graph see the View Table Up command 6 4 2 Compound Calibration Tables Calibration tables of individual compounds are available together with the calibration curves and other parameters from tabs of individual compounds in the Calibration window Used Compound Name oxalic Display the relevant tab by double clicking its name or the first grey field of the M citric E tartaric corresponding line in the main calibration table The table lists values for all levels of the relevant compound
16. Setup defines the parameters common to the printout in its entirety Report Setup Chromatogram Page Setup Black and White Print Cancel _ Lab Header IV Print Background Color of Graphs Report Header Help Method Form Font Value Font Calibration New Margins mm y Chromatogram Open Results Top 5 Save Sequence g SST Left 5 Between 2 Right 5 Save As Audit amp Signatures n Bottom 5 Printer Preview Print Print To PDF Send PDF Fig 35 The Page Setup tab Use the Form Font commands and the Value Font to select the type size and properties of the employed font Form Font will be used to print headings Value Font for the data items proper The commands in Margins section decide on the page margins the Between command specifies the space between individual parts of the printout all parameters are in millimetres Heading The second tab Lab Header contains the laboratory header Up to ten lines of text can be entered and will appear in the header of the first page or alternatively in the header of all pages in the printout according to how the On 1st Page Only item has been set The header can be framed using the Border item and printed on grey background using the Grey Background item The Number of Lines field specifies the number of lines per page A separate font type font size and characteristics can be selected for each li
17. User Guide 7 2 Report Style Files A report style is really a template that contains a list of all the sections to be printed and the report layout size and type of the font borders spaces etc During the printing process proper the actual values or files are merely inserted into the corresponding sections Each report style is then stored in the corresponding report style file where its contents can be displayed and modified The adapted report style can be saved under the same or different name as a new report style All activities are concentrated in the Report Setup dialog Report styles are stored in the COMMON subdirectory and are common to all instruments and projects 7 3 Printer Selection Printer selection is the only part of the Report Setup dialog that is not included in the report style and is shared by the whole station in other words it is not possible to set different printers or different print quality at individual parts of the station The list of available printers their set up and the connection with the computer all constitute a part of the Windows system and the station takes it over in its entirety Start the selection using the Printer command Select the appropriate printer using the button this will display a list of all printers that are registered with the Windows operating system While the station is running click the line that contains the requested printer to make it the current printer The Propert
18. again and hold down while dragging the cursor left or right to the desired location for the column As soon as a thin red line appears at the location where you want to move the left border of the column release the left button 3 613 253 325 How to sort items in a table Items lines of a column are ordered by default according to the first column or the order in which the lines have been created To reorder a table according to some other column double click the heading of that column to sort in ascending order repeat the process to sort the table YL Clarity User Guide in the descending order Some tables e g the Integration Table cannot be reordered or reordering must be first permitted by the Enable Sort command from the local menu Displaying and hiding columns The result tables in the Chromatogram window and tables in the Calibration window can be extensively reconfigured using the Setup Columns command from the local or Edit menu Once invoked the Setup Columns dialog will open From here the user can select the columns to be displayed and define their order Creating of new column with definition of calculation Invoke the Add Column command to open the Add User Column dialog Here the user can create a new column for the table using a predefined calculation formula User columns can be displayed in the Result and Summary tables 2 6 Clipboard Using the clipboard All data in tables and parameters may be transferr
19. be equipped with one starting input and one confirmation output Once a sequence has been run using the Run command from the Sequence window the station will send an authorising signal and await confirmation from the autosampler The station will begin a measurement after confirmation has been received The run will terminate after the time that has been specified in the Enable Autostop parameter from the corresponding method has expired and the station has remained in the DLE state for the period that has been defined in the d e Time field Thereafter a new authorisation signal will be sent to the autosampler and the station will await its confirmation The above cycle will be repeated for all the measurements listed in the sequence table If the sequence table has to be updated a sequence may be suspended using the Pause command the command can be invoked anytime but the sequence that is in the RUNNING state will only be suspended the next time the station switches over to either the DLE or the WAITING FOR READY state Invoke the Resume command to continue the sequence Conditions underlying start of an active sequence 1 A checked Active Sequence checkbox in the Sequence Options dialog 2 A checked Enable Autostop checkbox in each method included in the sequence table 3 Creation of a logical loop e the relevant digital output should be connected to the confirmation autosampler input e the output signal from the autosampler should
20. been manually shifted it may happen that the station refuses to place the point at the requested position since it detected that the baseline would intersect the signal and will place the point at the nearest possible location 39 YL Clarity User Guide Integration Table 0 CHROMA TOGRA M Y WORK T data1 911 Filter Ott Chromatogram Grp Time A Time ie Operation min min Peak Width min Default 0 050 Threshold m Default 0 200 Integration Interval 3 000 0 000 Min Area m 0 000 0 000 0 010 Min Height m 0000 0 000 0 010 Half Width min 0 000 0 000 0 020 Tangent Area Ratio 0 000 0 000 S01 O00 Valley Tovalley Slope 0000 0000 0200 Peak Add postive T 369 04a Results SUMMA Integration Measurement Conditions h SST Results Fig 17 Chromatogram Integration The order and hierarchy of parameters and commands that affect an integration 1 Peak detection using the Peak Width and Threshold parameters starts from the time indicated in the Integration Start parameter 2 An attempt then follows to draw the baseline to the valley according to the ValleyToValley Slope parameter followed by automatic tangential separation according to the remaining two parameters of the Separation section 3 The Integration Table is applied A check of possible baseline signal intersection is performed 5 Finally all peaks that fail to satisfy at least one of the parameters specified in the Rejections section are excluded
21. both are from the Chromatogram Overlay submenu The two straight lines displayed by the 3D View command are used to set up the angle and depth of the three dimensional view All chromatograms will be regularly displaced along the selected line The displacement is governed by the Offset X and Offset Y fields from the Graph Properties Signals dialog The Clear 3D command zeroes the above offsets and accordingly displays all chromatograms in their original positions The original positions of individual chromatograms are set using the Original command again from the Graph Properties Signals dialog 5 4 Chromatogram Modifications By default each chromatogram is integrated according to the parameters from the Integration Table displayed in the Chromatogram Integration window When using multi detector chromatograms each signal will have its own independent Integration Table The Integration Table contains all parameters from the template method These parameters can be modified and filled in either directly in the integration table or using the commands from the Chromatogram Baseline Peak and Integration submenus Note The station automatically checks for instances of baseline crossing After each operation the baseline will be corrected to prevent baseline crossing the station either shifts the peak beginning or peak end to the nearest possible point or refuses to perform the requested operation If the peak s beginning or end has
22. calibration subdirectory Rapidly switch between the subdirectories using the fis and iG icons in the Open Chromatogram dialog Note If you prefer not to have the chromatograms separated in the above manner select identical names of the two subdirectories Analysis Subdir and Calibration Subdir when establishing a new project in the Project Setup window To obtain detailed information about the active chromatogram invokes the Method Measurement command from the Chromatogram window 4 3 Fundamental Procedure of Analysis The following chapters present directives informing about various methods of analysis processing The basic procedure is also described in the Getting Started manual in the First Analysis chapter Additional information is also available in chapter 10 2 Signal Displaying and Measurement on page 75 4 3 1 Single Analysis This chapter describes a comprehensive procedure of analysis processing and takes most options the station has to offer into account Some additional variants are discussed in subsequent chapters Instrument selection Click the instrument icon found in the main YL Clarity window that represents the chromatograph you wish to use in the analysis Fill in your name or while in the protected mode select your User Name and enter the Password Then click the OK button to open the corresponding Instrument window Setting up measurement conditions All parameters and data items referring to t
23. command Both commands can be found in the Edit menu In addition to the serial peak number the retention time and width at half height of all peaks absolute calibration values and percentages names and types of compounds are displayed for uncalibrated results By setting the calibration file in the Calibration File Peak Table field using the Set button and selecting one of the calibration calculations in the Calculation item the absolute calibrated values and percentages as well as the names and types of compounds will also be displayed See Chapter 6 3 Types of Integration Calculations on page 50 and the Reference Guide for a more detailed description of individual calibration calculations Result Table 2506mutt U lt ESTD Reten Time Compound Response Name 3613 A oxalic 5 203 253 325 A 4 609 168 Ordnr citric 5 417 561 713 A 2 372 24 7 Ordnr tartaric 6 300 217 455 A 1 181 12 3 Ordnr malic 3 160 176947 A 1 125 11 7 Ordnr succinic 8 550 193 934 A 1 970 20 5 Ordnr lactic 10 347 152602 A 1 312 13 7 Ordnr acetic 12 710 A Ordnr methanol Total 9 595 100 0 Results Summary Performance Integration Measurement Conditions SST Results Fig 22 Example of Calibrated Results Table 49 YL Clarity User Guide 6 2 Table of Peak Parameters For the purposes of Good Laboratory Practice and to verify the suitability of the employed system calculations have been extended to include some special parameters such as asymmetry
24. compile the calibration equation for the given type of curve fit Change the type or normalise all amounts e g by dividing multiplying all values entering the calibration by 100 and then specify the Scale Factor 100 or 0 01 in each affected chromatogram 10 7 Calibrated Calculations The requested type of calibrated calculation was not used If the required type of calculation is not specified in the Results table all the conditions that underlie its use have probably failed to be satisfied See Chapter 6 3 3 Internal Standard Methods ISTD on pg 52 and the Reference Guide for additional details The following are the most often encountered underlying errors e Use of the incorrect calibration file or too narrow identification windows e For an ISTD calculation the calibration file must contain the compound marked S7D e InISTD calculations with different amounts of internal standard when it has either been set in only an unknown sample or only in the calibration file The station will then not be able to recognize whether it is missing from one or is surplus of another Therefore YL Clarity would rather choose an uncalibrated calculation instead of an incorrect variant of the ISTD calculation 79 YL Clarity User Guide e InISTD calculations with the same amount of internal standard when it has either been set in only an unknown sample or the calibration file The station is then not able to recognize whether it is missing from
25. create lines Paste Insert Erase the table field CT R DEL Display the previous cut out Previous Chromatogram Zoom Calibration R Data Acquisition CTRL H Display the next cut out Next Zoom i YL Clarity User Guide Display in original size Unzoom ee Start an analysis Run Single Start a sequence Start Run Sequence Pause a sequence Pause Resume running of a set sequence Resume Abort Sequence Data Acquisition CTRL HI Process the sample currently being measured without terminating the analysis Snapshot Terminate a sequence after the completion of a sample measurement Stop Downl Skip the current sample Skip CTRL Left Repeat an injection from the current vial Repeat Injection Sequence CTRL El Reset the flags in the Sts column Reset Status Sts Insert Adds the selected device to the instrument _ If no device is selected opens Add Device dialog System Configuration Clears the selected device from the instrument _ l 2 5 Tables Because tables in the Windows environment are not standardised the following essential characteristics of tables used in the YL Clarity program are presented below 2 5 1 Editing Entering new values Values can be directly entered in individual cells provided the table cells are editable Note Some tables such as the Result Table as well as tables
26. dialog Use the _ lt button or drag and drop with mouse to remove the selected device from the displayed instrument Use the lt lt _ button to remove all devices from the displayed instrument INT5 board setup The ISA board of A D converters INT5 is not equipped with a Plug and Play system and so the configuration has to be done manually Specify the connection between YL Clarity and the A D converter board Interrupt and Base Address items The values set here must coincide with the setting of the jumpers on the converter board otherwise data acquisition will be inoperative It is recommended that you note these parameters e g in the corresponding table provided at the end of the Reference Guide 12 1 1 Number of Instruments Up to 4 instruments may be set in the No of Instruments item regardless of the number of instruments in your version The excess instruments so called Offline instruments will be fully functional for evaluating analyses that are proceeding in other instruments although not for data acquisition 12 1 2 Description of Instruments and graphical symbols To make the work with the station more comprehensible the user can assign a name to each instrument using the Name field select the type of attached chromatograph in the Type of Chromatogram item and assign arbitrary images to represent opened and closed chromatographs by clicking the images below the Image for Closed Opened Chroamtogram inscriptio
27. dragged simultaneously e Point the cursor to the number of the line to be dragged The cursor will change to e Left click the mouse button hold and select the other lines to be dragged e Release the mouse button then click and hold it again anywhere over the highlighted lines e Drag the cursor to the newly desired location of the selected lines The location will be indicated by a red hairline e Release the mouse button The lines can also be moved using the Line Up and Line Down commands from the Edit menu Selection of lines for measurement In practice it may happen that you have defined a sequence table for more extensive analyses but you currently only need to use a few lines of this table One possibility is to mark the lines in the Run column Larger tables can be edited using the following commands from the Edit menu Mark for Run Includes selected lines for measurement the checkboxes in the Run column will be checked Clear Run Marks Excludes the selected lines from the measurement the checkboxes in the Run column will be unchecked Invert Run Marks Inverts the status of the checkboxes in the selected lines Lines that have been checked will be unchecked and vice versa Another option is to write the individual lines 1 3 7 or groups of lines 1 4 6 7 in the Run Lines field from the Sequence Options dialog 28 YL Clarity User Guide 4 3 2 5 Procedure of Sequence Measurements 1 O
28. expressed in any units The type of units is specified in the Units Compound field of the Calibration Options dialog The units stated there will be shown at all amounts in the table in the graph and also in the Results table in the Chromatogram window 62 YL Clarity User Guide Note The user can specify their own units in Units after Scaling item of the Results table 6 12 Correction for Differences in Injected Amount Different injected amounts of both the calibration and unknown samples can be adjusted to a common value If the Default Injected Volume checkbox has been checked and a value has been entered in the Calibration Options dialog each response used in calibration recalibration or evaluation will be multiplied by a correction factor calculated as the ratio of the above value and the value of Inj Volume from the chromatogram header Unless the Default Injected Volume checkbox has been checked the Inj Volume parameter serves for informational purposes only If you change the entered value you can invoke the Update Calibration Responses command to recalculate all responses by multiplying them by the ratio of the old and the new value If the Default Injected Volume checkbox has been unchecked the last recalculated values of responses will remain valid regardless of any changes made in Inj Volume item Owing to the linear interpolation that replaces the actual dependence between the amount and the response it is advisable
29. four detectors e The name of the calibration file and calculation parameters yi Full version e The parameters used for direct chromatograph and autosampler control optional 11 2 3 Calibration Files CAL The calibration files contain calibration curves for a practically unlimited number of compounds for up to four detectors Any calibrated chromatogram contains a link to the calibration file and also a copy of all the calibration files that where present at the moment of saving printing or exporting changed comparing to the last saved version yi Full version Note The calibration file also contains a record of all the changes performed Calibration Audit Trail 82 YL Clarity User Guide 11 2 4 Sequence Files SEQ The sequence files enable one to perform a series of measurements Each sequence file contains the relevant sequence table and some auxiliary parameters Each line of the sequence table in fact describes the method of measurement and evaluation to be used for one or more injected samples yi Full version Note The sequence file also contains a record of all performed changes in the Sequence Audit Trail 11 2 5 Report Style Files STY A report style decides what will be printed and how The following information can be printed as part of a report e The measurement description and conditions e The chromatograms and calibration curves e Tables of results e Sequence tables The user can a
30. from all detectors will automatically be identified and displayed within the range set in the Time and Voltage fields When the displayed range is unsatisfactory change the values in the Time and or Voltage fields and confirm the change by pressing where the signal will be displayed with the new Zoom Use the left mouse button to zoom in on any one of the cuts To resume from the original magnification that was specified in the Time and Voltage field double click the left mouse button The station will store selected cuts to see them use the Previous and Next Zoom commands respectively Note In a zoomed in cut the window will no longer be automatically redrawn the same is true when the base range of the window has been exceeded Starting an analysis Use the icon or the Analysis Single command to open the Single Analysis dialog where the analysis can be controlled Single Analysis C Clarity 2 4 4 WORK1 Wefault1 Analysis Sample ID 421 Sample Ethanol Amount 0 ISTD Amount 0 Dilution 1 Inj Volume ml 10 Calibration Standard Method Level Control ae ee ee ee Chromatogram File Name My LC 1 ze Zn gt m Enable File Overwrite Counter 1 Data Recovery OK Cancel Help Fig 3 The Single Analysis Window Fill in header of the analysis in the Analysis group If you check the Calibration standard checkbox the chromatogram will be automatically stored in the CALIB subfolder
31. from files that have been opened for reading only cannot be modified After first clicking a cell you may then enter a new value that replaces the previous one By double clicking or pressing the function key F2 the cell will be transferred to the edit mode lf after clicking an arrow button is displayed the cell represents a list of values prepared in advance Click the arrow and select the appropriate value from the list Move among the cells by means of the cursor keys Once the first cell has been entered the next row will automatically be created The row being entered is assessed in its entirety for error during these modifications and can only be abandoned after all errors have been corrected YL Clarity User Guide If the requested row is not visible locate it using of the vertical scroll bar displayed on the right or by using the cursor keys It is also possible to enlarge or maximize a window and display all rows of a table Changing values in cells without predefined values Click anywhere inside the cell and enter the new value the old value will be erased Text can be edited after double clicking anywhere inside the existing value or pressing F2 2 5 2 Adding and Deleting Lines A new line will automatically be created once the first cell has been filled in The user may edit the new line only after the accuracy of the preceding line has been verified The easiest way to delete a line is by first selecting it using
32. from the Chromatogram Overlay submenu or by using the and 3 icons Modification procedure Invoke the command place the mouse cursor at any part of the main graph click and hold down the mouse button while slowly dragging in the desired direction the chromatogram will move and change its size Once the requested location or size has been reached release the mouse button Displaying changing values The values by which the chromatogram has been changed are shown in the Line Charts tab of the Graph Properties window in parameters Offset X Y and Multiplier X Y The chromatogram can be directly modified by changing the values of these parameters Invoke the Origin command to return to the original size and location Saving the effected changes The chromatogram that has been modified as described above will become a mere graphical curve i e the baseline and the peak descriptions will disappear To create a full bodied chromatogram from the curve invoke the Overlay Operation Copy command followed by the File Save command See Chapter 5 3 2 Mathematical Operations for additional information 5 3 2 Mathematical Operations Some basic mathematical operations over chromatograms can be performed using the Overlay Operation command from the Chromatogram menu by clicking the i icon Mathematical Operations Operand Operation Operand B V The Whole Chromatogram The Whole Chromatogram Copy Example Signal 3 C Diffe
33. in the ID field and invoke the Delete command Use the displayed interval vertical lines to select the peak s to be deleted from the group If the selected group is a member of another group its membership remains intact List of existing groups The Existing Groups list specifies all groups containing at least one peak Group name If a calibrated calculation has been enabled and the employed calibration file contains calibrated groups the list will display their names as defined in the calibration file Editing the group name Group names cannot be changed in the Groups dialog since they are derived from the names shown in the calibration file and can thus be only changed in the main calibration table of the relevant calibration file 5 4 4 The Selection of Conditions That Restrict Integration The Rejection section in the Integration tab can be used to exclude from integration peaks that do not satisfy certain criteria All peaks whose Area Height or width at half height Half Width are smaller than or equal to the specified values will be excluded from integration in other words they are neither displayed in the chromatogram nor included in the Result Table This way particularly with the Height parameter you can get rid of small insignificant peaks that confuse the results without affecting the baseline that runs under the remaining peaks 5 4 5 Separation Parameters The Separation section in the Integration tab can be use
34. item select whether you wish to display the axis with a fixed scope of values Fixed or whether the station is to automatically convert values to decimal multiples these will be expressed by the prefix before the name of the unit e g mili micro kilo etc Auto 5 Ascertain what voltage corresponds to 1 AU and enter its inverse value into the Scale field For example if 1 AU corresponds to a voltage of 2V enter the value 0 5 into the Scale item 5 2 3 Descriptive Labels and Lines The main graph can contain descriptive labels and lines Both can be situated in the graph area or anchored to the active chromatogram Descriptive label location Invoke the Chromatogram Create Label Text command from the menu or from the local menu to display a dedicated cursor Move the cursor to the intended location of the new descriptive label Doubleclick to open the Text Label dialog where you can enter the text of the label in the Text field select the font in the Font item and decide which point the nearest chromatogram point or to the graph border will be fixed to 35 YL Clarity User Guide Anchoring to chromatogram To anchor a label to the active chromatogram check the Assign to Active Chromatogram parameter Invoke the Anchor Text Alignment command to decide which point the nearest chromatogram point or to the graph border will be fixed to Line location Invoke the Create Label Line command from the Chro
35. keys and key combinations striking multiple keys simultaneously Keyboard shortcuts of the MS Windows system Applies or implements the selected command The command that has been selected will be highlighted in the menu in a dialog the borderline of the button will be emphasized by a continuous or broken line YL Clarity User Guide From the menu the required command can be selected using the cursor keys and from a window using the Tab key Esc In a dialog the key substitutes for the Cancel key and will close a dialog without saving the changes Hides an expanded menu Tab Gradual selection of commands parameters edit lines and buttons in the active window A selection is usually completed using the key Spacebar Rapidly switches between selected parameters by checking or un checking them Alt Selects the first menu item Ali letter Rapidly selects a command or parameter that has the selected letter underscored Insert Switches between the insert and overwrite regimes When editing text lines you may use to decide whether new characters will be inserted at the cursor position or will overwrite the characters to the right Keyboard shortcuts of the YL Clarity shortest meon vay LS LZ EAE CTRL Close current file Close CTRL SHIFT W Close all opened files Close All LSJ LO N C CTRL Insert and
36. left clicking the mouse on the file name an second click will cancel the selection To select a contiguous list of files left click the first desired file hold down the key and click the last desired file all interjacent files will be selected Pay attention to Select All Ctrl A and Unselect All commands which are self explanatory Processing order The items in the list of files can be sorted alphabetically in ascending item Normal or descending order item Backward by filename Sort by Name or date saved Sort by Time Processing proper Start the processing using the Proceed command If no chromatogram or sequence has been selected the command will merely save the current settings of the Batch window The Open Chromatogram Window through Run Program checkboxes are the same as those in the Postrun Setting window See Chapter 4 3 1 4 Automatic Functions after Analysis on page 24 for additional details 4 4 DDE synchronization with other programs DDE Dynamic Data Exchange is a technique the Windows system uses for transferring data between individual applications running under Windows By means of DDE another application may follow the status of the YL Clarity station and control a co operating device accordingly The YL Clarity station behaves like a DDE Server Other programs can be connected to the YL Clarity station through the following variables Service Name Clarity Topic Name Status Item Names Cha
37. level number in the first column responses in the Response column and amounts at individual levels in the Amount column The Response Factor column contains level specific response factors equal to the amount divided into the response at that level The Rec No column displays the number of eventual recalibrations of the point Note The level specific Response Factor is merely an indicative value When the free calibration is to be employed the global response factor taken from the main calibration table will always be used Display and calculate areas or heights The base either the peak area or peak height of the displayed response of the level response factor of the correlation equation and of the displayed curve is determined by the Response Base field 54 YL Clarity User Guide My GC Calibration 250X8HR1 cal lt Statistical IEX H form 9 mM H2S04 0 5 ml min MODIFIED File Edit Display Calibration view Window Help fy fy Ai m EE E ao EE AIEE 1 JH Automatic Recalibration Response Amount Resp i oxalic 4 068 min 0 1012 0 0153 2 0 0115 6 6144 2 18 8121 0 2160 08316 0 071 120 0000 06592 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 3 0000 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 1 1 1 IWAAMIM900000 1004 gi e E Response Response Base Area Compound Type Ordnr X Curve Fit Type Linear
38. line will separate those peaks and its position will coincide with the new peak end If the peaks are separated by a vertical line or connected at the valley and the peak end is shifted closer to the apex the peaks will be separated Voltage 1E 3 mV a a o o o 2 84 Isopropanol Voltage 1E 3 mv 2 84 Isopropanol N o 44 YL Clarity User Guide Change the valley or vertical separating line The Both command or it icon defines a new position for a valley or the vertical line that separates the peaks The common point can be shifted to any location between the apexes of the two peaks Should the resulting baseline intersect the signal the peaks will be separated Voltage 1E 3 mv Voltage 1E 3 nV 3 2 25 2 50 2 75 3 00 2 25 2 50 2 75 3 00 Time min Time min Adding new peaks Interval lines set the beginning end of a new peak The apex is automatically determined at a location between the maximum and minimum depending on peak orientation between the peak beginning and end A new peak cannot be added in the area of tangentially separated peaks Adding a positive peak The Add Positive command or icon creates a new positive peak If the beginning or end of the created peak falls inside a neighbouring peak the peaks will be separated by a vertical line that may either be placed at the beginning or end of the created peak A 35 30 A 2 25 20 15 10 5 0 7 00 7 25 7 50 7 Adding a negative pea
39. peak of interest is at least 10x smaller that the voltage range set in the Range item in the Method Setup Acquisition dialog use a lower range Some peaks are not being detected e Check whether the limiting integration conditions are improperly set using the Rejection item in the Integration tab of the Chromatogram window These parameters are included in the method file and might even prevent integration of correct peaks if the selected method is inappropriate e lf you use the integration algorithm with the default values Peak Width 0 1 min Threshold 0 1 mV the very narrow peaks occurring at the beginning of analysis might be ignored Try reducing the Peak Width If this leads to the detection of many small spurious peaks set the Threshold to a value higher than the height of these spurious peaks It must be stressed that the detection of peaks always depends on an interplay of the above two parameters and changing only one of them not always produces the expected results see Chapter 4 2 for additional details e f none of the above two remedial measures was successful in recognising some undetected peaks the peaks involved are probably highly distorted so that their shape fails to satisfy the elementary conditions for peak detection In this event use manual integration Chromatogram Peak Add Positive Negative Too many peaks are detected For a very noisy signal the algorithm might erroneously interpret the noise as
40. provides a comprehensive review of all the possible ways to measure a single or a series of chromatograms 4 1 Measurement A complete measurement is comprised of the data acquisition from a detector the digital integration of the measured data and storage of the results on the hard disk Individually an Instrument window can be in any one of the following individual states regardless of the state of other Instrument windows STOP A measurement is not in progress and may not be started by an external signal WAITING A measurement is not in progress and the station is waiting for the external start signal before it can begin RUNNING An analysis is in progress PAUSED Indicates a suspended sequence RUNNING PAUSED The sequence will be suspended after the current analysis has been completed IDLE The state of active sequence after the measurement has been finished and before the confirming signal will be sent from the station to the autosampler The duration of IDLE state can be customized by the user CONTROL Data acquisition has completed and the control program of the directly controlled chromatograph or the LC pumps is concluding its run WAITING FOR READY The active sequence has been started station is waiting for the READY signal from the directly controlled device Measurement with the YL Clarity station is comprised of the following steps e The A D converter transforms the analog signal to a 24 b
41. same for all compounds and that all compounds present in the injected sample were actually detected Since the first assumption is very rarely met non calibrated calculations are primarily used to obtain a preliminary semi quantitative result Note Non calibrated calculations are also used by default in instances where a calibrated calculation has been selected but not all required conditions have been met no calibrated compound was identified in the chromatogram or the requested calibration file was not found The type of calculation that is actually being employed will always be indicated in the header of the table of integration results Results together with a reason for why the required calculation could not be performed 6 3 2 External Standard Method ESTD Calculating using the external standard method respects differences in detector sensitivity to various Compounds and provides the amounts of individual compounds and their percentages in the injected sample The drawback of the external standard method is that it is extremely sensitive to both the injected amount and measuring conditions To eliminate any possible errors it is mandatory to maintain the highest precision of injected amounts autosamplers and frequently rebuild the calibration files using recalibration so that they reflect potential changes in characteristics of the detector and the chromatographic system as a whole The above drawbacks are in part removed in the inte
42. saves the file under a different name and or in a different directory from which the file was opened When invoked the Save As dialog will display the original filename and directory of the file Enter a new name in the File Name field and select another directory using the Look In field also known as the combo box and use the File Type field to save the file in another format Note The File Type item converts files between the CSW17 CSW32 and YL Clarity stations in both directions Save as C Clarity WORK1 DATA Lookin DATA ezez ezi Boe ce i Name Size Type Created Last Change PRM Chromato 7 11 2003 13 45 1 10 2003 9 02 PRM Chromato 23 11 2003 15 55 24 11 2003 11 22 PRM Chromato 7 11 2003 13 45 26 9 2003 15 59 PAM Chromato 7 11 2003 13 45 26 9 2003 16 00 PAM Chromato 7 11 2003 13 45 26 9 2003 16 01 File Name 12506multi prm File Type Clarity chromatogram prm v CSW 17 chromatogram prm Analyst CSW 32 chromatogram prm SamplelD 71 ea chromatogram prm i 1250 mv 10 Hz Sample Ul standard wine mix 7 17 00 min Fig 1 The Save As dialog Note It is not advisable to save files outside of the current project folder 10 YL Clarity User Guide 2 9 Recording all station operations Audit Trail Station Audit Trail The YL Clarity station keeps a log of all of the operations that it performs Records of the Station s operations are saved in the LOG sub folder in the
43. sccsnrnnsareenn aeea ARE a EEEE ORERE RAEE 101 1 INDEX ceire E EE see eee ee E E A 103 VI YL Clarity User Guide 1 Introduction 1 1 Description of the YL Clarity Station The YL Clarity chromatographic station is an effective program used to acquire process and evaluate data from any standard commercially available gas liquid chromatograph The station can process analyses containing hundreds of peaks with varying widths from tenths of a second to tens of minutes Due to the adjustable range anywhere from 156 mV up to 10 V of the inlet A D converter the station can be directly connected to the output of almost any chromatograph YL Clarity collects chromatographic data independently in the background while the user analyses previously acquired data corrects the baseline performs calibrated or uncalibrated calculations or runs other programs Results can be printed on any printer and the printout layout adapted to the user s needs through a host of adjustable parameters Tables data and displayed chromatograms can be exported as files or inserted directly to other programs running under Windows Calibrated calculations by the external or internal standard method may be performed using the calibration files Each calibration file can contain an arbitrary number of components each calibrated at up to 20 concentration levels YL Clarity is also equipped to automatically process all data acquired from CSW stations The full
44. station CLARITY DSK A default station desktop file DSK A station desktop files of individual users TXT A text file that contains topical information The main directory contains the following subdirectories COMMON A subdirectory that stores common methods and report styles PROJECTS A subdirectory that contains a list of all projects BACK A subdirectory with backup copies of configuration files of the previous version after updating the station DOCPDF A directory with an electronic version of all manuals in PDF format CB20 INT7 UPAD SENTINEL Directories with backup copies of PnP device drivers IMAGES A directory with symbols of the selected chromatographs SOUNDS A directory with the default sounds assigned to selected events TMP The directory for storing temporary data during acquisitionand backup copies of the last two measured chromatograms from each instrument WORK The basic project directories assigned to one station instrument LOG A directory with the station audit trail files Each project directory can contain the following files MET Template methods SEQ Sequence files DATA Data subdirectory containing the following files PRM Chromatograms CALIB Calibration subdirectory containing the following files PRM Calibration standards CAL Calibration files A more detailed description of the structure of subdirectories can be found in Chapter 13 Working with Directories and Projects on page 91
45. tables The correspondingly coloured icon will be indented To select another chromatogram as active click on the correspondingly coloured icon or select the chromatogram from the Chromatogram List dialog Overlay EJ W m E E E E e amp Fig 15 The Overlay Toolbar Changing chromatogram colour To change the colour of any of the first eight chromatograms simply click the icon of the chromatogram whose colour you wish to change and then on an empty icon with the desired colour The colour of the icons and the chromatogram will change accordingly Closing a chromatogram To close the current chromatogram invoke the Close command from the File menu or click the X Icon Invoke the Close All command to close all displayed chromatograms Disabling the OVERLAY mode To disable the OVERLAY mode click the Overlay command from the File menu or the indented My Icon The station will invite you to save modified chromatograms that are about to be closed 37 YL Clarity User Guide When the OVERLAY mode has been disabled only the current chromatogram will be displayed in the graph 5 3 1 Resizing and Relocating Chromatograms The current chromatogram can be resized and moved independently in horizontal and vertical directions This makes it easier to match two chromatograms e g to subtract the solvent peak or to modify a chromatogram with erroneous retention times These modifications are made using the Move commands and Scale
46. the capacity factor column efficiency and resolution These calculations can be found in the Performance tab This tab is implicitly hidden use the View Show Tables Performance Tables or Results Performance Table commands to display it Column Performance Table 2506mutt UY calculated Statistical A 7 Unretained Peak Time 1 min Reten Centroid Variance Skew Excess Efficiency Effa Inet Time min min2 th pl t p m 100 4563 4590 00041 0 639 0 099 5146 51456 Bah Gru 5203 5200 0 0026 0 281 0 495 10551 105514 5417 5436 0 0091 2219 7577 3256 32563 Column calculation 4 6300 6309 0 0049 0152 0 950 8145 81449 Statistical Moments 6 573 6 619 0 0091 1 387 2 219 4828 48275 From Width at 50 6 7453 7457 00066 0195 0 813 8435 84351 7 7 853 7 795 0 0076 0 381 0 828 8020 80196 Results Summary Performance TETTA A Measurement Conditions F SST Results F Fig 23 Table of Peak Parameters Calculation method Use the Column Calculation parameter from the Performance tab to select one of the two available calculations 1 According to statistical moments Statistical Moments This constitutes the most accurate integral calculation based directly on the values measured for a given peak The calculation provides top quality results for well separated peaks at a reasonable signal to noise ratio and sufficient number of partial integrals for individual peaks The underlying formulae are listed in the Re
47. the time axis X Axis checkbox and either the chromatogram in its entirety or only the currently displayed part All Data or Displayed items to be exported In what format is the chromatogram exported The chromatogram is exported as one or two columns of values separated by a character selected from Text Format item The Fixed format adds the required number of spaces between values of different length to ensure that they are properly aligned in columns of equal width The first column contains time in minutes the second column voltage in mV The time increment is taken from Time Step field Each voltage is calculated as arithmetic mean of all voltages within the specified time increment If zero has been entered the data will be transferred with the minimum time increment of the chromatogram in question defined by the sampling rate Sample Rate If a value larger than the chromatogram duration has been specified as the time 71 YL Clarity User Guide increment the result will be a single number representing the voltage that is averaged over the entire chromatogram No other data baseline marks retention times descriptive labels are exported In this instance the Headers checkbox will insert headings of individual columns The Full Format checkbox will insert the chromatogram header at the beginning of the exported text In what format is the Results Table exported A character taken from the Text Format item will separate the
48. used for sorting data of certain compound determination for different series of samples or for data from certain time period Whenever an instrument starts it opens that project which was used the last time by any user on this instrument Projects contain paths to last opened chromatograms calibrations reports sequences and methods When a project is opened by any user these last opened files are opened automatically prj file The project files are named as prj They are contained in the PROJECT directory situated in the working directory by default CLARITY The main function of the project file is to specify another directory having the same name and containing relevant stored data Project directory The project directory contains template methods sequence files report styles and also two subdirectories DATA and CALIB The data subdirectory stores chromatograms the calibration subdirectory stores calibration standards and calibration files To switch between the calibration and data subdirectories when selecting files click either of the ff and fe icons in the File Open Chromatogram dialog By default files from the current project are displayed in each instrument Use the icons and commands from the File Open dialog to select a file from any other directory To facilitate sharing files common to several projects e g report styles the station contains the COMMON directory Click the f amp icon in the File Ope
49. values of individual cells of the table The Fixed format adds the required number of spaces between values of a different length in order to align them into columns of equal width The Headers item adds headers to individual table columns The Full Format item appends the name date and time of chromatogram creation to each line of the table Which characters may be used as separators Characters for separating individual columns are selected in the Text Format item If the Delimited by Comma Delimited by Semicolon or Delimited by Tab item has been selected the corresponding separator will be inserted between individual data items To preserve the layout of the table use the Fixed format this format inserts the number of spaces necessary for properly aligning values unless a proportional font such as the System font is being used between individual data items This selection is suitable for exporting data to text editors when creating final reports Note The Fixed format is suitable when a document is to be left as it is without further amendments To classify sections of reports into a document in the text editor create a separate style which for example could be named YL Clarity report and will use a disproportionate type font Then apply this style to passages that have been copied from the report of the station On the other hand the Delimited format is more suitable if further amendments to the report are to be ma
50. version involves these extra features Data can be acquired simply by using the control module from chromatographs with a digital output YL Clarity can be configured to allow measurement on up to four chromatographs simultaneously each of which can be equipped with up to 4 detectors YL Clarity is also equipped to support the cooperation between chromatographs and autosamplers and tools for supporting the requirements of the FDA s 21 CFR Part 11 guideline 1 2 Updating of program Updates to the purchased version of YL Clarity are provided free of charge We are constantly developing the YL Clarity station to meet the needs of our customers Should you have any problem with the station please do not hesitate to let us know Whether it concerns inadequacies in the existing functions or suggestions for improvements we welcome and take seriously user opinion as part of our job Who s afraid of the Internet For easier communication with the developer s team we have prepared special web sites on which you can learn about a range of interesting information and on which you can inform us of any improvements you would like made where you can meet other users and mutually exchange experience upon solution of ordinary problems with chromatographic work All sites are easily accessible from the home page of the Young Lin company at the address www younglin com We would like to draw your attention to several sections of the website YL
51. will occupy the entire page width and unless a fixed height is specified by the Fixed Height command the default height will be 2 3 of the page When the Landscape item has been selected the chromatogram will be printed on a separate page with the time axis along the longer side of the page Use the No of Pages parameter to print the chromatogram on several pages Printing in Colour The station is able to print on colour printers Chromatograms descriptive labels and lines will be printed in colour 69 YL Clarity User Guide 8 Import The YL Clarity station provides complex possibilities for chromatogram imports in the following AIA TXT and EZ Chrom formats Importation can be performed using the File Import Chromatogram command from the Chromatogram window Select the desired directory and file s to import in the Open Files to Import dialog Files can be filtered to display only the files of a selected type using the Files of Type listbox Attention mported chromatograms will be processed using the current template method opened in the Instrument window and not using the method of the currently opened chromatogram Importation of multiple files at once Multiple files can be selected at once in the Open Files to Import dialog A separate dialog window will subsequently be opened for each imported file AIA format The format of AIA files is quite strict in the form but the content is not fixed Thanks to this the AIA fi
52. you have installed Should a newer version now be available a dialog with the number of the new version will appear and you may download the new version After downloading the YL Clarity station will automatically shut down and run the installation program The program will take you step by step through the installation of the updated version These updates are only available to registered users Registration is accomplished by using the Help Register command YL Clarity User Guide 2 Station Control Although the YL Clarity station operates similarly to other programs that run in Windows we would like to provide brief descriptions of basic Windows concepts 2 1 Windows Main windows The YL Clarity station has a hierarchical structure Instrument consists of up to four major windows the Instrument Chromatogram Calibration and Sequence windows When any of these windows are opened the corresponding icon along with the name will be displayed in the MS Windows taskbar Note If you find too many icons displayed in the taskbar distracting uncheck the Show Windows on the Taskbar checkbox from the User Options General dialog accessible from the Instrument window using the View Options command Modal windows Some open windows called modal windows prevent the user from working in any other window until the modal window is closed The Open File dialog for selecting files is an example of a modal window MS Windows shortcu
53. 00 Pump Detectors l Driver An INT 1 Int A D Card driver CCA Instrument 2 Aa Digital 1 HP5890 GC Driver C2 Instrument 2 X Aa Detector 1 UPAD USB Driver LC3 Instrument 2 GC LC 4 Instrument 2 3 GCs HP5890 GC Driver 3E AS As 3 HTA Euro AS300 Sampler Se Sampler 1 HTA Euro AS300 Sampler _ Sampler 1 Instrument 1 Control Number Start In Int A D Card driver v fi X Ready Out intz A D Card driver x fi l Cancel Help Fig 38 The System Configuration dialog The command opens the System Configuration dialog Using this command will display a list of all installed and configured devices and control modules in the left and the configuration of individual instruments in the Instrument 1 4 tabs in the right How to add a device to the left list Below the list Setup Control Modules is the Add button which displays the list of all currently available device drivers in the Available Control Modules dialog The dialog contains all drivers that you have installed including those you can t use due to licenses not purchased Click the Add button or double click the name of a device to transfer it to the list Note Being listed in the file does not necessarily imply that the device is present correctly installed or properly connected The configuration dialog of the device involved will open first If an A D or D A converter is involved the station will attempt to find the converter during the set up If the
54. Clarity User Guide Downloads Product Updates Offers updates to the station Registered users may obtain the latest versions of their station Support Technical Support The easiest way to connect with our user support is via e mail You may of course also contact us by telephone or fax Technical support enables you to determine the source of a fault and notify us with information we need to be able to help you to solve any problem you may have Support Frequently Asked Questions The FAQ section summarizes and addresses some of our customers most frequently asked questions and provides the answers User Forum The Users Forum is a place where users are able to exchange experiences they have had with Young Lin chromatographic stations and any connected technical or methodological problems that may have occurred while measuring chromatographic analyses Naturally our technicians carefully monitor this forum and answer questions regarding the use of YL Clarity but it is also not impossible for another user to have had the same problem as you may be experiencing and have an idea of how to solve it Automatic check of last available version Should your computer be connected to the Internet you may make use of automatic checking of the last available update In the main YL Clarity window use the Help Check for Updates command The command will compare the number of the last available version on the Internet server with the version
55. DONT Ve FES E E EE A EEA E 67 Ted Pime SOS CON emeenin EEEE EEEE ESEE EEE 67 Te REDON Ve Sel OCHO N nese E 67 LO Repot oye Modic alO Messens ipia E a E enaeetesuchatss 67 8 IMPOR Toia a a E E S r eee eee re A eee eee a E 70 9 EXPORT cene A A E ene eee 71 9 1 Conjoint text export of Chromatogram and the Corresponding Results 0086 71 9 2 Exporting results to a database ccccccsscccccccssssececccseseceeseeeeeeeeeeaaseeeesssaaseseesesaaeeeess 73 9 3 Exporting the Summary table cece ccccececccseeseeeeeeeeeeseeeseeeeeeeesaaeaseeeeeeeessaaeaeeeeeeees 73 9 4 Exporting a chromatogram ssessssorerssersnsernrerarnnrnrnrernrnrernrernnnerennrernnrerennrernnrerennrennne 73 9 5 Exporting Chromatograms as Vector PICtUIeS cccccccceceseeeeeeeeeeeeeeeeesaaeeesesaaaeeees 73 10 ROUEN Ge ese eee eee ent 74 10 1 Running the PO GI AIM ic saesercties acinen codeantinaalscdeetteadanaatancidveinechadvutdnedsaustencdienselacelsiwandeettencaceds 74 10 1 1 YL Clarity Lite cicic icc da vescs cisncted eden seneececdaedetasieccedccadscevedeedsedaladersscdenceedsdesanesacdedesneciee 74 10 1 2 YL Clarity Fe i cicccccccceccecscsececerscscsecenscsusecensesesaversvsecacenseseceverees 74 10 2 Signal Displaying and Measurement ccceeeecceeceeeeeeeeeeeeeeeeeeeseaaeeeessaeeeeeeeesaaeeeeeeaas 75 ROS Mies 1 18 16 9 C t ene eee eee cn ene eee eee eee eee eee 76 10 4 Processing and Displaying ChromatOgrams cc
56. Integration Calibration File Set the calibration file that contains the table of compounds used for their identification as well as the calibration curves used to calculate the actual amounts in the Method setup Calculation dialog 20 YL Clarity User Guide Preparation for analysis termination Check the Setting Postrun command from the Instrument window regarding which activities will proceed after the processing of measured data See Chapter 4 3 1 4 Automatic Functions after Analysis on page 24 for additional information Invoke the Analysis Single command to open the Single Analysis dialog and inspect the Chromatogram File Name field Up to 254 characters including spaces and national characters may be entered The following characters are however not allowed J 2 l lt gt I When employed in the normal operation the automated naming option is very useful The station uses a set of variables such as the sample number and current date etc that are preceded by the character Once an analysis has been terminated each such variable will be substituted by the topical value Variables may be combined and the topical value will be displayed in parentheses above the Chromatogram File Name field and in the Information table of the Instrument window For additional details refer to the Reference Guide chapter Single in the Chromatogram File Name section Assistant for setting file name Click on
57. It is essential to keep in mind that when the Enable Overwrite toggle in the Single Analysis dialog has been checked newly created files will overwrite any old ones A completed chromatogram appears clipped from above or from below e First verify that the chromatogram is not clipped only clipped on the monitor because of the Properties Axes Range Fixed command e lf the chromatogram is clipped from above the detector signal was apparently cut off either because of a too low range setting in the Range item of the Method Setup Acquisition dialog or was already cut off in the detector because of an excessive preset range or the injection of an extremely concentrated sample 76 YL Clarity User Guide e f negative voltage values are missing from the chromatogram the Bipolar item in the Method Setup Acquisition dialog was probably left unchecked this item enables the measurement of a negative detector signal There is an excessive noise in the chromatogram A measurement was possibly made using an unsuitable connection between the chromatograph and the computer e g the detector cable of the YL Clarity station was not shielded Another reason might be a defective chromatograph or converter board Check the chromatograph e g using a recorder or contact your vendor Small peaks exhibit a staircase shape or excessive noise Possibly the full measuring range of the converter is not being utilised If the voltage of the maximum
58. Main station directory 98 Manual Calibration 59 Integration 78 modification of responses 61 Recalibration 60 Mathematical Operations window 38 Measurement preliminary processing 22 sampling rate 16 Method 17 Method Setup Acquisition 76 Measurement 75 Model method 98 Move 38 Next Zoom 19 56 No of Pages 69 Noise 19 excessive 77 setting parameters 16 Offline 75 On New Page 67 Only with export 25 Orientation 69 Over 61 Overlay disable 37 mode 37 Toolbar 37 PAD 99 Page Setup 68 Parameters 25 Password 98 Peak Adding new 45 delete Lock 41 Groups 46 User Guide Identification 63 Peak Type 63 Peak Width 16 20 40 77 problems with detection 77 Toolbar 44 Portrait 69 Postrun command 21 24 dialog 24 window 24 Previous Zoom 19 56 Print chromatogram 69 in Colour 69 printer selection 67 printer selection 66 Printout 98 Project directory 99 file 99 Protected mode 99 Range 18 Recalibration description 60 manual 60 Reference Peak method description 63 scheme 64 Reject Negative 43 Rejection 40 47 Report Setup command 66 Lab Header 68 Page Setup 68 window 66 67 Report Style 67 Reports description 66 Response Global response factor 62 manual modification 61 Response Base 54 Response factor 62 Response Factor 54 Response Factor 51 Restore Default Columns 49 Result Table description 49 YL Clarity Results Display 21
59. a high number of small peaks Working with such chromatograms is very confusing and the speed of all operations decreases dramatically e Increase the value of Threshold e Make the chromatogram more lucid by reducing the number of detected peaks using the Rejection command to appropriately set the integration conditions e In some instances it might be advisable to ban undesirable peaks using the Baseline Lock command Incorrectly detected peaks e When the Threshold value is too high the beginning of some peaks might be placed too high on the leading peak edge This can be corrected using the Chromatogram Peak Start command An alternative automatic remedy may be tried by entering a lower value in the Threshold field T7 YL Clarity User Guide e When the Threshold value is too high the narrow peaks may not be detected or a group of unseparated peaks may be integrated as a single peak If this happens decrease the value of the Peak Width parameter With very narrow peaks it is advisable to verify that the chromatogram was not measured with a too low sampling rate Sample Rate E g when the chromatogram has been measured using a 10 Hz sampling rate the decreasing of the Peak Width parameter under the value 0 07 min will have no effect It is then necessary to measure the chromatogram again with an increased sampling rate e lf the Peak Width parameter is too low a group of peaks might be separated the peaks in the group are not
60. agnified and contracted without any adverse effect on its quality or file size A detailed procedure for copying a chromatogram to an MS Word document 1 Display the requested chromatogram in the Chromatogram window 2 Invoke the Export Export as Picture to Clipboard command 3 Run MS Word and open the target document 4 Point the cursor to the location where the chromatogram picture is to be inserted and select Edit Insert from the main menu The inserted picture can be magnified or contracted and modified once double clicked 73 YL Clarity User Guide 10 Troubleshooting This chapter summarises problems most often encountered when working with the YL Clarity station Problems are listed in chronological order in which they might occur in a typical working procedure 10 1 Running the Program 10 1 1 YL Clarity Lite Demo inscription in the header of the Instrument window The demonstration version of the program has mistakenly been run The demonstration version will have the serial number displayed in the About dialog in the form 99 999 Open the window using the Help About command Message Demo Wrong S N in the Instrument window The serial number of the station listed in the About dialog open the dialog using the Help About command differs from the number on the A D Converter board Message Demo Missing HW in the Instrument window e The A D board has either not been found or has been damaged e INT7 board d
61. am Page Setup V Print Info _ Lab Header l On New Page Parameters Report Header Signals Summary Method All MV Levels Calibration f Current y Chromatogram C Only Active Signal Open Results Sequence x SST Audit amp Signatures Current s Save Save As Printer Preview Print Print To PDE Send PDF Fig 34 The Report Setup Dialog 2 Selecting a printer Check and if need be select a printer using the Printer command including setting the quality and size of the printout 3 What will be printed Look through all tabs in the left hand side of the Report Setup window and check or change what will be printed The name of the report style containing these settings will be displayed in the title bar of the window 4 Selecting a different report style In some instances it is more convenient to use a different report style instead of modifying the current report style Invoke the Open command to list all the report styles that are stored in the COMMON directory 5 How will the printout look Use the Preview command to see what will be actually printed 6 Printing reports To start printing the report invoke the Print command The dialog showing the printer settings will appear once again to enable the user to verify that the settings are correct determine the number of copies to be printed select the scope of printed pages etc 66 YL Clarity
62. am dig input Dig Inp DataApex 2 Down DataApex U PAD2 aes Event Table Measurement Acquisition Integration Calculation Advanced Cancel Apply Report Help Fig 6 Event Table A new line will automatically be appended once the previous line has been correctly filled in Active sequences use some of the digital outputs for synchronising the station with chromatographic equipment A N Should you use an active sequence ensure that you do not use those specific outputs in the Events Table Active sequences are described in chapter 4 3 2 2 Active Sequence without Control on page 26 Manual setting of control outputs Control outputs can also be manually managed using the System Digital Outputs command Invoking the command will open the Digital Output Control XXX Board dialog where XXX stands for the name of the A D board that is used or selected The first column Initial State is earmarked to set up the default state of the outputs each time the program is run The second column Current State sets the topical state of the outputs and enables the user to change it immediately Digital outputs of Data pex U PAD2 SN 2 Output Initial State Current State eee no Output Relay Output Relay escriptions 1 Qe Be A Digital Output 1 2 OW OW t Digital Output 2 Close Help Fig 7 Digital Output Control for the U PAD2 23 YL Clarity User Guide A Description column is pr
63. ameter Both parameters fundamentally influence the quality of the resulting chromatogram with regard of peak detection determination of peak beginning and end and the correct baseline Accordingly in creating atemplate method used for each class of analyses pay appropriate attention to the optimum setting of the two parameters Although the setting is not too critical the result will be the same within a certain range of values their incorrect selection must be subsequently corrected by operations with the chromatogram see Chapter 5 4 Chromatogram Modifications on page 39 These additional operations should not substantially change the selected baseline rather eliminate some phenomena that the peak detection algorithm is unable to cope with e g tangential separation identification of the solvent peak ban on detection during the period of column switching etc Some practical guidelines referring to setting up these parameters are in Chapter 10 4 Processing and Displaying Chromatograms on page 76 In general the minimal width of detected peaks expressed as the distance between the peak start and end is directly proportional to Peak Width and inversely proportional to Threshold Moreover the Threshold parameter prevents erroneous assignment of noise to spurious peaks 16 YL Clarity User Guide In addition to the above two obligatory parameters stated in the firs two lines of the Integration table a number of further parameters
64. and new units at both axes or display the chromatogram in a fixed rendition fixed range of the axes can be set in the Graph Properties Time Axis and Voltage Axis dialogs Fixed rendition Fixed rendition means that both axes will have a fixed range regardless of the actual chromatogram size The range is always supplied in base units milivolts and minutes using the From To parameters in the Range section The specified values will apply only if the Fixed checkbox has been checked Axis format Select the desired format for the axes in the Graph Properties Time Axis and Voltage Axis dialogs You may hide the axis by unchecking the Visible checkbox Enter the required title in the Title field It is possible to shift the axes Offset or change their scale Scale Using the Units field set the units to be displayed on the axes The units are only displayed on the axes of the main graph and not in the results tables and thus are for informational purposes only How to set actual units on the axis In chromatographic practice it happens that it may be better to display the absorbency units AU instead of voltage The procedure for setting AU is as follows 1 Open the Graph Properties Voltage Axis dialog 2 Verify that the Visible checkbox has been checked 3 Select the name of the axis in the Title field e g Absorbancy units and the abbreviation of units AU in the Units Type field 4 In the Units Type
65. ard The export mode depends on the setting in the Export Chromatogram dialog accessible using the Setting Export Data command from the Instrument window or the File Export Data command from the Chromatogram window Automatic running of another application If the Run Program field contains a name of an application e g EXCEL EXE and the Parameters field contains optional parameters of that application for Excel e g the name of the working sheet or macro file that application will automatically be run Use the By button to search for the required application including the relevant full path If the Only with export checkbox has been checked the application will only be run when the Automatic Export checkbox has also been checked 4 3 2 Batch Measurement of Analyses Sequence The station enables batch measurement of analyses also Known as sequence measurements or simple sequences to be performed in particular in connection with autosamplers For this it is possible to select an active or passive operation The running and duration of individual analyses is controlled either by the station active sequence or by the autosampler passive sequence 4 3 2 1 Passive Sequence Passive sequences can either be used with autosamplers that decide on the injection time or by manual injection In this regime the station will only react to signals that informs about effected injection This means that there are no special conditions re
66. attempt to communicate with the converter has been successful the configuration dialog of the converter is shown allowing the user to enter custom signal names and units Then the device is shown in 86 YL Clarity User Guide the left hand list of the System Configuration dialog and its free channels can be assigned to individual instruments of the station Note Communication with modules for direct control of chromatographs digital pumps and autosamplers will only be checked when the instrument from which the user would like to control these devices is being opened Accordingly during the configuration process one cannot establish whether the communication set up is correct How to assign individual devices to station instruments Switch to the corresponding instrument tab in the right part of the System Configuration dialog In the Setup Control Modules list on the left select the desired device and add it to the instrument using the __ button or the mouse to drag and drop the device Each station instrument you wish to use for measuring chromatograms must have the correct signal source assigned e Channel s of the A D converter internal INT5 INT7 or external U PAD e A digital output s from the chromatograph to which an available control module has been connected e g HP 6890 etc How to remove the device select the device to be removed from the list in the corresponding InstrumentX tab of the System Configuration
67. be connected to the corresponding external digital output The default Output pin Nr on the connector pin Nr on Output pin Nr on the connector connector assignment of INT5 INT7 UPAD INT7 UPAD digital outputs is Relay Relay as follows 1 oum 5 1 1 1230 827 sours a is Bs a ours ee a 635 m m cena fw Note Should you be using an active sequence be sure not to process these outputs in the Events Table 26 YL Clarity User Guide One injection cycle lt eeorororoeee Measurement analysis _ _ _ gt STOP IDLE Biisk RUNNING BREAK IDLE _ Autostop Resume 2nd inj 2nd time Start Run 1st inj enable injection program Sequence enable OUTO 6 digital L output Autosampler broadcasts injection The program returns the original digital output Given by the value ne 4 Initial from theDigital mee Outputs window input st 1st injection Fig 10 Time Scheme and Succession of Signals in an Active Sequence 4 3 2 3 Active Sequence with Control For selected types of autosamplers we supply a software module that directly selects the injection sequence and time The interconnection for active sequences is usually then made using a serial communication cable between the PC and the autosampler A detailed description will be found in a separate manual 4 3 2 4 Sequence Table and Its Creation A s
68. been started Automatic subtraction of Chromatogram In addition to comparing the measured signal with the background chromatogram see above the YL Clarity station also offers the ability to subtract a chromatogram automatically Set the desired chromatogram in the Chromatogram field and select the method for automatic subtraction in the Matching field from the Method Setup Measurement dialog The station will either simply subtract the chromatogram from the currently measured signal or will attempt to displace the subtracted chromatogram with the measured chromatogram A more detailed description is provided in the Reference Guide Display the subtraction chromatogram in the background of the Data Acquisition window by using the File Show Solvent Chromatogram command The status bar of the Data Acquisition window will indicate which chromatogram is to be subtracted Time min 2 983 voltage mv 18 284 0 000 Background chromatogram Subtraction Chromatogram Fig 4 Status bar of the Data Acquisition window Setting up the processing parameters The measured chromatogram will be integrated and evaluated according to the parameters of the template specified in Method Setup Integration and Calculation tabs Especially check the following parameters Peak Width Enter the width of the narrowest peak expected in the Method setup Integration dialog Threshold Enter the half height of the lowest expected peak Method setup
69. ble contains compounds already calibrated on previous level it will look for and eventually calibrate these compounds also at the current level Only the peak selected using the cursor will be calibrated Only the group containing the peak selected using the cursor will be calibrated Add All Add Existing 4 Add Peak Add Group 4 Supply known amounts Enter all Known amounts for all compounds in the Amount column below the calibration level Level x 58 YL Clarity User Guide 5 Repeat steps 2 to 4 for all calibration levels required Note Thanks to the character of the YL Clarity station any change in the calibration file will immediately be reflected in the result tables of all chromatograms that use it In other words it is not necessary to save changes using the File Save command to update the result table 6 How are peaks assigned to compounds in the calibration table The retention time of each peak you wish to calibrate using the Add Peak command will be compared with the identification windows of already calibrated compounds If identified with any of them i e if the retention time lies within the interval lt Ret Time Left Window Ret Time Right Windows gt its retention time will be added at the next level Otherwise a new calibrated compound will be established If the calibration proceeds under the Add Existing command only identified compounds will be calibrated in the above manner
70. can be set in the Integration table allowing for automatic integration of complicated chromatograms These parameters are described in detail in the chapter 5 4 Chromatogram Modifications on pg 39 4 2 1 Method The method file constitutes a tool used to achieve facile description and setting of all measurement conditions and to attain high reproducibility of measurements performed with the YL Clarity station The method is divided into a number of sections of which each is reserved one tab of the Method Setup dialog Event Table Section for control of the inputs Measurement Section with description of measuring conditions and possible setting of length of measurement or automatic subtraction of desired chromatogram Acquisition Section with parameters that are related to a signal measurement This includes attenuation sampling rate control of digital outputs through the Event Table etc Integration Section with integration parameters for the correct identification of peaks and determination of the baseline Calculation Section summarising calculation parameters for setting the type of calibration calculations Advanced Section with settings of chromatogram subtraction and column calculations AS Control Section for potential direct autosampler control LC GC Control Section for potential direct control of a chromatograph or pump The template method file is accessible from the Instrument window using commands fr
71. cated and controlled using the ef sign next to the Ae icon in the Instrument window must be checked Note All parameters and commands of the Single Analysis dialog will be ignored if a sequence is running Displaying chromatograms printing exporting and running other applications during the sequence run are also defined in the Postrun Setting dialog or by the f and O signs from the Instrument window and are thus common to the entire sequence 4 3 3 Batch Processing of Analyses The station allows for batch processing already measured chromatograms Chromatograms selected for batch processing will be subject to operations that are analogous to those included in the Postrun Setting dialog The Analysis Batch command from the Instrument window will open the Batch dialog My GC DEFAULT1 Batch a Options File Type V Reprocess by Instrument Method Chromatograms x i Open Chromatogram Window Select All Open Calibration Window Print Results Unselect V Export Data Show Alerts Sort by V Export Chromatogram in AlA Format Name Hania Export Chromatogram in TXT Format Export Chromatogram in EZChrom Ascii Format C Time C Backward sae 3 Run Program Only with export Parameters Fig 12 Batch The File Type command determines what should be processed chromatograms calibration standards or sequences A list of the corresponding files in the current project is then shown in the left column Seq
72. cccccceecssseeeeeeceeeeeeeeeeeeaeeeeessaeeeeeeeeas 76 10 5 Chromatogram Modification rz cccccenzesevececdenebacsencaved genet eadstiestasescnestableenoteadcedsiateceeebecneneet 78 1O00 OAD O eee ence eee eee ne ee noe eee ee een ee ee ee eee 79 YL Clarity Contents 10 7 Calibrated Calculations ccccccccssseeccceeeeeeeeesseecceeeeseeeeseeeeeeeseeeeaeeeeeeeeesseeaseeeeeeeeesaaas 79 11 YL CLARITY FILES AND DIRECTORIES 000cccce esses sss s sss aaaaaaaaaaaneeeeeeeeeeeeeeeeeeee 81 Ved TIC CIOMC S e E E tnd animeniaianiuncassnctess 81 Tee oy gt ene eee eee ee eee ee 82 11 2 1 Chromatograms PRM ccccccscceeeeecseeeeeeeeeseeeseeeseeaseceeesseaseeeeesseaseeeeesaeaneeees 82 11 2 2 Template Method Files MET cccccccssescceecsesseeeeeeeeeeseeeeseeeeeeeesseeeeeeeesaaaneeees 82 11 2 3 Calibration Files CAL ccccccccccccecscesesseeceeeeseeeeeeeseeeeeeeeeeeseeeeeeesseeaaeeeeeeeesaaas 82 112A Sequence Files SEO srssccscencccosccsenensctoosudesnadeocssctntscmberosssdeseedaseseesnskicnsmedsnenselnocbdes 83 11 2 5 Report Style Files STY oo eccccccccccsssssseeeceeeeeeeeeeseeeeeeseeeeseeeeeeeseeeaeeeeeeeeeessags 83 11 2 6 Password File CLARITY PSW AME ooo cccecececeseeseseseeeseserersestseneeeees 83 11 2 7 Configuration File CLARITY CFG ccccccccccccsssssseeeeeeeeeeseeeeeeeeeeeseeeeeeeeeeeeeeeaaas 83 11 2 8 Desktop File CLARITY DSK cccccccccccccccceeeeeeeeeeeeeeeeeeeee
73. ckup dialog From which location will be files restored The source location other directory disk or computer can be specified in the Source item Either enter the path directly or use the button to browse 94 YL Clarity User Guide Backup WORK1 Create Archive Restore Archive File List Selected Size rene oae se ar 25 10 1994 2 32 KB DataApex Ltd Default project for Channel 1 25 10 1994 115KB Data4Spex Ltd Default project for Channel 3 i Select All Files File Type 7 i 5 Calibration Standards JW Without compressing Source D backup uae E To Common E Move from Archive Cancel Restore Help Fig 41 The Backup Restore Archive dialog The other items and commands are analogous to those listed in the Archive tab described in Chapter 14 Backing up and Restoring Files and Projects on page 93 95 YL Clarity User Guide 15 Glossary The following list of often used or differing terms is providing to prevent misunderstandings and errors 21 CFR Part 11 This is a directive stipulating the conditions under which a company may use electronic records and signatures The directive is mandatory for companies that use computer system designed for manufacturing or distributing products that are subject to regulation by the FDA known as regulated products Access rights A system that governs the activities that specified users are allowed to perform
74. d to change the baseline below non separated peaks See the Reference Guide for additional information 47 YL Clarity User Guide Valley To Valley Slope Specifies the maximum slope of the baseline Tangent Area Ratio Constitutes the first condition imposed on tangential separation Tangent Slope Ratio The condition is satisfied if the ratio of slopes of the second and the first peak exceeds the specified value 5 4 6 The Integration Table The Integration Table contains a list of manual chromatogram modifications i e the commands from the Baseline Group Integration and Peak submenus Each operation is identified by its name and the range of validity For commands with a range of validity that is defined by an interval Lock Add Positive etc the integration table contains the limits of the validity interval For commands that are defined by a single point Start End and Both the integration table contains the retention time of the peak that is involved and the new distance relative to the retention time Note This approach to a certain extent removes any potential inaccuracies that originate from differences in retention times determined in various analyses The Integration Table for new chromatograms You can prepare the integration table for new chromatograms before measuring the chromatogram in the Method Setup Integration dialog This dialog you may open using the Method Integration command from the In
75. de by removing or adding lines in tables etc Most of the advanced text editors contain a function that formats text that is separated by a selected symbol into a table Destination of exported data The Clipboard item exports the data to the Windows Clipboard To export to a text file select the File item and specify the filename in the File Name field If you wish to enter the name of an existing file invoke the Browse command to search for the file Automatically assigned filenames If the File Name field has been left blank data will be transferred to a file of the same name as a chromatogram with the TXT extension Target directories for export If File Name field does not specify a path the text file will be stored in the same directory as the exported chromatogram Export to a single file The user can append the exported data at the end of an existing file to do that check the Append item 72 YL Clarity User Guide 9 2 Exporting results to a database If dBase File item from the Export Data dialog has been checked the data will be exported in the DBF format In this case only the Results Table will be exported to the file in the full format regardless of whether or not Full Format has been checked 9 3 Exporting the Summary table The Export Summary Table command will invoke the Open File to Export Summary Table dialog for entering the filename and directory Individual items of the summary table are found sepa
76. de the file is CLARITY DSK and is common to all instruments See Chapter 11 2 8 Desktop File CLARITY DSK on page 84 for additional details 5 2 1 Chromatogram Description and Display Select the information to be displayed in the Graph Properties Graph dialog Graph Properties Peak Tags Background Colors if Preview Graph i Retention Time Chart W Show Labels W Mame lf Windows Default Show Grid Peak Number W Show Legend W Group ID __ Select Baseline w Li Font m Line So Border W Marks Windows Default Color Color As Active Signal As Active Signal select E Select Select i Cancel Help Fig 13 Graph Properties Graph 5 2 2 Description and Format of Displayed Axes The display of axes can be specified in the Graph Properties Axes Appearance dialog Graph Properties Graph Axes Appearance Time Axis Voltage Axis Signals Gradient Title Font Line Width 1 Value Font Color Units Font IV As Active Signal a Fig 14 Graph Properties Time Axis dialog 34 YL Clarity User Guide The thickness and colour of the axes are set using the Line Width and Color commands The Title Font Value Font and Units Font commands determine which fonts will be used for axes description values and units Note Further settings such as the customisation of descriptive labels units and determining whether to convert between the original
77. e the displayed range Change the Time and Voltage parameters preferably to their respective maximum values Alternately you may select the floating range using the View Floating Axes command which enables the station to choose the appropriate setting for displaying the signal e A cut that lies outside the signal is being displayed Cancel the cut by using the Unzoom command Ctrl or the 4 icon e You have mistakenly set the same colour for both the curve and the background Invoke Properties from the local menu and check the assignment of colours Data acquisition terminated prematurely Verify that the Enable Autostop has not been enabled in the Method Setup Measurement Data acquisition has prematurely terminated or started repeatedly Probably a false start signal has occurred in the instrument where an external signal start has been enabled contact your vendor 75 YL Clarity User Guide Redeeming data from an analysis An emergency situation might occur during while acquiring data power failure computer malfunction disk error disk full etc Causing an interruption If you consider data from the interrupted analysis to be important you can redeem it First remove the cause of the underlying failure and then invoke the Data Recovery command from the Single Analysis dialog The interrupted analysis will then be saved as a valid chromatogram Disk full If a requested operation cannot be performed because the d
78. each user can have his or her station appearance settings customised The settings of all windows graphs and tables are instrument specific The parameters specified in the User Options are common to all instruments used by a user 90 YL Clarity User Guide 13 Working with Directories and Projects The station enables a base directory to be assigned to each instrument as well as for the storage of analyses in different projects 13 1 1 Instrument Directory Selection Invoke the Directories command in the Main station window to specify a different base directory for storing projects for each instrument The above command is especially suitable if the YL Clarity station is a part of a computer network where either several stations or several YL Clarity Offline evaluation programs are operative By default all instruments use the main station directory usually C CLARITY Instrument directories are stored in the CLARITY CFG configuration file At least one project directory is assumed to exist in the instrument directory the former is described in PROJECT subdirectory If no instrument directory no PROJECT subdirectory and no project directory exists you will be queried as to whether or not you wish to create the corresponding directory or project 13 1 2 Projects A project is an ensemble of different analysis data and accessories used as basic organisation unit for sorting data and auxiliary files For example it may be
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80. ed to other locations in the station or even to and from other programs simply using the Cut Copy and Paste commands Within the YL Clarity station it is possible to use the clipboard to copy text labels and lines between chromatograms Note A typical example of this feature is the use of the table calculator Excel to easily prepare an extensive sequence table This can then be easily transferred using the Copy and Paste commands into the Sequence window Copying data to the clipboard The values of all parameters and the content of any fields of the tables may be transferred to any other places or other programs of the Windows system with the help of the clipboard The Clipboard is a temporary memory that is shared within the entire Windows system into which you enter the selected value using the Copy amp or Cut 4 command You then locate these in another place using the command Paste fJ In some tables you also use the Paste Insert function keys 1 which does not rewrite the original content of the table but instead adds new lines above the currently selected line These commands can be found in either the Edit or the local menu of the tables Also using the Copy Ctrl C Cut Ctrl X and Paste Ctrl V commands is possible Selecting an area to be copied Use the left mouse button and the grey buttons at the top and to the left of all tables to select a contiguous area All cells passed by the mouse cursor wi
81. eeeeeeeeeeeeeeeeeeeeeeeeeeees 84 11 2 9 Archive Files DGZ AME cc ceccccececsccececsesesecersesesesecevsteeseversesececenees 84 12 10 Project Files PRJ cennin E REA 84 TM Fie SNA eea E EE E E E E E E 84 TA MPU EOC ING eee E A E E E E E S 85 11 5 Marking Changes in a File Not Yet Saved cccccccccsssesseeceeeeeeseeeeeeeeeeeesseeeeeeeeeeesaaas 85 12 STATION SETTINGS YAM aaneneneeeeeeneeenneneooennuneoounnnnnernneneoonnnnnnernnnnnneonnnnnneernnnnnnen 86 12 1 System Configuration Setting ccceccccccccccsssssseecceeeeseeeeseeceeeesseeeeeeeeeeeeesseeeseeseeeeeessaas 86 1241 N MmMDer Os SMS tunmente soceensosre isc 87 12 1 2 Description of Instruments and graphical SyMDOIS ccccsseeeeeeeeeeeeeeseeeeneeeees 87 122 User Accounts Protected MOG cocineran eE AE 88 Mees e NONE LOCK ea a S E E 89 t24 eer SUNOS eeni a E E EEEE AET 90 13 WORKING WITH DIRECTORIES AND PROJECTS 0 0 c cists assassins 91 13 1 1 Instrument Directory Selection c cc cceecceccceeeeeeeeeeeeceeeeeeeeeeeeeeeeessaeaeeeeeeeeeesaaas 91 WSileZ PR O CClS E 91 14 BACKING UP AND RESTORING FILES AND PROJECTS AAMS eessssccssssseeeeeees 93 Wet Med ASIC e saneaatua rigecisalcaminctaiea tancina ee E ieee oan aneadiaies tncadicueuncaaneaunn ais 93 Wale Fae SOMO FUSS siresatocieercciasanstegs nats saduesahinoasseotesssatconttsainetbesetnsyeteansdesavocsiaamerans cate 94 15 GLOSSARY Gurernnnennl ann nents ene een 96 eee O08 oy Ogg s
82. eeeeseeeaeeeeesseeseeesessaageeesessaaaes 48 6 CALCULATIONS AND CALIBRATION uw eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseesesseeseeeeeeeeeeeeeees 49 oT Ae TADO eee eee eee eee E E ee E meen eee eee eee ae eee es 49 6 2 Table of Peak Parameters CMe iio cecccccccsssscceccceesseeecceaueeecseausecesessaseeesessaaaes 50 6 3 Types of Integration Calculations ccecccccccccecccesesseeeeeeeeeceeeessceeseeeeaeeseeeeeeeeeesaeaegees 50 6 3 1 Non calibrated Calculations Uncal cccccccccccceeeeseeseeeeeeeeeseeeeeeeeeesesaeaeeseeeeees 52 6 3 2 External Standard Method ESTD cccccccceeecceeeeeeeeeeseeeeeeeeeeaeeeeeeeeeeessaaeeeees 52 6 3 3 Internal Standard Methods ISTD cc cccccceceeecceeeeeeeeeeeeeeeeeseeeeeeeeeeeeeessaeaaeees 52 6 4 Description of the Calibration File ccccccccsccccsssssseceeeeeeeeeeseeeeseeeeaeesseeeeeeeesaeassees 53 6 4 1 Main Calibration Table cccccccccsccccccccceeceeeesseeceeeeeeseeseeeeeeeeeeseeeseeeeeeesesseaeseeeeeees 53 6 4 2 Compound Calibration Tables cccccccccccccccsssssseeceeeeeeeaeeseeeeeeesseeeeeeeeeeeesssaaesaees 54 6 4 3 Calibration Curve cccccccccccccceseseeseeceeeeeeeeaeeeceeeeeeseeeaeeeeeeeessaaeeseeeeeeesssaaanseeees 55 YL Clarity Contents 6 5 How to Create Calibration ccccccccccccccssssseeeceeeeeeeeeeeeeeeeeeeseeeeseeeeeeeesseaeeseeeeeeessssaeaseees 57 6 6 Creating Additional Concentration LeVelS cccccccccececcceeeecseesseeeeeeeesseeeeeeeeeeessa
83. eport The layout is defined by the employed report style 98 YL Clarity User Guide Project directory Used to store all working files of an instrument in which the homonymous project has been opened Project file extension PRJ The file specifies the directories in which all user files will be stored Protected mode A regime that enables only authorised users users who have an account assigned in the User Accounts dialog to work with the station and access data Raw data file RAW A file used in previous versions of the CSW10 17 and for the external PAD unit containing non analysed and non adjusted data of the analysis The CSW32 and YL Clarity stations save raw data directly into the chromatogram file Report style An outline determining which and how analytical results will be incorporated into a report and subsequently printed Each report style will be stored in a separate report style file Report style file extension STY A file storing information that determines what to print and how to print it Sequence file extension SEQ A file that defines an automatic sequence of analyses Splitter A resettable bar that divides certain windows e g the Chromatogram or Calibration windows into individual panes The bar can be moved to change the size of individual panes SST The System Suitability Test is an integrated module designated to validate the chromatographic system on the basis of evaluation of chromatogra
84. equence measurement is defined in the sequence table where each line specifies the measurement of one or several samples The table including the auxiliary data is stored in a sequence file In order to perform a certain measurement it is sufficient to select a suitable sequence file and start the sequence Displaying the Sequence window To display the Sequence window click the gil icon or invoke the Analysis Sequence command from the Instrument window The last used sequence file will be displayed My GC Sequence Ethanol in blood MODIFIED File Edit Sequence View Window Help va F Ak Val FEE Ae E F Pibe me sce ee e 0 000 1 000 2 000 Blank Ethanol in blood Sequence 0 000 1 000 2 000 Cal04 1 Ethanol in blood Sequence 0 000 1 000 2 000 Cal09 2 Ethanol in blood Sequence 0 000 1 000 2 000 Cali4 3 Ethanol in blood Full 0 000 1 000 2 000 Calg 4 Ethanol in blood Sequence 0 000 1 000 2 000 Cal24 i Ethanol in blood Full 0 000 1 000 2 000 Cal26 6 Ethanol in blood Full 0 000 1 000 2 000 Pers014 Ethanol in blood Sequence 0 000 1 000 2 000 Pers016 Ethanol in blood Sequence On oanm fw hw On ananmn hw h M M M M r C M IV m For Help press F1 vial No 5 Inj No 1 File Cal19 State Waiting Sequence Active Format Auto Fig 11 Sequence Editing a sequence table A new line will automatically be appended each time the SV Start Vial cell has been filled in or the Run checkbox has bee
85. etention Indexes with Unretained Peak Storno N pov da Fig 29 The Calibration Options Dialog How to set the recalibration mode Set the recalibration mode in the Recalibration section of the aforementioned Calibration Options window The result of recalibration can be either the arithmetic mean of all previous values and the new value Average a weighted mean of the original and the new value Weight or finally the old value can be replaced by the new one Replace How to prevent recalibrating using incorrect values The maximum allowable difference in per cent between the new and the existing value can be specified in the Search Criteria field in this manner you can forbid automatic recalibration using values that fall outside the permitted range In manual recalibration the Over message in Departure column will appear if the permitted difference has been exceeded Enter zero to disallow the condition 6 9 Manual Recalibration As with calibration you may choose between manual and automatic recalibration In the former instance the appropriate Recalibrate Peak Group dialog containing all data that can be changed directly will open each time a compound has been selected 60 YL Clarity User Guide Recalibrate Peak 14 29 Curent Level 8 Recalibration 1506 Compound Name Peak 14 29 od new Val Val Units 0 000 2197 O70 mvs 2197 O70 0 000 608 431 m 608 431 0 000 0 009 gkg Skip
86. etention times brought about by changes of measurement conditions use of different methods changes in characteristics of the chromatographic system or simply by random error The method of reference peaks eliminates a substantial part of these complications resulting in reliable identification of peaks in the chromatogram Compounds marked as reference in the calibration file will be identified first The difference between the retention time of a reference compound and that of the corresponding reference peak in the chromatogram is then used to correct the retention times of the other non reference compounds listed in the calibration file The non reference compounds are then identified according to the retention times so corrected The reference peak method will automatically be applied if at least one compound in the calibration file has been marked as reference either in the main calibration table the Peak Type item or in the tab of the relevant compound of the Compound Type item accessed by selecting Refer The peak of the internal standard can also be marked as reference peak by selecting RISTD 63 YL Clarity User Guide If several peaks fall within the identification window of the reference peak the largest of them determined according to how the peak area or height has been set in the Response Base item will be identified A A reference peak not originally identified in the chromatogram cannot be subsequently identified in
87. faults Dialog ccceeeeeecceeeeeeeeeeeeeeeeeesaseeeeeeeeees 62 Fig 32 Scheme of the Reference Peak Method ccccccccssssseeceeeeeeeeseeseeeeeeessaseeeeeeeeees 64 Fig 33 Resolving Overlapping Identification WINGOWS cccccseesceeeceseeeeeeeseeeeeeeessaaeeess 65 Fig 34 The Report Setup Dialog yi ache eth ee a ea a 66 FIGs 30 INe PAGS Setup TAO x ces ccticcte ac ce cece on E a sexe lesen Oe base Ree aN 68 Fig 36 An Example of a Laboratory Header cccccccssssseeeeceeeeeceeeceaeeseeeeeeseeesseseeeeess 68 Fig 37 The Export Chromatogram Dialog spisie tainn aiiai aii aa ai aa 71 Fig 38 The System Configuration Gialog ccccccccssssssccceeeeecaeeseeeceeeeesseeseeeeeeeeessaeaseeeeeees 86 YL Clarity User Guide Fig 69 The User Accounts Dialog lt 284i wee eek eA ee 88 Fig 40 The Backup Create Archive Dialog ccccccccceececeeeeeeeeeeeeeeeeaeeeeeeeeeeesaeneeeeeeees 93 Fig 41 The Backup Restore Archive dialog ccccecccseeeeeeeeeeeeeeeeeeeeeeeeeesaaaeeeeeeeaaeeeess 95 102 YL Clarity 17 Index User Guide 3D View 39 Access rights 96 Acquisition see Data Acquisition Active Sequence 26 Add All 57 Group 57 Negative peak 45 Peak 57 Positive peak 45 Amount 51 Analysis Batch Processing 30 description 15 external control 22 preliminary processing 22 processing 16 Anchor Text Alignment 36 Area 47 Arrows 36 Assign to
88. ference Guide 2 From width at half height From width at 50 This represents the standard calculation method based on the measured width at half height and the assumed Gaussian peak shape This method often leads to deviations from the actual efficiency for real chromatographic peaks Note To ensure that the capacity factor has been correctly calculated do not forget to specify the dead retention time Unretained Peak Time and also the column length necessary for calculating the relative efficiency Column Length 6 3 Types of Integration Calculations Generally speaking the result of a chromatographic analysis representing the amount of a compound is either the area or height of the corresponding chromatographic peak or group of peaks However the same amounts of different compounds elicit different detector responses To take this fact into account while calculating the amount one must know the detector sensitivity under the given measurement conditions In other words the calibration curve of the compound in question representing the response as a function of the amount of the compound Calibration curves are stored in a calibration file the latter can contain an arbitrary number of calibration curves that correspond to the compounds that are present in a mixture The Calibration window is earmarked for creating and modifying calibration curves Calibration calculations respect the differences in detector sensitivity vis a vis i
89. fter the end of the analysis in progress 4 3 1 3 Control of External Devices The YL Clarity station when using A D converter is able to control external devices equipped with control inputs pumps temperature programmers autosamplers etc The Event Table included in each method can control up to eight inputs on the internal or four inputs on the external A D converter Each line of the table defines a single condition event and if the condition is satisfied a set a specified output to the prescribed value Examples of events the expiration of a preset analysis time Time the decrease of a detector signal below or increase 22 YL Clarity User Guide above a preset value measured either from zero Input or from the value at the start of the current analysis Input Rel When contradictory requirements involving a single output occur the last command issued will be in control When using a multi detector measurement there will be a separate Event Table controlling the outputs of the A D converter and containing the corresponding channel for each detector Event Table creation and modification To display the Event Table invoke the Method Setup Event Table dialog command from the Instrument window Method Setup C Clarity 2 4 4 WORK1 WDefault1 MODIFIED Common for all detectors gt 10 000 min Command upad2 2 400 000 mY DataApex U PAD2 upad2 2 0 020 m Run Program gt upad2 2 100 000 m Run Progr
90. g Additional Concentration Levels Once the first calibration level has been created continue to calibrate at the next levels Any number of compounds can be calibrated at each level regardless of whether or not they have been calibrated at the lower levels Moreover compounds from different calibration standards can be calibrated at a single level 1 How to set another calibration level Each time a calibration file is opened the first calibration level will always be selected Use the arrows from the toolbar or Calibration Set Level command to change the calibration level If the Automatic Calibrate regime has been enabled the current calibration level will change in conformity with the following rules The Add All and Add Existing commands set and calibrate the first completely free level The Add Peak or Add Group commands always set and calibrate the first free level of the relevant compound To prevent the program from automatically selecting calibration levels enable the Manual Calibration regime on the toolbar See Chapter 6 7 Manual Calibration for additional details 2 Reading in another calibration standard Invoke the Open Standard command to select and display another calibration standard corresponding to the preset calibration level 3 Transferring compound data to the calibration table Invoke any of the following commands Add all peaks identified in the calibration standard If the calibration ta
91. he OVERLAY inscription in the right hand part of the status bar Displaying multiple chromatograms A practically unlimited number of chromatograms can be simultaneously displayed using either the File Open command or by clicking the 4 icon Chromatograms can be displayed by repeatedly invoking the Open command or by selecting several chromatograms in the Open Chromatogram dialog Each chromatogram will be displayed in a dedicated colour The BJ BI SEB E E icons are assigned to the first eight displayed chromatograms Refer to the Chromatogram menu for a comprehensive list of all displayed chromatograms To select multiple files hold down the key while left clicking the mouse button a second click will cancel the selection To select a contiguous sequence of files left click the first file to be selected with the mouse button hold down the key and then click on the last file to be selected Note The number of chromatograms that can be simultaneously opened in the Overlay mode is in fact limited by the Maximum Chromatograms in Overlay field from the User Options General dialog The implicit value is 20 and the maximum can be set to 10 000 Active chromatogram One chromatogram signal usually the last one displayed is active and all displayed information and commands will only refer to that chromatogram The name of the active chromatogram will be displayed in the title bar of the Chromatogram window and in the headers of all
92. he measurement are summarised in the Method Setup Measurement and Acquisition tabs of the template method These are first displayed using the and g icons or by using the Method Measurement Acquisition command from the Instrument window The name of the template method will be displayed in the Information table If you prepare another template method during the measurement the name of this current template method will be displayed in the header of the Instrument window Setting up the maximum input voltage The input range attenuation is defined by the Range item in the Method Setup Acquisition dialog and must be higher than the maximum output voltage of the employed detector On the other hand it is improper to measure small voltages with say the 10 V range since this would reduce resolution and accuracy of the measurement If you intend to measure negative voltages 18 YL Clarity User Guide check the Bipolar checkbox in the A D converter setup dialog accessible from the System Configuration dialog by double clicking on the A D converter INT 7 U PAD etc icon Note In case of multidetector measurement it is necessary to set the range values for each detector separately using Select detector item in the Method Setup Acquisition dialog Monitoring the baseline drift and noise Open the Data Acquisition window using the J icon or the Monitor Data Acquisition command from the Instrument window The signals
93. hived files will be compressed and stored as a single file under a selected name 93 YL Clarity User Guide Will the files be copied or moved If the Move to Archive item has been checked the file s will be moved to the destination specified in the Target field i e deleted from the original directory What is the total size of files to be archived The overall size is indicated above the list of the selected files in the Selected Size item How to sort files in the list Double click the header of each column to sort the entire table according to that column Double click again to sort the files in the reverse order Backing up calibration standards lf chromatograms are to be archived the Calibration Standard item displays the contents of the calibration subdirectory Archiving files from the COMMON directory Check From Common item to archive files that are stored in the COMMON directory How to delete files Invoke the Delete Selected Files command This command cannot be reversed from within the YL Clarity station 14 1 2 Restoring Files The File Restore command from the instrument window restores files from any directory to the current project When invoked the Restore Archive tab from the Backup dialog opens This is very similar to the Create Archive tab To which location will be files restored The Restore command always restores files to the current project whose name is shown in the title bar of the Ba
94. hived is specified using the File Type item Also in addition to all the YL Clarity files entire projects can be archived i e all files identified in a specified project directory and all its subdirectories Backup WORK1 Create Archive Restore Archive File List 25 10 1994 2 32 KB DataApex Ltd Default project for Channel 1 25 10 1994 1 56 kB DataApex Ltd Default project for Channel 3 25 10 1994 115KB DataApex Ltd Default project for Channel 3 25 10 1994 971 B DataApex Ltd Default project for Channel 4 f Select All Files File Type Projects si V Without compressing cr Target d BACKUPS ees M Move to Archive Cancel Archive Help Fig 40 The Backup Create Archive Dialog How to select files to be archived The list shown in the upper part of the Archive tab contains all the files of the selected type from the current project Select a file by clicking the filename Several files can be selected by clicking their names one by one while holding down the Ctrl key The meaning of the Select All Files button should be self evident Where will the files be archived Specify the destination another directory disk or computer in the Target item The path can either be entered directly or selected using the button In what format are files stored in the target location lf the Without Compressing item has been checked files will be stored unchanged as individual files otherwise all arc
95. hod for logging station activities Most commands in the main YL Clarity window are enabled only when all Instrument windows are closed 3 1 2 Instrument Window All tools necessary for working with a single chromatograph are brought together in the Instrument window The Instrument window contains an information table status line and analysis processing diagram e Each Instrument window opens independent dialogs so it is possible to control the proceeding of analyses on multiple instruments simultaneously e Windows are distinguished by line colour in the analysis processing diagram and instrument name in the header or potentially in the project directory name in the Status bar 3 1 3 Chromatogram Window This is the fundamental window for displaying modifying and evaluating chromatograms Open the window by clicking the icon in the Instrument window or at the end of menu bars in other YL Clarity windows 3 1 4 Calibration Window The Calibration window is designed to create modify and display calibration curves Open the Calibration window using the icon from the Instrument window or using the Window Calibration command from any window Refer to the Getting Started manual for hints on how to create and use a simple calibration 3 1 5 Sequence Window This window defines the sequences of multiple analyses Open the window by clicking on the ji icon from the Instrument window or the Window Calibration command f
96. ies command beside the line with the printer name opens a dialog where the print size quality and other parameters can be set The layout of the window differs among individual printers 7 4 Report Style Selection The name of the preset report style is displayed in the title bar of the Report Setup dialog Invoke the Open command to see a list of all the available report styles Click the name of the report style to display some additional data items like the author s name in the Created By field or a description of the report style in the Description field Select the style either using the OK button or directly by double clicking the style name Alternatively you can enter the name of the style in the Filename field The New command creates a new empty style 7 5 Report Style Modification Each report style is divided into individual segments and a separate tab is reserved for each such segment to the left of the Report Setup window Segments preceded by the y symbol will be printed Double click the tab of the corresponding tab to include or exclude that segment from the report The y symbol corresponds to the Print item in the top left corner of each tab Most segments are further subdivided The On New Page checkbox decides whether the segment will be printed on a new page or not 67 Page Setup ab Header Report Header YL Clarity User Guide Global parameters that apply to all segments The first tab Page
97. ignations Sans Serif boxed RUNNING Available states of the station uppercase Italics Istd Values of parameters Italics Passages that do not apply to the Lite version of YL Clarity Young Lin Instrument Co Ltd YL Clarity Contents Contents 1 INTRODUCTION wisesoccdscendecesccs lve ccceadecescsctcedcesadecescne ced ceeedeescndccedcenelececcwesdecescsccesdenseececcactes 1 1 1 Description of the YL Clarity Station ccccccccccccceeeeeeeeeseeeeeeeeesseeeeeeeeeeessseeseeeeeeeeeeeaas 1 1 2 Updating of program ccccccccccseseeceeeeeeeeeeeeecaeeseeeeeseeeceeesseaseeeeessaaeeeeseesaaeeeeesaageeeeseaaees 1 2 STATION 6s I 5 Deneeemnrine atin Sele leprae teens tile nite een eae ene eee eee ee 3 Ziv AN OOW o eaea extn veaycousarest consaspeaeinaracssneses 3 22 AGOMS AG FOOD ANG a sascctcsecensccdencavncsecesesshuseosteseagtssosssnessscbsseqceeseapeuceacesausayscneeestessnedsscaenee 3 20 MOUSE 226 9 0 ene ne ne nee ee eee ee ee eee ee eee eee eee 4 24 Keyboard Contolera a debncnediadon dacs i E a EREE 4 2 ADCS E A A ee eee eee eee 6 2 5 1 EOIN e E E T E A E A E 6 2 5 2 Adding and Deleting LINGS cccccccseeecccccssseecececsessececseeeceesseeageceesesaasecessssaseees 7 2953 Local menus OF SS sania REAREA AARE E E RAE 7 eae COMUNN ec 9 aeiia E REE EE 7 2C PO aa E E E E EE A eee 8 2I PING SOLS CUO A poreden E E EEE E E E E E AES 9 26 O NNG FES eenen E E E E a e E E E 10 2 9 Recording all s
98. il also functions as a journal of sorts If for example you are unable to recall the name of a file to which you had exported the results of a performed analysis you can search for that file in the Audit Trails for the given period arrange the lines according to type of events and check the exports 11 YL Clarity User Guide 3 Structure of YL Clarity station windows The following Figure shows the fundamental structure of YL Clarity stations aj 1 r l l Dersa ii an g l jicduyeegi dui tii reeled ls a eee TE Audit Trail PEATAS Create User Column Instrument Control Fig 2 Fundamental Structure of YL Clarity Stations 3 1 Structure of YL Clarity windows YL Clarity stations are organised hierarchically The full version can measure on multiple instruments simultaneously After starting the station the main YL Clarity window will appear and display the symbols of up to four instruments The Instrument window for measuring and processing analyses from connected detectors can be opened by clicking the chromatograph icon and if need be entering the user s name and password 12 YL Clarity User Guide 3 1 1 YL Clarity window The fundamental purpose of the main YL Clarity window is to select which instrument is to be used for a particular measurement The window can be also used to configure the station select the base directories for data storage set up the digital outputs and select the favored met
99. ill also be kept within manageable limits a feature that will effect the speed of additional modifications 10 6 Calibration Some peaks have not been calibrated New peaks can be added to an already calibrated file only by using the Add Peak or Add Group commands but not by using the Add All command The latter only calibrates all peaks from the calibration standard for an empty calibration file in other instances the command only calibrates the already existing peaks A peak has been erroneously calibrated as a new compound The deviation in the retention time of the affected peak exceeds the size of the identification window Increase the values stored in the Left Right Window items or alternately use the reference peak method see Chapter 6 13 1 Reference Peak Method on page 63 Note When applying the reference peak method keep in mind that the modified retention time of a compound might differ significantly from the retention time actually measured Thus also if two original retention times are identical the peak identification could fail because the modified retention time may wander outside the limits given by the identification window Neither the calibration curve nor the corresponding calibration equation is displayed e The Curve Fit Type item is set to Free Calibration The curve fit for new compounds is set using the Curve Fit Type parameter in the Calibration Options Defaults dialog e The system was unable to
100. imultaneously displayed in the Overlay mode and subsequently subjected to mathematical operations 5 1 Displaying a Chromatogram Chromatograms are displayed in the Chromatogram window which is opened using the A icon from the Instrument window or the Window Chromatogram command from other windows It is also possible to have the window open automatically after the completion of a measurement Unless the OVERLAY mode has been enabled the chromatogram that is currently displayed will close before another one can be displayed The size of the chromatogram is such that it will fill the entire area of the graph To close the displayed chromatogram s invoke either of the File Close or Close All commands Indicative graph In addition to the main graph a smaller indicative graph can be displayed using the Preview Graph command from the Display menu or through the local menu The chromatogram will always be shown in the indicative graph at the base magnification and will contain any cut displayed in the main graph Zooming in Point with the mouse to any corner of the cut that is to be zoomed in on Left click and hold the mouse button then drag the cursor to the opposite corner of the cut Release the button so as to display the magnified selected cut in the main graph The station will remember the last cuts so that they can be displayed one by one using the 4 and icons or the Display Previous Next Zoom commands The icon o
101. in a File Not Yet Saved For most files the MODIFIED notice after the filename indicates that the effected modifications have not yet been saved The station always alerts to situations where such changes may be lost e g when the station is closed or when a new file is being opened and will offer the option to save the changes 85 YL Clarity User Guide 12 Station Settings In the interest of extensive utilisation the station contains a number of commands that allow settings to be customised These features include everything from selecting the number of instruments and connected detectors to creating users access rights customising the desktop appearance and configuring the settings of individual instruments and current projects 12 1 System Configuration Setting Invoke the System Configuration command from the main window to display the system settings of the YL Clarity station saved in the CLARITY CFG file A foundation set up will have already been made during the installation procedure System Configuration Setup Control Modules Number of Instruments 3 aD A Instrument 1 Ay Instrument 2 Aa lnstrument3 Instrument 4 etectors Tup ki ot driver E Type of Chromatograph 3 nstrumen fn INT 2 Instrument 2 fe GC Pee Name MyGO B UPAD USB Driver 00888 An Detector 1 Instrument 1 Aa Detector 2 36 GC HP5890 GC Driver Y GCs Instrument 1 Aa Digital 1 Instrument 1 Aa Digital 2 5 LC la FLUX RHEOS 20
102. in the sample Identification windows relative to the retention times so corrected are used to identify non reference peaks The method used to resolve overlapping identification windows construed in the above manner is described in the following chapter The reference peak method will provide the most reliable results if reference peaks are distributed fairly uniformly across the entire chromatogram The calculated corrected retention times of non reference peaks apply only to identification during calibration recalibration or calibrated calculations and are not substituted for retention times of compounds in the calibration file or the sample Updating retention times of compounds included in the calibration file is described in Chapter 6 13 3 64 YL Clarity User Guide 6 13 2 Resolving Instances of Overlapping Identification Windows It is not necessary to monitor whether or not the neighbouring identification windows overlap Prior to the identification process proper the YL Clarity station will check the identification windows of individual compounds and resolve instances of overlapping by reducing some identification windows This method is elucidated in the following Figure Overlap divided uniformly between the retention times LW RW left right identification window Fig 33 Resolving Overlapping Identification Windows The corrected identification windows remain in effect only during the identification process and do no
103. indows depends on the setting of the corresponding checkboxes from the Postrun Setting dialog Open the windows manually using the A and icons and then have the chromatograms displayed using the File Open or File Open Standard commands 21 YL Clarity User Guide Data evaluation Invoke the Results Result Table command to display the table of integration results in the Chromatogram Integration window See Chapter 6 Calculations and Calibration on page 49 for a detailed description including the procedure used to obtain calibrated results Presentation of results The results of an analysis can be automatically printed exported see Chapter 7 Reports on page 66 and processed by another program e g Excel which will be automatically run after termination of the analysis All based on the settings in the Postrun Setting dialog See Chapter 4 3 1 4 Automatic Functions after Analysis on page 24 for additional details 4 3 1 1 External Control of Analysis Run Analyses can also be run and terminated using an external signal from a chromatograph an auxiliary button on the cable or a sampling valve depending on your configuration and program installation The External Start Stop checkbox from the Method Setup Measurement dialog enables external control Items in the synonymous section decide on the external control mode The Down and Up items decide whether the station will react to the ascending leading or descending
104. is sufficient to use the standard Open File dialog manually navigate to My Network Places and to then select the desired computer yi Full version For a regular access of files over the network it is better to use the System Directories command from the main YL Clarity window In the displayed dialog use the button next to the desired instrument to select the main directory of the distant station When opening this instrument you will only have to select the desired project Note Files cannot be shared among instruments within a single station The only exception is files of the report styles which can be shared Note Since files are stored in project directories the same name of a file that is open in several instruments does not necessarily mean that the files are identical since in most instances each instrument has its own project directory The same holds true of chromatograms in the data and calibration subdirectories 84 YL Clarity User Guide 11 4 File Locking In some instances the ability of the station to work with certain files is restricted to prevent a collision that may corrupt measured data e The parameters of the current template method from the tab in the Method Setup Acquisition LC GC or AS dialogs cannot be modified while an analysis is in progress e While a sequence is in progress all already measured calibration files including the one in progress will be locked 11 5 Marking Changes
105. isk is full you have several options e Delete files that are no longer needed from any directories other than YL Clarity e Archive or delete unnecessary chromatograms or entire projects With the Archive command in the Instrument window open the Backup Create Archive dialog Either archive the older chromatograms on another disk or erase them using the Delete Selected Files command 10 3 Sequence The Run command and icon are inactive dimmed A Single Analysis is running Check the status in the Instrument window Single Analysis can be terminated from the Single Analysis dialog or Data Acquisition window See the first bullet of the chapter 10 2 Signal Displaying and Measurement 10 4 Processing and Displaying Chromatograms A saved chromatogram has been lost Chromatograms are either stored in the data or calibration subdirectory depending on the setting of the Calibration Standard parameter in the Single Analysis dialog When selecting a chromatogram do not forget to display the corresponding subdirectory using the fi or fie icons A file contains an incorrect chromatogram e Verify that the correct project has been selected since files of identical names can exist in several directories e Maybe you have overwritten the original chromatogram using another one by entering the name of an already existing chromatogram in the Chromatogram File Name field inadvertently ignoring the warning against possible overwrite
106. it binary number representing the integral value over a given time e Due to the design of the converter it is possible to obtain a true integral The Young Lin A D converter permanently integrates the input voltage while standard sampling converters with approximation transfer only sample voltage at discrete time intervals Wi Full version Note This does not apply to detectors with digital outout for which a control module is available e g HP 5890 6890 etc where the data is transferred to YL Clarity through the RS 232 serial line e The above binary number will then pass through a digital filter that filters out all parasitic components originating e g from power voltage fluctuations 15 YL Clarity User Guide e Individual binary numbers data items are read from the converter at a specified rate Each partial integral occupies four bytes e Data samples are temporarily stored in the operating memory and then sent to the hard disk approximately once per minute as a buffer In the TMP subdirectory of the main station directory C CLARITY TMP by default a file CHXRUN RAW where X stands for the instrument number is thus created for storing the so called raw data This ensures that very long chromatograms can be measured since the capacity of the hard disk is much higher than the capacity of the operating memory Selecting the sampling rate In the field of fast measurements on capillary columns and microcolumns in particu
107. k The Add Negative command or icon creates a new negative peak If the beginning or end of the created peak falls inside a neighbouring peak the peaks will be separated by a vertical line that may either be placed at the beginning or end of the created peak 275 8 00 8 25 8 50 Time min 0 Time min 45 YL Clarity User Guide Manual apex determination Owing to the automatic determination of peak apex the following procedure must be used to place the apex at a specific location especially when defining monotonic peaks First using the Lock command cancel the peak with the incorrectly assigned apex and add a new peak using the Add Positive or Add Negative command as required This is done so that its beginning or end depending on the position of the maximum of a positive or minimum of a negative peak will coincide with the position of the intended apex To finish shift the beginning or end of the peak to the appropriate location using the Start or End commands The Solvent peak The Solvent Peak command or icon designates a peak to be a solvent peak The letter S before the peak number in the graph indicates the designation of the peak Solvent peaks are neither included in integration nor listed in the Result Table More than one peak may be designated as a solvent peak Voltage mV Voltage mv 1 0 1 5 2 0 2 5 3 0 Time min Recording accomplished modifications All operations accomp
108. kip button The Abort button terminates the whole calibration process The amount of the calibrated compound is entered in Amount field in the displayed dialog 59 YL Clarity User Guide 6 8 Recalibration The YL Clarity station provides for facile recalibration modification of calibration files The procedure is similar to that which has already described for calibration What does recalibration mean Recalibration means repeated calibration at a given concentration level The purpose is either to update the calibration points or increase precision by repeated averaging at individual calibration levels Calibration Fig 28 The Calibration Window Toolbar How is the recalibration mode set The mode of recalibration is set in Mode Recalibration field in the Calibration Options dialog T The command can be opened by invoking the Calibration Options command using the Ei icon or directly in the main toolbar of the calibration window Calibration Options ETHANOL Calibration Options Defaults Calibration Description Display Mode DEMO Example Ethanol in blood ESTD Number of Signals 2 X Recalibration C Replace Calibration Mode ers Average f Automatic C Calibrate tag No of Points C Manual Recalibrate fo Units C Weight Weighting Factor Compound gl Search Criteria V Enable Response Value Change 0 Update Retention Time Default Injected Volume ml r IV R
109. lar you would be glad to make use of one of the preset sampling rates The setup is a part of the method file and can be changed using the Method Acquisition Sample Rate command from the Instrument window Changing the sampling rate affects the chromatogram size Note The available scopes of sampling speed depend upon the type of converter used 4 2 Processing the Analysis Processing chromatographic data means identification of all peaks in the chromatogram its identification and quantification and determining the proper baseline The YL Clarity station is equipped with a standard algorithm for processing chromatographic data The algorithm requires that the Peak Width and Threshold parameters be set These parameters are a part of the template method file and will be transferred to the chromatogram after an analysis is terminated Peak Width The parameter decides on the peak width at half height expressed in minutes of peaks occurring in the processed analysis The value should approximately correspond to the parameter W05 peak width at half height For peaks of different width the value should be set according to the narrowest one Threshold The parameter is entered in millivolts is independent of peak width and discriminates between a useful signal and noise If a peak has to be included in integration or measured then the height between the beginning and apex of that peak should be at least twice as high as the value of this par
110. le inscription will be displayed instead of results in all chromatograms that have been evaluated according to this calibration Note lf the amount of internal standard was only filled in on one side the ISTD Amount parameter is left blank in the header of the relevant chromatogram or the Amount column in the internal standard compound in the calibration file the internal standard method cannot be applied In all chromatograms that have been evaluated according to this calibration only the uncalibrated calculation will be used 6 4 Description of the Calibration File The calibration file contains data items needed for the compilation of calibration curves In addition to the table of amounts and responses other information like the compound name retention time number of recalibrations etc is listed for each compound The data contained in the calibration file is presented in two tables The main calibration table lists data of all compounds that are common to all calibration levels while the compound tables contain data referring to individual compounds at all levels including the calibration curve Note All data items that are stored in several locations will always be updated after each change Naturally when a modified calibration file is used to process the displayed chromatogram the changes will immediately be taken into account Multidetector calibration For multidetector chromatograms the calibration file can simultaneous
111. le may contain various customized items The Import AIA File dialog is designed to include an unpacking tree to make it easier to verify which items are present in the file The AIA format is designated for single detector chromatograms only Text format A chromatogram saved in the text format may but does not have to contain a header that describes the conditions of the measurement and obligatory data of up to four subsequent chromatographic curves which come one after another Data can be in one column voltage or in two columns time and voltage The conversion program determines according to the content of the individual imported text files the most appropriate settings for importation The automatic setting can be manually modified Text format EZChrom ASCII This format utilizes the ASC suffix and from the text format used by the YL Clarity station only differs in the header with different names of individual items 70 YL Clarity User Guide 9 Export The YL Clarity station allows conjoint text export of results and chromatogram to either the Clipboard or a file export of results to a database file text export of the summary table It is also possible to export the chromatogram in various formats AIA Text EZChrom ASCII moreover chromatograms can be exported in the vector picture format 9 1 Conjoint text export of Chromatogram and the Corresponding Results The Export Data command invoked by clicking the X ico
112. lete 9 Demo Demo Missing HW 74 Demo Wrong S N 74 message 74 Departure 61 Descriptive label 35 Digital Output Control window 23 Digital Outputs setting 23 Dilution 51 Directory 9 Down 22 Drift 19 Enable Autostop 22 26 Enable Sort 8 End 44 Equation correlation 56 curve fit 56 EV 27 Evaluation Version 97 Event Table 23 creation amp modification 23 description 22 Export 71 as text 1 chromatogram in vectors 73 Export Chromatogram window 71 formats 71 Results Table 72 User Guide to database 73 to MS Word 73 External Devices 22 Standard Method 52 Start Stop 22 26 Files CHXRUN RAW 16 CLARITY EXE 98 Filtering 9 Information 9 multiple files 10 Open 9 Ordering 9 Saving 10 Fixed Height 69 Form Font 68 Forw Horizontal 42 From width at 50 command description 50 From To 35 Front Tangent 42 Graph Properties Axes 35 Graph 34 Groups 46 Half Width 47 Height 47 Hidden window 97 98 I V 27 Identification Windows 65 Ignore Origin 56 Indicative graph 33 Inj Volume 28 63 Instrument Directory 98 window 13 Integration Calculations 50 conditions 47 Integration Table 46 48 manual 78 Start 40 Table Description 98 Internal Standard Methods 52 ISTD ISTD2 53 ISTD3 53 YL Clarity Keyboard Shortcuts 5 Landscape 69 Line Style 36 Line Width 35 36 Lock 41 97 98 Locked File 98 Locked Instrument 98 Look In 9 Lvi 28
113. lished will be stored in the integration table and accordingly any operation can be cancelled or corrected An Integration table from another chromatogram or another method can also be used See Chapter 5 4 6 The Integration Table for additional details 5 4 3 Working with Groups of Peaks Peaks can be combined in groups and subsequently integrated together Each group is assigned a single letter identifier and accordingly the maximum number of groups is 26 The Chromatogram Peak Peak Groups command or amp icon from the Peak toolbar are earmarked for working with groups and will open the Groups dialog ID fB Existing groups Delete Cancel Help Fig 20 The Groups Dialog 46 YL Clarity User Guide Adding a peak to a given group Enter the group identifier in the ID field and invoke the Add command Use the displayed interval vertical lines to select the peak s to be included in the group By repeated use of the command other then neighbouring peaks can be added to a group To highlight the fact that a peak is included in a group the corresponding group identifier will be shown after the peak number The Result Table also then comprises the integration results for the created groups No peak may be included in more than one group If a selected peak has been previously assigned to a certain group it will be transferred to the new group Voltage mv Deleting peaks from a group Enter the group identifier
114. lso e Select page characteristics borders numbering and font e Define the headers printed on individual pages The station is supplied with a number of pre defined report styles The user can modify them at will or create his or her own 11 2 6 Password File CLARITY PSW Vuli version Access rights of all users are stored in this file provided the station operates in the protected mode To change the access rights invoke the User Accounts command from the main YL Clarity window Refer to Chapter 12 2 User Accounts Protected Mode on page 88 for additional details 11 2 7 Configuration File CLARITY CFG This file stores the current settings especially the hardware configuration of the YL Clarity station yi Full version Note A backup copy BACKUP CFG is created during station installation In the event the CLARITY CFG file is for any reason damaged you will be notified and the backup copy will automatically be used It contains e The number of displayed instruments and their names e The list and configuration of the installed A D and D A converters modules for direct control of chromatographs pumps and autosamplers e Assignment of the above devices to individual instruments e Configuration appearance of the main YL Clarity window 83 YL Clarity User Guide 11 2 8 Desktop File CLARITY DSK The CLARITY DSK file contains the following e Settings referring to size visibility and location of all no
115. lues at some levels if any will be displayed with asterisks the number of recalibrations is apparent from the Rec No column 55 YL Clarity User Guide nhexan 1 000 min D D mn o D pas Response ISTD Response 0 0 05 1 0 15 2 0 25 Amount ISTD Amount Fig 26 Example of Relative Calibration Curve for the ISTD Method Any part of the curve can be zoomed in using the left mouse button return to any of the previous magnifications or to the original cut using the Previous Zoom commands 4 icon Next Zoom icon or Unzoom icon respectively or display a grid using the synonymous command All the above graphical functions are the same as in the Chromatogram or Data Acquisition windows e g Chapter 5 1 Displaying a Chromatogram on page 33 Type of curve fit equation The type of correlation is defined in Curve Fit Type item Origin item decides on how the co ordinates of the origin will be handled the gnore Origin option ignores the origin while with the Compute with Origin option the origin is considered to be one of the calibration points this means that the resulting curve is influenced by but need not pass through the origin the Curve Passes Through Origin option will always force the correlation curve to pass through the origin Correlation equation The Equation item displays the plot of the calibration curve and the corresponding correlation equation except for the Point to Point segmented line ty
116. ly contain a set of calibration curves for up to four signals The number of displayed signals can be set in the Number of Signals item from the Calibration Options dialog All displayed figures apply to the current signal whose name will be displayed in the header of the global calibration table or in the header of the graph of the calibration curve Select the desired signal using the Calibration Set Signal command or the coloured button from the toolbar The figures that are common to all signals will be displayed in black The figures that are specific for each detector will be displayed in the colour of the appropriate signal 6 4 1 Main Calibration Table The global calibration table is available from the Compounds tab of the Calibration window Open the window using the Window Calibration command or the icon The table summarises data about all compounds that are common to all levels The name of the compound retention time the two identification time windows compound type Peak Type 53 YL Clarity User Guide global response coefficient Response Factor used in free calibration The columns labelled Level X contain data of the current calibration level My GC Calibration C Clarity WORK1 DATA 2506MULTI PRM lt ESTD IEX H form 9 mM H2S04 0 5 ml min Sel File Edit Display Calibration view Window Hel A fl ALY m jJ4H SX eam QoQ BPs 1 afautomatic Recalibration _ EsTD Lx EAST 21 Detector 1 Left Right
117. matogram menu or from the local menu to display a dedicated cursor Move the cursor to the location of the future line beginning left click and hold the left mouse button to draw a line Release the button once the desired end point has been reached and the Line Label dialog will open This is where you can specify the type of line end as well as the colour and type of the line and its thickness in Arrows Line Style and Line Width items Note Lines with a thickness exceeding one pixel will always be shown as continuous You may anchor the line to the active chromatogram by selecting the Assign to Active Chromatogram parameter Modifying descriptive labels and lines A previously created label or line can be modified anytime by double clicking on it with the left mouse button or right clicking on it with the mouse button Labels and lines can also be moved or resized using the handles similar to those used in standard drawing applications which can be invoked by clicking any point on the label or line Hold down the left mouse button and drag to move the object and then release the mouse button to drop it at the desired location The object size can similarly be changed using the relevant handles When a label height has been changed the font size will adapt accordingly Deleting labels and lines Delete the selected label or line that with the displayed handles using the key or the Remove Labels Selected command from the Chromatogram
118. matographs and autosamplers and pumps Data processing string A series of operations comprising the entire procedure used for everything from processing data from an analysis to printing the report This procedure is graphically displayed in the Instrument window using icons that represent the main commands Desktop file extension DSK A file used to store the size location and appearance of all windows and parameters of the instruments Direct control of chromatograph autosampler pumps An integrated additional module for selected chromatographs pumps and autosamplers enabling the direct control and monitoring of selected parameters Electronic signature An electronic signature is an analogy for doing to electronic documents what we do to paper ones and must fulfil the same function as a handwritten signature Meaning that it is a similar process of marking a document for protection and that it must be unique clear and ensure the immutability of the document File sharing YL Clarity enables file sharing between multiple stations Any changes saving of such files are enabled only in the station that first opened it Modifications performed with the shared file will take effect in the other stations only after the file has been reloaded YL Clarity does not enable file sharing between instruments of a single station YL Clarity does enable projects to be shared between multiple instruments of the same station Attention Using the sa
119. me file name in multiple instruments at once does not mean that you are using the same file because each instrument must have a different project directory In other words it is not possible to share projects or files among instruments of the same Station GLP Good Laboratory Practice GLP is an internationally agreed upon system for ensuring and monitoring the quality of laboratory work This is verified and its fulfilment confirmed by the issuance of a certificate 97 YL Clarity User Guide Hidden window A window that is not visible or has been hidden Its activity has not been terminated but rather suspended or is proceeding in the background Click the minimise button E to hide a window cf Closed window Information table A table in the Instrument window displaying the name the measurement methods and the identification of the measured chromatogram Instrument a A part of the program designated to measure and evaluate analyses that share a common time base from one chromatograph The instrument is indicated by the Instrument window see chapter 3 1 2 Instrument Window on pg 13 from which further windows can be opened e g Chromatogram Calibration etc Detectors and control modules can be configured into individual instruments see b Sometimes also a chromatograph Instrument directory The directory identified in the main YL Clarity window for each instrument where projects i e project directories a
120. menu or the local menu To delete all labels and lines from a graph invoke the Remove Labels From Workplace command To delete all labels and lines from an active chromatogram invoke the Remove Labels From Active Chromatogram command To delete all labels and lines invoke the Remove Labels Remove All command Note Labels and lines anchored to an active chromatogram will be stored with that chromatogram Labels and lines attached to the graph area are a part of the desktop file extension DSK Printing descriptions and lines Set which type of descriptions and lines are to be printed in the print style found in the Report Setup Chromatogram dialog Either the lines or descriptions that are linked to the chromatogram and or to the workplace or simply as they are currently displayed on the screen will be printed Note This feature may also be used for hiding of your working symbols and notes that should not be printed in the final print output 5 3 Operations Involving Several Chromatograms Overlay The OVERLAY mode is where several chromatograms can be simultaneously displayed 36 YL Clarity User Guide OVERLAY mode enable To enable the OVERLAY mode use the Overlay command from the File menu the 4 icon or double click the OVERLAY inscription displayed to the right on the status bar The active OVERLAY mode will be indicated by the activated icon the coloured E3 and icons in the Overlay toolbar and t
121. ms obtained from the YL Clarity station Station configuration Determines the number and arrangement of instruments and their interconnection to the A D converter board directly controlled and description of connected detectors Status table A table displayed in the Instrument window containing the names of system files the status of the analysis currently in progress potentially the retention time and identification number of a sample System files The decisive files for working with the station and individual data files project method report style sequence and calibration files Tabs A tab is where several windows are stacked The system is frequently used in dialogs and also in the Chromatogram and Calibration windows Click the corresponding tab to switch over to another tab Template method A method file that serves as a template for new analyses It is always stored directly in the project directory Its name is displayed in the Information Table and its contents are always copied to the newly created chromatogram 99 YL Clarity User Guide Toolbar A block of icons that lead to commands Each toolbar can be situated anywhere on the screen and be configured by accessing the View Customize command in the window or by right clicking the mouse button to access the local menu Unprotected mode A regime of the station that enables any user to work with the station and access its data Window title bar Title bar i
122. n checked At the same time the following remaining mandatory items will be automatically filled in i e copied from the preceding line except for EV and I V items e EV End Vial the last position e I V the number of injections from the position 27 YL Clarity User Guide e Sample ID Inj Volume the values that are included in the chromatogram header e File Name the name under which the chromatogram will be saved e Std Lvl the calibration standard and the level to be recalibrated e Method Name the name of the method to be used for measuring the analyses performed according to the given line e Report Style the name of the report style used Automatic numbering for multiple measurements from a single line If more than one sample is to be measured from any given line EV should by at least one higher than the SV or if several injections are to be effected from any given line I V higher than one the template of the chromatogram name should contain the v and i variables In the default set up the program will automatically add the missing variables To switch off this automatic correction change the Format item from Automatic to Manual in the Options dialog Sequence Options Save the completed sequence file using the File Save command or Save As Changing the order of lines The order of lines in the sequence table can be changed using the drag and drop function with the mouse Multiple lines can be
123. n dialog to switch to the COMMON directory Instrument directories There is a possibility to set different working directories for different instruments This can be done in the Instrument Directories for Projects dialog which is opened by the System 91 YL Clarity User Guide Directories command in the YL Clarity window The directories specifications are stored in configuration file clarity cfg and are common for all users roi 4 Clarity GJes_pemo pry Instrument Directories for Projects Gq Bac lcs Beno E cezo GI Poa _DEMO pri Instrument 1 C Clarity ae 5 O COMMON El workt prj ates a E CTRLTHERM El work pri Inst t2 AWMuColleaguesPC LC Carit ahs netrumen y g y DOE por El work3 prj Instrument 3 oe O bece z q El work4 pri EA DEMO j Instrument 4 an an AlAs Instrument 1 O GPC_DEMO 3 2 IMAGES Audit Trail CAClarity LOG ee INT G Loc Cancel Default Help PDA DEMO 2 PROJECTS ROCKEY Working drectory 1 contains the PRO ECTS directory 2 with alist of available 4 fom SENTINEL projects 3 each projects then specifies directories for storing data 4 5B SOUNDS All projects fromthe same working directory share report styles stored in the COMMON directory 4 O TMP i UPAD UTILS amp G wore gt CALIB O DATA Note n the above image the Instrument 2 shares projects with another YL Clarity station that has been installed on a networked computer
124. n from the Instrument window or in the Chromatogram window is used to export data as text In the Instrument window the Export Data command will only set up the mode to export automatically Postrun function after an analysis has terminated The Export command in the Chromatogram window is earmarked for manually exporting the active chromatogram In both instances the Export Data dialog will open Export Data Export Content Chromatogram Text Format MV Result table c 2 Fixed width In fixed format Delimited by Summary table Ta l Column Iv Moments Time Step Calculation Parameters D min Chromatogram Decimal separator lt Window s Locale gt l Automatic Export To v Chromatogram Header Append Clipboard TextFile dBase File Result table only Table Headers Character Encoding Full Format ANSI X File Name Export Cancel Help Fig 37 The Export Chromatogram Dialog What may be exported The Export Data command enables the user to export data from the Results Table Result table checkbox from the column parameters table Column item chromatogram header Chromatogram Header checkbox calculation parameters Calculation parameters checkbox statistical moments Moments checkbox and also the chromatogram Chromatogram checkbox all in a user defined format When a chromatogram is to be exported the Chromatogram section will be made available where the user can select
125. n modal non dialog windows of the station e A configuration of all graphs and tables e A user specific configuration of the station available from the User Options dialog e Name of the project to be opened prj e Print styles These are not dependent on the project you may use the same print style in several projects The full version features e Inthe protected mode any user can use his or her own dedicated DSK file The filename is specified in the Desktop File item of the User Accounts dialog 11 2 9 Archive Files DGZ The DGZ archives are files to which all the archived data are compressed DGZ archive is not the same as ZIP archive in the fact that files cannot be added to it Instead the files from the archive have to be extracted the old archive must be deleted and finally a new one with the Original and added files should be created 11 2 10 Project Files PRJ These files contain the information on the directories to which the user files will be stored as well as on recently opened files 11 3 File Sharing The YL Clarity station allows files to be shared with another station Sharing means that the station that first opens the file can modify it In all other stations the file will be opened only for reading indicated by an READ ONLY inscription after the filename How to facilitate file sharing over a LAN network For the occasional display of individual files from other YL Clarity stations it
126. n the calculation and ensures high reproducibility of the obtained results The YL Clarity station uses two procedures for calculating the internal standard method The appropriate method is automatically selected depending on whether the same amount of the internal standard in all calibration standards and in unknown samples is being used 52 YL Clarity User Guide a The same amount of the internal standard is used and it is neither specified in an unknown sample nor in the calibration file A relative calibration curve is compiled and used in the calculation where the ratio of responses of the compound in question and the internal standard is plotted against the internal standard response on the vertical axis and the Amount of the compound on the horizontal axis b The different amount of the internal standard has been set both in unknown sample and in calibration file The actual amounts are calculated from a relative calibration curve where the ratio of responses of the analyte and the internal standard on the vertical axis is plotted against the ratio of the amount of the analyte and the amount of the internal standard on the horizontal axis Note The compilation of both types of variables requires that the calibration file contains at least one level at which both the analyte in question and the internal standard have been measured If this condition is not met the relative calibration curve cannot be compiled and the N A not availab
127. n will sort the list in reverse order The ordering mode is indicated by the Icon in the column heading Filtering displayed files While the filename is being entered in the File Name field only files beginning in the already entered text will be displayed If you wish to find files containing a given text not at the beginning of the filename start by entering either in the File Name item or the corresponding number of question marks YL Clarity User Guide Filtering file types The File Type field selects the type of files to be displayed Selecting All Files will display all of the files in the current directory regardless of whether they have the same extension that has been ascribed to the relevant file type Simultaneous opening of several files If the OVERLAY mode has been enabled several chromatograms can be selected in the Chromatogram window To affect a contiguous selection click the first file then press and hold down the key and click the last file to be selected All chromatograms will be highlighted and subsequenily read in by clicking the OK button or striking the key Use the key to select files other than contiguous files Press and hold down the key while clicking on the files to be selected one by one Confirm the selection by clicking OK or pressing Enter 2 8 Saving Files Use Save to automatically save changes effected in the file without changing the name or directory of the file The Save As command
128. named MyColleaguesPC Each item specifies the working directory for the corresponding instrument If an item is left blank the working directory will be set to the directory from which the executable file CLARITY EXE was run C CLARITY by default This directory may be set any time by the command Default How to establish a new project Create a new project in the Instrument window using the File Project command which opens the Project Setup dialog and in this dialog press the New button After first entering the project name you may then modify the names of the data and calibration subdirectories How to store chromatograms and calibration standards in the same directory Select the same name for the two subdirectories in the Project Setup dialog the Analysis and Calibration Subdir items How to open another project Select a new project using the File Project Open command A project can be opened in several instruments and can be shared by other YL Clarity programs across a computer network 92 YL Clarity User Guide 14 Backing up and Restoring Files and Projects The YL Clarity station provides tools for backing up and restoring all data and working files 14 1 1 Backup The File Archive command from the Instrument window is earmarked for backing up data When invoked the command will open the Archive tab of the Backup dialog How to select the type of files to be archived The type of files to be arc
129. nating peaks from an integration 40 YL Clarity User Guide Baseline ES ee ee A ATAA Fig 18 The Baseline Toolbar Validity Interval Two vertical lines delimit the interval of validity Once the command has been invoked the left vertical line will appear Use the mouse to drag the line to the desired position and confirm the move by left clicking the mouse button Move the right vertical line to the desired position using the same method The confirmation of the move will invoke the command The command can be abandoned at anytime by right clicking the mouse button or pressing the key AN Operations involving peaks will only be performed with peaks that are completely enclosed between the two vertical lines Records of modifications All accomplished modifications will be stored in the integration table where any operation can be subsequently cancelled or corrected An integration table from another chromatogram or another method can be also used See Chapter 5 4 6 The Integration Table on page 48 for additional details Peak deletion Using the Lock command or icon will exclude all selected peaks from an integration Only peaks that are completely contained in the selected interval will be excluded Voltage mV 8 8 Time min Time min Baseline through a valley Use the Valley command or icon to force the baseline into all the valleys situated between the interval lines In the event this might resul
130. ndividual compounds at various concentrations Concurrent calibration of several compounds from a single injection may register potential interactions between the calibration compounds as well If a tentative evaluation of the amount of the compound is sufficient for your purposes use the uncalibrated calculation where no calibration curve is required 50 YL Clarity User Guide The YL Clarity station offers two fundamental calibration calculations the external standard method ESTD and the internal standard method ISTD Each can be based on peak height or peak area It is always mandatory to select the appropriate calibration file and enter any additional parameters that are necessary for the selected type of calculation This can be done either in advance in the template method Method Setup Calculation dialog or in the right hand section of the Chromatogram Results window for already measured chromatograms Note The calculation method is defined using the Calculation item in the right hand section of the Results tab and not by the Display Mode parameter from the calibration file in the Calibration Options dialog since the latter merely decides on how the calibration curves are displayed Regardless the calibration file always contains all data necessary for any type of calculation Calculation of percentages The ratio of Amount and Dilution fileds from the chromatogram header specified in Single Analysis or Sequence windows
131. ne using the 4 icon and the text aligned using the and icons Report Setup Chromatogram See i EET tt 2 EE JE ee aaa a Clarity Chromatography SW a V Border Datadpex 2006 Method oe i aor ray Backgroun www dataapex com Calibration d 7 E New y Chromatogram Open Results Help Save Image on the Left i SST iv Options Save As Audit amp Signatures Sequence Printer Image on the Right granm r M Options Print Print To PDF d Send PDF a Fig 36 An Example of a Laboratory Header The contents of all printed segments outside the Report Header can be specified in more detail in the corresponding tab The Method and Sequence segments always comprise several parts of the relevant files The Results segment enables the user to decide whether the table of integration results summary table or the table of column parameters will be printed The Calibration segment allows the user to decide whether all valid or only current level and calibrated compounds will be printed 68 YL Clarity User Guide Printing the chromatogram Parameters from the Chromatogram segment define the orientation and size of the printed chromatogram Orientation item is used to select the orientation location and size of the chromatogram When the Portrait item has been selected the chromatogram will be printed across the page with the time axis parallel to the text The chromatogram
132. nnels Channeli through Channel4 The item Channels assumes values from 0 to 4 depending on the number of open Instruments The items ChannelsxX with X 1 4 indicate the status of individual instruments as follows Value Meaning 2 Instrument not installed 1 Instrument closed 0 Instrument is disabled 1 Instrument is in S OP state 2 Instrument is in VW A T NG state 31 YL Clarity User Guide 3 Instrument is in RUN state 4 Instrument is in DLE state 5 Instrument is in BREAK state You may use one of the following Clipboard formats for transferring data cf_ Text cf_CSV and cf_X Table 32 YL Clarity User Guide 5 Chromatogram The YL Clarity station enables the user to apply a number of operations to chromatograms Among them are baseline modification including the method used for drawing the baseline shifting peak beginnings and ends creating new peaks combining peaks into groups as well as subsequent joint integration and selecting limiting parameters for peaks to be included in integration The effected operations will be stored with the chromatogram and may be used in subsequent analyses thus enhancing reproducibility of the obtained results Because of YL Clarity s intuitive mouse operations and the auxiliary icons all operations are simple and facile Any part of the chromatogram can be zoomed in to define the exact location of the intended operation Multiple chromatograms can be s
133. ns Once the configuration is saved the main YL Clarity window will display the assigned names and the symbol of each instrument 87 YL Clarity User Guide 12 2 User Accounts Protected Mode The station can operate what is known as the protected mode Advantages of the protected mode include the following e The data and station configuration are protected against intervention from unauthorised or inexperienced persons e The station can be locked during a proceeding measurement to protect it from being used by unauthorised persons e Several users can work with the station simultaneously and independently e Customised settings can be saved for each user e Ability to electronically sign a chromatogram Invoke the System User Accounts command from the main YL Clarity window to open the User Accounts dialog where changes can be made and the protected mode set User Accounts Password Restrictions Common for ll Administrator V Min Length Chars Kleofas Maja M LifeTime 90 4 Das V Expiration Warning 5 Days M Password Reuse 365 Days User Details for Petr User User Info User Name Petr Password Submitted Desktop File Petr Password Changed 09 z 2003 Description Lact Logi 09 z 2003 Other Users Can Access To Change Password Read amp Write Instrument 1 Instrument 2 Bao Instrument 3 Thawte Freemail Member kohutek dataapex Certificate Instrument 4 User Acces
134. ns command to open the Calibration Options dialog and then click the Defaults tab Calibration Options 250x 8hr1 Calibration Options Defaults Response Base Area o l Zero Type Curve passes throught Origin v Curve Fit Type finer o amp Weighting Method None v Left Identification Window Right Identification Window 0 100 0 100 Set All Now For Current Signal Cancel Help Fig 31 The Calibration Options Defaults Dialog Default values of some selected parameters for new compounds in the current calibration file can be selected here 6 11 2 Response Factor and Free Calibration The calibration file lists two response factors for each compound Level specific response factor For each calibrated level the compound table lists the response factors in the synonymous item The factor is calculated as amount divided into response at a given level and is only indicative Global response factor The main calibration table contains the column for setting the global response factor Response Factor used instead of values calculated from the calibration equation when the Free Calibration applies Free calibration can be selected in the selected compound tab of the Curve Fit Type item Free calibration is indicated with the Free inscription in the Peak Type column from the Result table in the Chromatogram Results window 6 11 3 Selection of Calibration Units The amount entered in the calibration table can be
135. ntal concepts of which are explained below Clicking Clicking is a term for pressing the left mouse button when the mouse cursor the arrow is pointing to the desired location such as an icon a button an edit line etc In most instances left clicking will replace the function of the key Double clicking e Clicking the left mouse button twice in rapid succession in the same location is most often used to select a file or highlight an entire word in the edit line e Customized function of the double click can be set in all graphs using the Doubleclick means command from the User Options General dialog accessible from the Instrument window using the View Options command Clicking with the right mouse button e Typically displays the local menu e In graphs Right clicking to zoom can be set using the Zoom button command from the User Options General dialog accessible from the Instrument window using the View Options command Mouse wheel The standard scrolling function of the mouse wheel has been extended for the YL Clarity station to facilitate navigation in Chromatogram Data Acquisition and Calibration graphs Wheel only Shifts a chromatogram cut out up or down SHIFT wheel Shifts cut out left right CTRL wheel Enlarges or reduces a chromatogram cut out 2 4 Keyboard Control The station may also be operated strictly from the keyboard The following is an illustration of the functions of some of the
136. ogram Description and DISPIAay ccccccsseeeceeecaeeeeeeeeeeeeeeeeesaaeeeeeessaaees 34 5 2 2 Description and Format of Displayed Axes ccececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaaeeeeeeees 34 5 2 3 Descriptive Labels ANd LINES cccceeccccccceeseeeeeeceeeeeeeeesseeeeeeseeaeeeeeesaaeeeesessaaees 35 5 3 Operations Involving Several Chromatograms Overlay cccccseeeceeeeeesseeeeeeeeeeees 36 5 3 1 Resizing and Relocating Chromatograms ccccccccsseseeeeeeeeeeeeeeeeeeeeeeeeseeseeeeeeas 38 5 3 2 Mathematical Operations ccccccccccccccceeccssessseceeeeeessesseceeeeessseeeeeeeeeesssseageeeeeeees 38 5 3 3 Three dimensional View of Chromatograms cccccccceceseeeeceeeeeeeeeeeeseeeeeeeeaeaees 39 5 4 Chromatogram Modifications ccccccccssseecceeceeseeeeeeeeeeeeeeeseeseeeessaeeeceesssaaeeeessesagseeees 39 5 4 1 Baseline Modifications cccccccssseeceeeeceeeeeeeeeeeeeeeesaeeseceeeeseaeeeeeessaeeeeeseseeeeeeenaas 40 542 Peak ModifIiCatlOnNS sisri nee eee ee eee a 43 5 4 3 Working with Groups of Peaks ccceccceccceeeseeeeeeaeeeeeeeesaeeeeeeseeeeseeeeeseaeeeeessagees 46 5 4 4 The Selection of Conditions That Restrict Integration cccccseeeeeeeeeeeeeeeeeeeeees 47 5 4 5 Separation Paraimelers icc ccicesesscccneraceecictacdnnestatceewietaciicedatninedcegoresddncededscneatcaedeeetacicness 47 5 4 6 The Integration Table cccccccsssccccccsssececcceesseceeseee
137. ol from the toolbar It is not necessary to fill in all figures for each signal For example the Compound Name Retention Time and Amount are common for all signals Common columns are displayed in black type Note A multidetector calibration can also be created using the single detector calibration standards Then you will have to enable the calibration of further signals in the calibration file using the Number of Signals command from the Calibration Options dialog 6 11 Calibration File Modification All data in calibration files can be changed unless dimmed The manual modification of responses The Enable Response Value Change checkbox from the Calibration Options dialog must be checked prior to any manual modification of the values of responses The number of recalibrations is reset to one 1 when a response has been manually changed Deleting a compound To delete a compound invoke the Calibration Delete Compound command or click the Icon 61 YL Clarity User Guide Artificial calibration lt is not a problem to create a calibration curve from the known response factor or response without using a calibration standard Add a new compound to the global calibration table by simply filling in any cell in the last free line Once the entry has been confirmed using the key the remaining data will be automatically supplemented and can be subsequently modified 6 11 1 Default Parameter Settings Invoke the Calibration Optio
138. om the File menu Note Carefully select the method for measuring a chromatogram in particular with regard to attenuation duration of analysis the limiting integration parameters and the selection of the calibration file For example the parameters from the Acquisition tab should be checked prior to starting an analysis since they cannot be modified later Once an analysis is terminated a copy of the method file will be stored with the created chromatogram This ensures that most parameters will be available and may be changed in the already measured chromatogram These are found in the relevant tabs of the Chromatogram window using commands from the Method and Results menus Note The layout of individual commands does not completely correspond to the tabs of the Method Setup dialog This is mostly due to the fact that parameters from the Chromatogram Acquisition dialog serve for information only and cannot be changed 17 YL Clarity User Guide 4 2 2 Chromatogram Raw data processing results in the creation of a chromatogram file extension PRM Chromatograms consist of three basic parts a copy of the model method the raw data and the chromatogram with identified peaks and a marked baseline Chromatograms can be displayed in either the Chromatogram or the Calibration window printed and the file contents exported to the Clipboard or to a text file Chromatograms of individual projects are stored in either the data or the
139. ommand When the window is then closed the station will be unprotected and files with originally restricted access will now be accessible What if you forget the password In this instance transfer the station to the unprotected mode by copying the CLARITY PSW file from the PGM directory on the installation disk to the main station directory This remedy however cancels all user access rights previously set 12 3 Instrument Locking In the protected mode any open instrument can be locked to protect it against unauthorised intervention during the user s absence To lock an instrument invoke the Lock command from 89 YL Clarity User Guide the Lock menu in the main YL Clarity window All activities running a sequence printing a report batch processing etc will continue unabated in the locked instrument Unlock the instrument by either repeatedly invoking the Lock command or by clicking on the chromatograph symbol and entering the password of the user who opened that instrument 12 4 User Settings The station automatically saves the settings of visibility size and location of all non modal windows the configuration of all graphs and tables and all user specific settings available from the User Options dialog The settings are saved in the CLARITY DSK desktop file In the protected mode the settings are saved in the file specified in Desktop File field for each user listed in the User Accounts dialog Thus in the protected regime
140. one or is surplus of another So YL Clarity would rather choose an uncalibrated calculation instead of an incorrect variant of the ISTD calculation The type of a peak is displayed as Free in the Results Table e The free calibration has been used in the Fit Type item of the relevant compound This means that the amount of the relevant compound has not been read off the calibration curve instead the global response factor Resp Factor from the main calibration table was used 80 YL Clarity User Guide 11 YL Clarity Files and Directories Since the chromatographic station uses a relatively large number of directories and files of various types and moreover these can be shared in several windows it is prudent to present an overview 11 1 Directories The YL Clarity station can be installed in any directory on any hard disk After an installation has completed the main directory will contain the following fundamental files CLARITY EXE The executable program of the YL Clarity station Clarity Lite EXE The executable program of the YL Clarity Lite station DLL Dynamically loaded auxiliary libraries that contains in particular modules for data acquisition and direct chromatograph control HLP CNT GID Online help files DTA Data files of simulated analyses used in the demo version CLARITY PSW The file that summarises the access rights of all users including their passwords CLARITY CFG The configuration file of the
141. oolbar contain peaks operations with 43 YL Clarity User Guide Fig 19 The Peaks Toolbar The positions of peak beginnings and ends as well as of valleys or separating vertical lines can be changed Invoke the command move the cursor to the required location and click to confirm Abandon the command may be at anytime by right clicking the mouse button or hitting the key Since only a single peak beginning or end can be shifted to any place selected on the chromatogram without shifting the apex it is unnecessary to specify the peak to which the operation refers Note The preceding sentence does not apply to tangential separations where if the required location lies inside the main peak modification of the tangentially separated peaks is given preference Shifting the peak beginning The Start command or icon defines a new position of the peak beginning In the event the peak beginning is shifted before the end of the preceding peak a vertical line will separate those peaks and its position will coincide with the new peak beginning If the peaks are separated by a vertical line or connected at the valley and the peak beginning is shifted closer to the apex the peaks will be separated Voltage 1E 3 mV an So Voltage 1Z 3 mv 2 84 Isopropanol Shifting the peak end The End command or icon defines a new position of a peak end In the event the peak end is shifted behind the beginning of the following peak a vertical
142. orbid all existing peaks across the chromatogram using the Baseline Lock command then divide the chromatogram into individual segments by repeatedly invoking the Add Positive Negative command and tune up the segments by editing the integration table In some instances the commands for baseline modification may be needed The peak beginning end cannot be shifted to the requested location or the required baseline modification cannot be accomplished A command aimed at baseline or peak modification will sometimes not conform to the user s desire because the algorithm employed for automated baseline modification will not allow it The reason for this is that the station has detected an attempt that would cause the signal to cross the baseline and so it automatically shifts the point in question out of the way A new peak cannot be added There was probably an attempt to add a new peak to an area occupied by the apex of another peak or to the region of tangential separation 78 YL Clarity User Guide Cancellation of a command in the integration table had unexpected consequences All of the commands involving baseline or peak modification including those that do not have the required effect are incorporated in the integration table At the moment a command is cancelled the originally ineffective commands may assert themselves It is therefore recommended to maintain only functional commands in the integration table In this manner the table w
143. ovided so that notes explaining the meaning of individual digital outputs may be entered 4 3 1 4 Automatic Functions after Analysis Termination The station always allows actions to be performed after each analysis has terminated Note Similar actions can be performed with batch processed chromatograms using the Batch command See chapter 4 3 3 Batch Processing of Analyses on pg 30 for additional details My GC PostRun Setting Options V Open Chromatogram Window Open Calibration Window Print Results V Export Data Export Chromatogram in AIA Format Export Chromatogram in TXT Format Export Chromatogram in EZChrom Ascii Format lexcelexe wee Parameters c Cancel Help Fig 8 Postrun Setting Set up is accomplished using the Setting Postrun command from the Instrument window Invoking the command will open the Postrun Setting dialog that contains commands for the automatically displaying the chromatogram printing a report exporting the chromatogram and running another application The setting of the first three items corresponds to and can be controlled by the and D traffic signs next to the corresponding j and ae icons in the Instrument window Automatic displaying of the chromatogram To set a chromatogram to be automatically displayed in the Chromatogram window check the Open Chromatogram Window checkbox from the PostRun Setting dialog or switch to the ES sign next to the A icon in the Ins
144. pe of fit Free Calibration and Sigmoid interlining with X representing the amount and Y the response The curve and the corresponding equation need not to always be displayed and especially in instances of third order polynomial correlation the algorithm that is used to calculate the coefficients of the equation may fail for some extreme values of amounts and responses To remedy such situations use another curve fit type or normalise the entered values Tightness of fit The Correlation Factor item contains the calculated correlation coefficient a number from the interval lt 0 1 gt characterising the tightness of fit Note In the event that the degree of the correlation equation is the same as the number of calibration levels for the gnore Origin option already for a degree less by one the correlation coefficient will be one 1 since such a curve will pass through all points Weighting This method can increase the influence of points with lower concentration on the calculation of the interlined curve Weighting can be related to either the amount of compound in the given point of calibration curve 1 Amount or 1 Amount or to the response of the compound in the given point of the calibration curve 1 Response or 1 Response 56 YL Clarity User Guide 6 5 How to Create Calibration The following chapters describe the procedure used to create and modify calibration files The station provides for both automatic and man
145. pening the sequence window To open the Sequence window either click the ji icon or invoke the Analysis Sequence command from the Instrument window 2 Selecting a sequence file Open the requested sequence file using the File Open command or by clicking the icon 3 Inspecting the content of the sequence table and the files used Inspect all parameters in the displayed Sequence Table eventually also check all method files used click anywhere in a line with the required template method and display its contents either using the Sequence Edit Current Method command or by clicking the 2 icon 4 Inspecting the validity of the Sequence Table YL Clarity automatically inspects whether it will be possible to perform the analyses from the displayed Sequence Table It controls the existence of specified template methods validity of chromatogram names the possibility of overwriting files Invalid lines are indicated with a cross in the Sts column Point the mouse cursor to the respective cell to display a detailed description of the problem Detailed description can be also displayed using the Sequence Check Sequence command icon 5 Running the sequence To run the sequence use the command Sequence Run Sequence icon from the Sequence or Data Acquisition window The sequence will turn to the V A NG state only then will it be possible to start the measurement of the first sample using an external signal from autosam
146. pler AN If the external signal arrives before the sequence is run using the Run command i e in the S OP state a single analysis will be run according to the setting in the Single Analysis dialog 6 The measurement process Measurement proceeds along individual lines of the table Each line may define several measurements of the same sample in I V item or measurements of more than one sample under identical conditions SV and EV items 7 Information about the running sequence Information will both be displayed in the status bar at the bottom of the Sequence window and in the Information table of the Instrument window Both places will display the name of the analysis in progress the position of the vial and potentially the serial number of the injection from that position The Instrument window also shows the template method used and the first two items of the chromatogram header Sample and Sample ID 8 Measurement processing in sequence analyses The template method file listed in the current line of the sequence table in the Method Name column determines the method of measurement and sample processing Printed reports if requested are controlled by the Report Style cells Two conditions must be met for printing 29 YL Clarity User Guide The report style must be selected in all lines of the Sequence table from which you would like to print report The Print Results checkbox from the Postrun Setting dialog also indi
147. quired to make an additional connection between the autosampler and the chromatograph Once a sequence has been started using the Run command from the Sequence window the sequence will pass from the STOP to the WAITING state where it awaits the external starting signal from the autosampler Once that signal arrives the analysis starts and the station assumes the RUNNING state One injection cycle As Measurement analysis F a STOP gt RUNNING WAITING RUNNING WAITING WAITING time Run 1st injection Autostop 2nd injection Sequence Fig 9 Time Diagram of a Passive Sequence 25 YL Clarity User Guide If the External Start Stop from the Method Setup Acquisition dialog of the corresponding template method has been set to Start Restart the next external signal will run the following analysis An analysis can be also terminated by checking the Enable Autostop checkbox in the Method Setup Measurement dialog of the corresponding template method 4 3 2 2 Active Sequence without Control Active sequences are used to increase the reliability of co operation between the station autosampler and chromatograph when an autosampler without autonomous control is being employed An active sequence is also necessary for the intelligent control of some selected autosamplers by means of a special control module see the next chapter 4 3 2 3 Active Sequence for additional details The autosampler must
148. quisition or Calculation tabs in the Method Setup dialog with the help of the Select Detector field The field is only visible when performing a multi detector measurement Calibrated group A group of peaks calibrated as a single component Calibration file Calibration Contains calibration curves and further data for calibrated calculations When performing a multi detector measurement each substance will have its own calibration curves for all detectors Calibration standard A chromatogram containing Known amounts of some compounds that is used to calibrate recalibrate at a specified calibration level Channel Part of the converter that enables the independent collection of data from one single detector 96 YL Clarity User Guide YL Clarity Offline Eval Lock Evaluation Version etc A version of the YL Clarity station that although otherwise fully functional does not allow for data acquisition This version utilises a protective key that is inserted in the printer or USB port of the computer Clipboard A Windows tool that uses the Copy Cut and Paste commands for the simple transfer of data between items including those in other applications Closed window A closed window is invisible and its activity has been terminated A window is usually closed using the Close command cf Hidden window Configuration of the station Sets the number of instruments and their allocation to the A D converter directly controlled chro
149. r chromatogram 48 YL Clarity User Guide 6 Calculations and Calibration The YL Clarity chromatographic station offers several types of calibration and non calibration calculations and is able to assess the quality of a measurement using calculated peak and column parameters Extensive mixtures can be calibrated at up to twenty concentration levels including the calibration of groups of compounds Semi automatic calibration and automated multiple recalibrations of the same level are also possible even for sequential analyses The YL Clarity station incorporates the reference peak method for reliably identifying calibrated compounds 6 1 Result Table The Result Table is in the Results tab opened or hidden using the Results Result Table command and always contains the topical values that refer to the current chromatogram any changes will immediately be reflected in the table Result Table Pers02 lt Uncal 157 639 50 947 776 75 8 2 305 0 05 1 307 0 270 0 6 0 4 2 557 0 06 42 514 15 699 20 9 23 3 2 860 0 04 203 083 67 242 100 0 100 0 Total Results Summary Integration Measurement Conditions SST F Fig 21 Table of Uncalibrated Results Results are displayed depending on the parameter settings in the right hand side of the tab The arrangement of columns is governed using the Setup Columns command In the following text we describe the default layout of the table which is the result of the Restore Default Columns
150. r the Display Unzoom command will display the chromatogram in the original size Note The implicit size is determined by the Scale Y Mode field from the Graph Properties Signals dialog or when the Range Fixed item has been checked using the From To fields from the Graph Properties Axes dialog 5 2 Display Characteristics In view of the many available options for displaying chromatograms axes tags and other information a separate dialog Graph Properties containing several tabs is devoted to these settings Open the dialog by the command Display Properties from the main menu or Properties from the local menu to pop up the local menu click with the right mouse button Parameters are organised in several tabs described below 33 YL Clarity User Guide Global setting lt is convenient to set a number of parameters common to other graphs chromatograms in other instruments the Calibration and Data Acquisition windows the station therefore offers a global setting for some parameters by the command View Options in the Instrument window The opened User Options dialog offers the Graph Axes Appearance Signals and Curves and Gradient tabs devoted to the setting of graphs If you check the items Use User Options on synonymous tabs in Chromatogram Calibration and Data Acquisition windows the corresponding parameters will be taken over from this global setting Note The setting is stored in a file in the unprotected mo
151. rated by a tab in the exported file 9 4 Exporting a chromatogram Exportation of the chromatographic curve to the AIA CDF text TXT Multidetector text format CHR or EZChrom ASCII ASC format The Export Chromatogram command invokes the Export Chromatogram dialog where the file format detector and target directory are to be entered Note If you do not set any filename the name of the exported chromatogram with the appropriate suffix will be used as default 9 5 Exporting Chromatograms as Vector Pictures The Export Export As Picture to File or Export As Picture to Clipboard commands export all displayed chromatograms including all descriptive labels headers and lines in the vector format WMF Windows metafile What is a vector format In the vector format a chromatogram can easily be incorporated modified and printed at a high quality using a text editor or a graphical application Word Excel Corel Draw etc since it is exported as a set of individual line segments connecting all its points What are the advantages of the vector format over the bitmap format Displaying and printing a vector picture is not restricted by the size of the graph in the Chromatogram window which otherwise affects the quality and size of data exported as a bitmap The size of the exported WMF file will be smaller than the size of the bitmap file Note In other words contrary to a bitmap a vector picture can be arbitrarily m
152. re sought Integration Table Constitutes a part of the method and contains a list of all modifications of the baseline or peaks that have been or will be affected in the chromatogram measured by that method Locked file READ ONLY A file that can only be read and never modified Locked instrument An instrument in the protected mode with locked control Lock mode can be activated using a command from the Lock submenu in the main YL Clarity window An instrument is both locked and unlocked by the same password Main station directory The directory where the executable file of the station CLARITY EXE is stored C CLARITY by default The same directory contains the project directories including the project directory PROJECTS the common directory COMMON and all configuration files Method file extension MET A template method file with a description of all parameters affecting an analysis Model method A chromatogram method marked as Model Method that can be easily used with other chromatograms by invoking the Copy from Model command Multi detector configuration measurement The ability to measure save and evaluate a single analysis by simultaneously using a signal from multiple detectors Password A string of a maximum of eight characters that are necessary for working in the protected mode with the station Printout The layout of individual parts of analysis results and the setting of parameters controlling the resulting r
153. rentiate A B BA Result Fig 16 The Mathematical Operations Dialog 38 YL Clarity User Guide In the opened Mathematical Operations dialog click the colour of the first chromatogram in the left Chrom A column select the required operation in the middle Operation column and select the second chromatogram if any in the right Chrom B column The Result field will display the automatically suggested name of the resulting curve The created chromatogram will not be saved and will be cancelled when the window is closed If you want to preserve it save it using the Save or Save As command If you check the Save As checkbox the resulting chromatogram will be automatically saved under the name displayed in the Result field which will be then editable The result is automatically integrated and evaluated according to the template method selected in the Instrument window The method associated with the original chromatogram will never be used when a copy has been created or differentiation A N performed using the Copy and Differentiate commands respectively Itis only used for a copy that has been created using the File Save As command Any chromatogram created or modified in this way will be labelled in the report with the Mathematically reprocessed inscription 5 3 3 Three dimensional View of Chromatograms To display chromatograms in a 3 D view invoke the 3D View command to cancel the view invoke the Clear 3D command
154. river has either not been installed or is inoperative 10 1 2 YL Clarity Demo inscription in the header of the main station window The demonstration version of the program has mistakenly been run The demonstration version will have the serial number displayed in the About YL Clarity window in the form 99 999 Open the window using the Help About command from the main YL Clarity window Message Demo Wrong S N in the main station window The serial number of the station listed in the About dialog open the window using the Help About from the main YL Clarity window command differs from the number on the A D Converter board or in the protective Sentinel key Message Demo Missing HW in the main station window e The A D board or the protective Sentinel key has either not been found or has been damaged e INT7 board driver or the protective Sentinel key has either not been installed or is inoperative e The driver module of the A D board or the protective Sentinel key has not been registered e The A D board driver has not been activated e The driver of the INT5 board has not been configured e A different base address or interrupt has been set on the board and in the INT5 driver 74 YL Clarity User Guide e A conflict has occurred between the base address or the interrupt of the INT5 board and the base address or the interrupt of some other computer device e The interrupt set on the INT5 board is not reserved for ISA slot
155. rnal calibration methods 6 3 3 Internal Standard Methods ISTD Calculations that use the internal calibration method respect the different detector s sensitivity to various compounds and to a certain extent eliminate errors that originate from differences in the injected amount The methods provide the amounts of individual components present in the sample and their percentages In the internal standard method a compound internal standard will be added to the calibration mixture That compound is known as the internal standard A Known amount of the internal standard must be then added to each analysed sample It thus follows that the internal standard itself must not be originally present in the calibration mixture or in the analysed sample Note In selecting the internal standard take into account the sample composition and the chromatographic conditions The internal standard should be very pure and stable must not react with any analyte and should provide a well separated peak Furthermore it must be soluble in the sample and the sensitivity of the detector vis a vis the internal standard and other components of the sample should be similar Since the internal standard is present in the calibration mixtures and in each sample changes in chromatographic conditions and in the injected amount affect the peak of the internal standard in the same manner as the peaks of other injected compounds This circumstance is taken into account i
156. rom any window 13 YL Clarity User Guide 3 2 Structure of YL Clarity Lite windows When using the YL Clarity Lite version the Instrument window labeled as YL Clarity Lite will appear after starting the station instead of the main window for selecting the instrument In contrast to the full version you will find here commands that are in the full version part of the main YL Clarity window e Inthe File menu the Digital Outputs command e Inthe Help menu the Register Check for Updates Send Report by Email User Code YL Clarity Online and About commands For Chromatogram Calibration and Sequence windows applies the same description like in the full version chapters 3 1 3 3 1 5 In contrast to the full version YL Clarity Lite does not contain the following features e Simultaneous measurement on multiple instruments e Logging of the station s activities Audit Trail e Advanced setting of access rights layouts User Accounts e Setting up the Station System Configuration e Offline batch processing of multiple chromatograms Batch e User columns in result tables Create User Column e Direct control of GC LC and AS using add on control modules GC LC AS Control GC LC Monitor e Backing up of files and projects Archive e Electronic signatures Sign e Additional advanced functions useful for working in bigger laboratories 14 YL Clarity User Guide 4 Chromatogram Measurement and Evaluation This Chapter
157. rom which the cut off is to be affected B a0 Voltage 30 20 lt 42 YL Clarity User Guide The Tail Tangent command or icon cuts off all peaks riders that situated on the tailing edge of the last peak and before the selected interval Place the left interval line inside the peak that carries the tailing riders to be cut off the right interval line behind the end of the last peak to be so cut off m Voltage mv 5 Time min Interchanging positive negative The Clamp Neg command or icon interchanges all apexes that are inside the interval to valleys and vice versa thus turning negative peaks from a group into positive ones Voltage mV lt 3 00 3 25 3 50 3 75 4 00 4 25 4 50 3 00 3 25 3 50 3 75 4 00 4 25 Declaring negative peaks to be disturbances The Cut Neg command or icon eliminates from integration negative peaks that are in fact disturbances Neither the beginning nor the end of the preceding positive peak will be affected 4 00 Time min Time min Declaring peaks to be baseline The Reject Negative command or icon excludes negative peaks from an integration without declaring them to be disturbances The beginning of the subsequent peak or the end of the preceding peak if any will be shifted to the original apex of the negative peak 4 00 Time min Time min 5 4 2 Peak Modifications The Peak submenu and the corresponding t
158. s Rights Open User Accounts Edit Sequence Open Configuration Edit Report Style Select Certificate Clear Certificate Edit Method Select Method Edit Chromatogram Open Audit Trail Settings Edit Calibration Cancel Help Fig 39 The User Accounts Dialog How to establish a new user account Open the User Accounts dialog Press New Fill in the following items User Name The name of the analyst entered here will be stored in all files created by that user Desktop File The name of the customised desktop file is entered here Several users may share the file If no name is entered the desktop file created by copying the CLARITY DSK file will have its name entered in User Name field Each newly created desktop file is a copy of CLARITY DSK file What activities should be banned allowed Once a new user s account is established that user can enjoy all rights Some access rights or rights for modifying specified parts of the station can be banned in the User Access Rights section It is advisable to ban standard users from accomplishing the following activities 88 YL Clarity User Guide e Access to setting user passwords User Accounts e Access to system configuration of the station Configuration e Access to setting the station log output Audit Trail On the contrary any ban on chromatogram modification Chromatogram is unnecessarily restrictive How to allow certain users to only work with certain instrumen
159. s ccse scons cee cenwsteahon ceuzceoun R N 37 Fig 16 The Mathematical Operations Dialog cccccccccceeccssseeeeeeeeeeeeaeeeeeeeeeeessaeaeeeeeeees 38 Fig 17 Chromatogram Integration sinsin a a i aa ia 40 Fig 18 The Baseline Toolbar sc ects ccosccnc se sacbasiosineancennncassedcceteeienceeeatatuctssmedsaoneesersaactuceeaateds 41 F19 The PFeakS TOODI e nena a a a ae 44 Fio 20 THe Groups Dialoger a a aa de ces need 46 Fig 21 Table of Uncalibrated ReESUIts cccccccccssseseecceeeeseceecceeeececesseaseeeeeseeseeesseaaaeeeess 49 Fig 22 Example of Calibrated Results Table cccccccccccccccsssseeeeeeeeeeeeaeeeeeeeeeseaeeseeeeeeees 49 Fig 23 Table of Peak Parameters cccccccsseecceeceeeeceeeeeeeeseeeeseaeeceeessaaeeeeeesseaseeeesesegseeees 50 Fig 24 The Main Calibration Table ccccccccccccccccsssseeeceeeeeeseeeeeceeeeesseeeeeseeeeeesessaeaseeeeeeess 54 Fig 25 The Compound Calibration Table ariii a a a 55 Fig 26 Example of Relative Calibration Curve for the ISTD Method ccccceeeeeeeees 56 FIGs 275 The Calibrate Peak Dialog reuera aE a a a ade 59 Fig 28 The Calibration Window Toolbar sssrini a aa aa 60 Fig 29 The Calibration Options Dialog ccccccccsseeeeeceeeeeesaeeeeeeeeeeseeeeeseeeeeeeessaeaseeeeeeees 60 Fig 30 The Recalibrate Peak Dialog n00nnnnonnnnnnnnnnnnnnnsnnnnnsnnnnsrnnnsnnnnsnnrrnsnnensnnnrrsnnersnnner 61 Fig 31 The Calibration Options De
160. s in the BIOS setting of the PC You have either forgotten the password or intend to cancel the password protected mode If the station is operating in the protected mode and you have forgotten the password copy the original CLARITY PSW file from the PGM subdirectory of the installation CD to the main station directory This will shift the station to the unprotected mode but be aware that all the settings in the User Accounts dialog will be lost 10 2 Signal Displaying and Measurement The 4 icon is dimmed and accompanied by the Disabled message and the Data Acquisition command is inoperative e No source for the detector signal has been assigned to the instrument usually a channel of the A D converter board Open the System Configuration dialog using the System Configuration command and select the appropriate signal source on the Instrument1 2 4 tab in Acquisition item e The instrument you are you using has exceeded the number of instruments purchased e g it is impossible to measure on a third instrument if only two have been purchased e You are using the Offline version of YL Clarity Invoke the Help About command from the main YL Clarity window to display the About dialog and check the serial number The serial number format of the Offline version is 98 XXX No signal is being displayed in the Data Acquisition window e Probably an incorrect range has been selected so that the current value of the signal lies outsid
161. s the upper band of each window It is comprised a button to used activate the control menu of the window the window name and the minimise and maximise buttons 100 YL Clarity User Guide 16 List of Pictures FIGS As TWAS SAVEAS dialogissa a a a a e 10 Fig 2 Fundamental Structure of YL Clarity Stations 00 0 cccccecceceeeceeeeessseeeeeeeeeseaeeeeeeees 12 Fig 3 The Single Analysis WiINdKOW ccc c sccccccssssececceeseeeeeeceueeceeceseaseceesssaaseeeesssaseeess 19 Fig 4 Status bar of the Data Acquisition WINGOW ccccccccceeeeeceeeeeseseceeeeeeeeeeesaeaeeeess 20 Fig 5 External Start Stop section of the Measurement tab ccccceeeeeeeeeeeeeeseeseeeeeeees 22 FiO Event TapE eenen aa 23 Fig 7 Digital Output Control for the U PAD2 ariris ainia 23 FIGS Ob POSUN SO MI aces tecitees ah ogy teh ied ees eats Sw ashen lanai ene eee 24 Fig 9 Time Diagram of a Passive Sequence cceccccccsseeeceeeeeeeeeeeeeseeeeeeeesaaaeeeesessaeeeess 25 Fig 10 Time Scheme and Succession of Signals in an Active Sequence 0ccccceees 27 PIGS TS SD CGUCIICC coisa cect dice n eset eevee dance ents de doses ade ease hitacci end eter canadensis 27 PIGS We AUC Missutsasetetasrserchatinna dati e 30 Pigs 13 Graph Properties Gra Pisica n eee ae ieee ee eee Ge 34 Fig 14 Graph Properties Time Axis GidlOg ccccccccsssseeeeecceeseceeeceueseeessaaaeeeeeessaeeeess 34 FIG 15 The Overlay TOODA cri
162. separated by a vertical line If this is the case raise the value of the Peak Width In general the width of detected peaks measured as the distance between the peak beginning and end is proportional to the value of the Peak Width and inversely proportional to the value of the Threshold see Chapter 4 2 Processing the Analysis for additional details 10 5 Chromatogram Modification Added peaks or other chromatogram modifications have been lost e You have probably failed to save the chromatogram after effected modifications e The integration table was mistakenly deleted or replaced by another one The manual integration procedure In the event that manual integration commands have been invoked Chromatogram Peak Add Positive Negative keep in mind that the manually added peaks will be stored exclusively in the integration table just like all other chromatogram modifications How to shift the peak apex As the peak apex location is automatically determined no instruments will be available for shifting it If it is still necessary to shift the peak apex to some other location use the procedure described at the beginning of chapter 5 4 2 Peak Modification on page 43 Dividing the chromatogram into regular integration areas slices In connection with some types of data evaluation it is necessary to divide the chromatogram into segments of equal length and integrate them separately The simplest way to achieve this is to f
163. side the newly calculated intervals The method used to correct the retention times of the non reference peak is apparent from the following Figure New retention times Te lt lt A conversion curve obtained by comparing the retention times of reference peaks An ideal conversion curve n expected if the retention times Ti and Ti are equal T i Retention times of reference peaks in the calibration file Ti Retention times of reference peaks identified in the chromatogram Original retention times A T1 B Tx T2 C T Fig 32 Scheme of the Reference Peak Method The difference between the actual retention times of reference peaks Ti and the retention times listed in the calibration file T i is used to determine by linear interpolation linear extrapolation for non reference peaks past the last reference peak the correction that is to be applied to the retention times of non reference peaks The following relations apply to the i th peak in individual segments between the A B C etc reference peaks In segment A before the first reference Tc To T2 peak In segment B between two reference Tce T 1 To T1 T2 i l T2 T1 peaks In segment C behind the last reference Tc To L12 peak TO Original retention time of peak i TC Corrected retention time of peak T Retention time of the reference peak in the calibration file Ti Retention time of the reference peak
164. station s main folder All operations performed during a single day 24 hour period are saved into a file that is named by the date the operation was completed using the LOG suffix This file can be displayed in the Daily Audit Trail tab The Session tab limits the displayed operations only to those that have been performed since last running the session Local Audit Trails of individual files Apart from recording all station operations the station also keeps detailed records of all operations of sequence calibration and chromatogram files These records are part of each file and can be displayed using the corresponding Window Audit Trail command from Sequence Chromatogram or Calibration windows What are the Audit Trails useful for e Logging station activity is one of the essential steps that need to be made in order to fulfill the conditions of Good Laboratory Practice GLP e Due to the existence of recorded information in the log table we can easily analyse the conditions that may lead to errors or instability in the station The program also enables you to send information regarding system settings and a record of the last two days of station operations when the station has been improperly terminated Note Before sending an e mail with information regarding error s you have the option to check and modity its content or add comments for our user support The message will be sent only after you have approved it e The Audit Tra
165. strument window Using an integration table from another method to measure new chromatograms Display the integration table in the Method Setup dialog using the Method Integration command from the Instrument window Here the local menu contains the Copy From command After invoking this command select the corresponding chromatogram or method This operation is irreversible Note t is necessary to differentiate between the creation of an entire new method from the current chromatogram using the Save as Template command from only copying the integration table using the Copy From command Using a method or only the integration table from another chromatogram The Method menu in the Chromatogram window contains amongst other elements two sets of commands for copying methods or only the integration tables alone from other chromatograms Copy Integration Table from a Model Copying a method or only an integration table from a chromatogram which was previously indicated as the model using the Set Model command Above all this possibility is used when cloning an integration table from one chromatogram to several various chromatograms Copy Integration Table from Template Method Use the method or only integration table from a template method Template methods are saved with the MET suffix and are used for measuring new chromatograms Copy Integration Table from Chromatogram Use the method or only integration table from anothe
166. sults A Summary Integration Measurement Conditions SST Results Thus if the sample weight will be entered in the Sample field and the volume used for dissolving the sample in the Dilution field using the same units as are used in the calibration i e Calibration is in mg l weight in mg solvent volume in litres the user will get the percentage of compound in the original sample in the Amount column of the Results table For example The amount 5 mg l was found for 100 mg sample dissolved in 100 ml 0 1 The result in the Amount column will be 5 mg 0 1 100 mg 0 5 Attention n evaluation of peak groups the total response used in the calculation of percentages includes contributions from individual groups and separate peaks i e peaks not included in any group It is important to keep this fact in mind when some peak is calibrated separately as well as a part of some group Calculation of unidentified peaks For peaks that are not identified in the calibration file the Response Factor parameter is used in the calculation instead of a value read off the calibration curve The default value is 0 so the unidentified peaks will not be applied 51 YL Clarity User Guide 6 3 1 Non calibrated Calculations Uncal Without a calibration file the amounts can be only expressed as percentages of the overall area or height of all chromatograms The two types of non calibrated calculations assume that the detector sensitivity is the
167. t in having the baseline intersect with the signal the station will prevent the intersection by automatically shifting the peak beginning or end This operation is opposite to the Together command 41 YL Clarity User Guide Baseline between separating verticals The Together command or a icon introduces separating verticals to all valleys that are situated between the interval lines This operation is opposite to the Valley command Horizontal baseline The Forw Horizontal command or r icon forces a horizontal baseline from the beginning of the first peak inside the selected interval beneath all peaks inside the interval Voltage mv SS _ __ __ _ _ _ E 7 0 7 5 8 0 8 5 7 0 7 5 8 0 8 5 9 0 Time min The Back Horizontal command or icon draws a horizontal baseline from the end of the last peak that is inside the selected interval beneath all peaks inside the interval 9 0 Time min 8 5 9 0 9 5 Time min Note Should the horizontal baseline intersect the signal inside a peak no forced horizontal baseline will possible for that peak Tangential separation The Front Tangent command or icon cuts off all of the peaks riders that are situated on the leading edge of the first peak and after the selected interval Place the left interval line to left of the first peak to be cut off and then place the right interval line inside the starting of the peak f
168. t replace the windows specified in the calibration file 6 13 3 Updating Retention Times Retention times of compounds tend to eventually shift and accordingly difficulties with the identification of calibrated compounds in the chromatogram may sometimes be encountered To avoid this problem the YL Clarity station provides for an automatic update of the retention times of calibrated compounds in each subsequent re calibration by registering any potential shifts in retention time This process results in the reliable identification of calibrated compounds Enable the automatic update by checking the Update Retention Time checkbox in the Calibration Options dialog The retention times listed in the calibration file will be updated as an arithmetic mean of the new time and all times established in previous re calibrations of the given compound 65 YL Clarity User Guide 7 Reports The YL Clarity station provides for an arbitrary part of the obtained results to be printed at any printer registered in the Windows environment 7 1 Reporting Procedure 1 Where to initiate a report The YL Clarity station enables reports to be printed from many dialogs The menus of most windows contain the Report Setup command 24 icon or the Report button Always select the window that contains the data you wish to include in the report Different report styles are preset in each dialog but can be modified or replaced at will Report Setup Chromatogr
169. tation operations Audit Trail VAMSI 11 3 STRUCTURE OF YL CLARITY STATION WINDOWS 0 ccccc titties 12 3 1 Structure of YL Clarity windows Waar i icccccccceeeceseeseeeceeeeeseaeeeeeesesssuaaeeeeeeeess 12 3 1 1 YL Clarity Ula re 6 Full version ee 13 3 1 2 Instrument Window CMa oe ceccccseececcseeeecceseeeseeseeecaseeeeeaeeeessneeessagseeeseass 13 3 1 3 Chromatogram WINOW c ccccccccceccseeeeceeecaeeseeeeecueeeeeeeseaeeeeeesseaeeeesessaaeeeesessaaees 13 3 1 4 Calibration WiINdOW cccccccccceccccaeeseeeceeeeeeeeeeeeceeeeeseaeesseeeeeeeessaeaaseeeeeeeesaaaaseeeees 13 3 1 5 Sequence WINKOW cceeeeeccccceccesesseeeeeeeeceeaeeseeceeeeeaeessseeeeeeesseeeseeeeeeeesssaaaaseeeeeees 13 3 2 Structure of YL Clarity Lite WINGOWS cccccccccseseeeceeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeessaaaeeeeeeess 14 4 CHROMATOGRAM MEASUREMENT AND EVALUATION sseeeeeeeeeees 15 Al Mea Some eea T steer cibesntecisarebasasapsiesnretaincstannin 15 4 2 Processing the ANnalySIs ccccscccccsssccccsssececeesseecceueeeceaseeecsaseeeesaseeessageeessegeeeesenseeess 16 4 2 1 MOMO sirssterctnautuneseoninenansnnibeausuiiasendadies genau sadensas sean saleee E E esas 17 Bee GONO een E EE E T E E 18 4 3 Fundamental Procedure of AnallySiS ccccccsssssececceeeeeeeeeceeeseeeceeeeseceeseeaueeeessaaageeeess 18 4 3 1 Sa EEA EI E EEE E E AE N E E 18 4 3 1 1 External Control of Analysis Run
170. th the left button held down will be highlighted The grey buttons to the left select the entire row those on top select the entire column the top left button selects the entire table To select a contiguous area use a combination of the key and the cursor key The combination A or the command Select all from the local menu selects the entire table see Chapter 2 5 3 Local menus of tables p 7 Note Editable tables are after selecting all cells of the table copied to the Clipboard without header Non editable tables are copied with header YL Clarity User Guide Automatically filling table fields with repeating values When entering data into the tables it may occur that you need to fill in an area of the table with periodically repeating information The Paste command automatically supports this need It is sufficient enough to copy information into the clipboard that is to be repeated and then indicate the area where data is to be inserted using the Paste command Note Automatic data entry applies to both lines and columns Should you thus wish to insert periodically repeating lines remember to insert them whole into the clipboard including any empty columns Deleting values Often times selected values can be deleted by the Delete command or the Dell key 2 File Selection Open any file using the Open command The Open X dialog will first be displayed where X stands for the type of file a chromatogram a method etc
171. the gt licon next to the File Name field in the Single Analysis dialog to open the assistant that will utilize individual variables to compose file names Simply select the required function click on it and the assistant automatically adds the corresponding variable to the file name 1 In some instances the application will save the chromatogram under a special name using the first free eight digit number starting at 00000000 This is designed specifically for situations where a risk that measured data might be lost or existing data overwritten exists The user has cancelled the invitation to enter a new chromatogram name using the Cancel command The application was unable to display a message requesting that the new chromatogram name be entered since e g some other message was displayed at that time End of analysis Activate the Stop button in the Single Analysis dialog Depending on the settings affected in the preceding two articles the analysis will then terminate and the measured data will be saved potentially evaluated displayed and printed Activation of the Run button will terminate the analysis in the same way run the next analysis and continuously measure a series of analyses Note An analysis can also be terminated using the Analysis Stop Abort commands De icons from the Data Acquisition window Displaying results The ability to have chromatograms automatically displaying in the Chromatogram and Calibration w
172. the grey button at the beginning of the row and then pressing the key 2 5 3 Local menus of tables Invoke the local menu by clicking any cell with the right mouse button The local menu contains commands from the Edit menu e The Select All command for selecting all cells in the table Select All e Fuction Undo Redo for cancelling or renewing applied changes in tables Copy Add user column e Commands for working with the Clipboard Copy Cut Paste and Paste fe econ Inse rt Restore default columns Setup columns e Commands for configuring the table Setup Columns Restore Default Columns Hide Column s Show Hidden Column s show hidden column s e Commands specific for the given table 2 5 4 Configuring Tables All tables enable the user to adjust the width of columns the order of columns potentially also the sorting method How to change the column width To change the width of a selected column move the mouse cursor to the right border of the grey field of the heading the cursor will change its shape to Click and hold the left mouse button then drag to change the column width Double click at the above location to adjust the column width to accommodate the longest string of text Several columns may also be selected at once changing the width of any one will change the widths of all How to change the order of columns 7 oe ty iss tee Left click on the grey header of the required column Click
173. to only use the above correction for small deviations originating e g from the difficulty of achieving a reproducible injection in gas chromatography 6 13 Peak Identification in Calibrated Calculations This chapter deals exclusively with the identification of separate peaks since the identification of peak groups proceeds according to respective single letter identifiers One may reasonably expect that compounds contained in a calibration file will be identified with peaks in the measured chromatogram To this end the user specifies identification windows relative to the relevant retention time for each compound in the calibration file If a peak exists in the chromatogram whose retention time falls within the identification window it will be assigned to the corresponding compound from the calibration file In calibrated calculations the calibration curve for that particular compound will subsequently be used for the peak thus identified If there are several peaks inside the identification widow the peak whose retention time is the closest to the retention time of the calibrated compound will be identified Peak identification is used not only in calibrated calculations but in recalibration and multilevel calibration as well Chapter 6 13 2 explains how the station resolves possible instances of overlapping identification windows 6 13 1 Reference Peak Method The process of peak identification may sometimes be complicated with changes in r
174. trument window If the OVERLAY mode is operative chromatograms will be displayed one by one and overlaid To set a chromatogram to be automatically displayed in the Calibration window check the Open Calibration Window checkbox from the PostRun Setting dialog or switch to the Gi sign next to the icon in the Instrument window The automatic display will be suspended if the OVERLAY mode is not operative and a chromatogram is currently opened that contains some unsaved changes or if the number of displayed chromatograms has reached the limit 20 by default set in the Maximum Chromatograms in Overlay from the User Options General dialog Note When the Maximum Chromatograms in Overlay limit has been reached the first opened chromatogram will be closed 24 YL Clarity User Guide Automated reporting Use the Print Results checkbox from the PostRun Setting dialog or the Gi traffic sign next to the icon ae in the Instrument window to enable automatic chromatogram printing printing will be done according to the report style set by the File Report Setup command from the Instrument window In a sequence analyses the report style must be defined in the corresponding line of the sequence table Printing is conditional on both the report style specified in the Sequence Table and the checked Print Results checkbox Automatic export Check the Automatic Export checkbox to have selected data automatically exported to a file or to the Clipbo
175. ts It is possible to allow certain users only to work with certain instruments by using the Access to item How to restrict certain users from using or updating files Permit files to only be read using the Read Only item or to be read and updated using the Read Write item If no item is checked your files will be inaccessible to other users Under which conditions do files cease to be protected e Files are protected as long as your account exists and cease to be protected once the mode has been changed to the unprotected state e Files read into another YL Clarity station where you do not have an account will be accessible How to cancel an existing account Select the name of the user to be eliminated from the list in User List Invoke the Delete command It is still possible to cancel elimination from the list by striking the Cancel button All files created by the eliminated user will then be accessible to all users after the station is run for the next time lf all users are eliminated the station will pass to the unprotected regime when run for the next time How to change the access rights of a user Select the name of the user whose rights you wish to modify from User List All items will then refer to that user and can be changed The effected change may still be cancelled using the Cancel command How to transfer the station to the unprotected mode Eliminate all users one by one from the list using the Delete c
176. ts The following fundamental key combinations used to facilitate work with windows Alt Closes the current window Esc Closes a dialog Alt Tab Switches between windows of all currently running programs F1 Invokes the context sensitive online help 2 2 Icons and Toolbars Icons Icons are small graphical symbols that facilitate invoking some functions or windows All icons have the corresponding counterparts in menu commands Toolbars Toolbars are panels containing icons Toolbars are usually situated below the title bar but can be moved to any place on the screen The YL Clarity station contains several predefined toolbars that may be customised icons can be added or removed the user can also create his her own toolbar Scheme of data processing y The Instrument windows display a special arrangement of icons that reflect the typical ns E Enc procedure of a measurement and chromatogram processing The corresponding A YL Clarity User Guide commands can be invoked in any order the displayed arrangement merely facilitates orientation and assists one in following the appropriate procedures for working Note the three E or O symbols that correspond to the first three items of the Postrun Setting dialog 2 3 Mouse Control As with most Windows programs the YL Clarity station is most easily navigated and controlled using the mouse YL Clarity makes use of both the left and right mouse buttons the fundame
177. ual calibration and recalibration of individual peaks or groups or jointly for all compounds peaks and groups 1 Create the calibration file Create a new calibration file using the File New command from the Calibration window 2 Display a calibration standard Unless you intend to create an artificial calibration you must display in the calibration window the relevant calibration standard at a certain level To do that invoke the Open Standard command or click the y icon to display a list of all chromatograms from the calibration subdirectory of the current project Use the fg icon to display chromatograms from the data subdirectory 3 Selecting calibration parameters Check the toolbar to determine whether has been set 1 fautomatic calibration The number box indicates the calibration level Automatic means that data for individual compounds will automatically be transferred to the calibration table and Calibration indicates the calibration regime contrary to recalibration regime 4 Transferring individual compounds data to the calibration table Use any of the following commands from the Calibration submenu or the corresponding icon to transfer compound data contained in the calibration standard to the calibration file Add All Add all peaks identified in the calibration standard lf the calibration table is empty all peaks and groups from the calibration standard will be calibrated If the calibration
178. uence processing If a sequence is to be batch processed all chromatograms measured during the sequence s last run will be included Any missing chromatograms not measured deleted or measured at any of the preceding runs of the selected sequence will be ignored Note Chromatograms are sought according to an internal hidden list of actually measured chromatograms It is because the File Name column may contain variables that would prevent the relevant chromatogram to be unequivocally identified date time serial number etc Also processing here will only be comprised of the selected operations that are listed in the right hand part of the Batch dialog 30 YL Clarity User Guide Comprehensive sequence processing The Complete Processing command performs repeated processing according to the topical contents of the sequence table The headers of all chromatograms will be overwritten and the method actually specified in the sequence table will be employed recalibration will be carried out if required Processing according to the current template method If you wish to process chromatograms according to the currently opened template method in the Instrument window check the Reprocess by Instrument Method checkbox from the Batch dialog all parameters listed in the Method Setup Integration and Calculation tabs will be used Selection of multiple chromatograms to be processed To select multiple files hold down the key while
179. z Origin Curve passes through Ori Weighting Method None ba Equation Y 135 95252x Correlation Factor 0 997573 Compounds oxalic A citric A tartaric glucose A malic fructose A succinic A lactic A glycerol A acetic methanol ethanol For Help press F1 Chromatogram Fig 25 The Compound Calibration Table Optional validity of points Individual points may be temporarily left out or on the other hand included into the calculation of the calibration curve A point is omitted from the calculation by cancelling the indication in the Used column in the calibration table of substance An invalid point is illustrated in the graph by a circle Note An invalid point in the calibration curve behaves as if it were not present For example indicating an invalid point at the end of the curve will change the scope of the axes This will cause the circle representing an invalid point to be shown outside of the displayed area of the graph Only the circles of those invalid points behind which will still be at least one valid point cross can be seen 6 4 3 Calibration Curve The calibration curve is displayed together with the compound calibration table The curve is plotted as the dependence of the response on the amount The curve will be not displayed though if the correlation equation cannot be compiled for the selected type of correlation Each calibrated level is displayed using a cross in the graph points for recalibrated va

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