GC Chromeleon SW Gamal A. Hamid

Contents Introduction Chromeleon client Chromeleon Console Chromeleon Studio Simple analysis 1. Start Chromeleon 2. Start the instrument 3. Create a sequence 4. Acquire data 5. Process data 6. Review and report results eWorkflow Getting started

Is a chromatography data system that allows you to control chromatography instruments and evaluate, process, report, and backup data. Chromeleon

Chromeleon Software Components: Instrument Controller Service Client Services Manager Instrument Configuration Manager Administration Console

Instrument Controller Service The Instrument Controller (Service) controls the data exchange to and from the Instruments, such as reading the instrument method from a Data Vault and sending it to the instrument, then writing back the raw data delivered from the instrument Data Vault Instrument Controller Process Run Start / Stop Services Manager Client

Client The Chromeleon Client provides the user interface for all tasks related to instrument operation, data analysis, and data management.

Service manager Monitor the status of the Instrument Controller and other services. Start/Stop the Instrument Controller service. Launch the Instrument Configuration Manager tool. No. Icon Description 1 Stopped 2 Starting or stopping 3 Running idle 4 Active 5 Error

Instrument Configuration Manager The Instrument Configuration is the tool in Chromeleon to configure chromatography Instruments before they can be controlled by Chromeleon.

Administration Console The Chromeleon Administration Console is the central access point for all administrative tasks in Chromeleon. In the Chromeleon Administration Console, you can: Manage users in the User Manager. Allocate licenses in the License Manager. Plan and organize tasks with the Scheduler. Define global policies. Configure the discovery service and monitor other Chromeleon services. Manage data vaults. Create and manage Organizational Units

Client

Chromeleon Client The Chromeleon Client provides the user interface for all tasks related to instrument operation, data analysis, and data management. The Chromeleon Client contains two main components: 1. Chromeleon Console 2. Chromatography Studio

Software Sequence Order Level 1 order access to the categories “Categories bars” . Level 2 order navigate through the objects “navigation Pane”. Level 3 order work with that object “Work area”.

1. Chromeleon Console The main Chromeleon window that appears after starting Chromeleon. The Console comprises three major areas: The Category Bars which provide access to the categories Instruments, Data, and eWorkflows where you can control instruments, navigate through all data and use or manage eWorkflows. The Navigation Pane where you can navigate through the objects related to the selected category. The Work Area which shows the content of the object that was selected in the Navigation Pane, and allows you to work with that object.

Console Components

1. Category Bars – These provide direct access to a. Instruments b 1. Category Bars – These provide direct access to a. Instruments b. Data c. eWorkflows 2. Navigation Area – This displays all objects associated with a specific category bar. Details are provided in the relevant section for the category bars. 3. Work Area – This displays details about the selected object in the navigation area. More details are provided in the relevant section for the category bars. 4. The Filter Toolbar offers different views of the list in the Navigation Pane: a. Local: Items available on the local Chromeleon station. b. Global: Items available on the Chromeleon Domain. c. Custom: Filter based on text input. 5. Menu Bar – provides major commands relevant to the console. 6. The Sequence Toolbar is available when a Sequence is selected in the Navigation Pane. 7. The Sequence Status Bar indicates the sequence status. 8. Status Bar shows general information such as the currently logged on user and role.

2. Chromatography Studio A separate window that is launched from the Console, in which you can work with data and objects related to a selected sequence. Here you can view and optimize all aspects of the data, modify instrument methods and processing methods, define and generate reports, and manage spectral libraries.

Studio Components

Chromatography Studio In the Chromatography Studio you can edit all objects related to the selected sequence: Injection List Instrument Methods Data Processing View Settings Report Templates Electronic Reports Spectral Libraries

Injection List The injection list is the primary element of a Sequence. The injection list groups injections in the order in which they will be processed and includes injection variables (name, type, etc.) that characterize each injection.

Instrument Methods The instrument method contains the control commands that are executed in chronological order by an instrument when running an analysis. The tool used to create an instrument method is the Instrument Method Wizard; the tool used to view and modify methods is the Instrument Method Editor. Double-clicking an existing instrument method automatically launches the Instrument Method Editor in the Chromatography Studio.

Instrument method An instrument method contains the control commands that are executed in chronological order by an instrument when running an analysis. The tool used to create an instrument method is the Instrument Method Wizard; the tool used to view and modify methods is the Instrument Method Editor.

The Data Processing

View Settings View settings define how the results for a sequence are represented in the data processing window. This includes information such as: The panes displayed in the data processing window, The zoom level and any layout properties of the chromatogram plot, calibration plot, spectral plot, contour plot, and 3D plot, The sheets (tables), columns, auto formats, and properties of the interactive results tables.

Reports and libraries Will cover later. Report Templates Electronic Reports Spectral Libraries Will cover later.

Simple Analysis

Simple Analysis Every analysis using Chromeleon follows the same 6 basic steps: 1. Start Chromeleon 2. Start the instrument 3. Create a sequence 4. Acquire data 5. Process data 6. Review and report results

1. Start the Chromeleon Start Chromeleon Controller (in the notification area). Wait until the Instrument Controller is running idle before stopping the service. (To stop the Controller Right-click the Chromeleon tray icon in the notification area of the Windows taskbar. Click Stop Chromeleon Instrument Controller.)

Configure Instruments Configure instruments to open the Instrument Configuration Manager, where you can add new instruments or change the current instrument configuration.

Modules Selection Select the modules according to the configuration of the system Retrieving the configuration from module given the right setting of each module.

2. Start Instrument To start the Chromeleon software: Double-click the Chromeleon 7 icon on the desktop: The Chromeleon Console window opens. If user management is active, you will be prompted to log on to the software. Enter the credentials provided by your Chromeleon administrator to proceed

Establishing a Connection Before you can control an instrument, communication must be established between the modules and the Chromeleon Instrument Controller. For all installed modules, the Connect command is executed automatically when the Chromeleon instrument service is running. To connect the modules follow these steps: 1. In the Console, choose the Instruments category and click your instrument’s name in the Navigation Pane. 2. Select the ePanel tab for the required module in the Work Area .

Controlling and Monitoring the Instrument To issue instrument commands follow these steps: In the Console, choose the Instruments category. Select the instrument by clicking its name in the Navigation Pane. 2. In the Work Area select the ePanel tab for the required module. 3. Use the controls on the ePanel to issue instrument commands (for example setting the of detector .

e Panels An ePanel is the window where you monitor and control a module's operation. ePanels are displayed on the Console in the Instruments view. If an Instrument includes more than one module, ePanels are grouped into collections, called ePanel Sets.

Monitoring

Other Commands Command Most common commands are available from the ePanels. If you need to execute a command that is not available in the ePanel, you can access all available instrument commands from a dialog box that is accessible via the Command button in the Instruments toolbar

3. Creating a Sequence A sequence determines how a group of injections should be processed. Sequences can be created in the Console or by using an eWorkflow. You create a sequence using the Sequence Wizard within the Console. the following files should be created: Instrument Method (Must) Processing Method Report Template But first

Instrument Method The instrument method contains the instrument commands that will be executed for a sample analysis. All data entry values are checked against the allowed values. The commands available depend on the instrument that the program file is connected to.

Creating an Instrument Method 1. In the Instruments category of the Console, select the instrument from the Navigation Pane 2. On the Create menu, click Instrument Method. 3. Complete all wizard steps and click Finish. The created instrument method opens in the Chromatography Studio. 4. Review the instrument method by selecting the module views in the Navigation Pane. 5. Edit settings, if required. 6. Save the instrument method 7. Close the Chromatography Studio.

Instrument Method Wizard Create Instrument method Select Instrument System General Setting Pump Flow Gradient Pump general Setting Sampler General Setting Sampler Injection Mode Sampler Temp. Control Column Oven general Setting

Processing Method A processing method is used to detect and quantify peaks and to evaluate the recorded chromatographic data. The processing method contains all the data processing instructions (e.g. detection parameters, peak names, etc.).

Creating a Processing Method 1. In the Console, on the Create menu, click Processing Method. 2. Select one of the predefined layouts and click Next. 3. Enter a name, select a file location and optionally enter a comment. 4. Click Finish to save the processing method and close the wizard. The new processing method opens in the Chromatography Studio.

Processing Method Wizard Create Processing Method Processing Method Template Named the Method & Finish Processing Method in Studio

Processing Method Components Detection Components Table Calibration Unidentified peak G. table Chromatogram Subtraction Advance Setting SST/ IRC

Detection Parameters Cobra Wizard Integration area Baseline noise range Smoothing width Minimum Area Channels and Injection types

Creating a Report Template 1. In the Console, on the Create menu, click Report Template. 2. Select one of the predefined templates and click Next. 3. Select a file location and enter a file name. 4. Click Finish to save the report template and close the wizard.

Report Pages

Sequence A sequence determines how a group of injections is processed. The following elements can be included in a sequence: Injection list (a group of injections that are analyzed) Injection results (the chromatographic data acquired for each injection) Instrument method (the commands used for controlling the Instrument) Processing method (the parameters used for evaluating the injection results) View settings (the settings used for displaying data in the Chromatography Studio) Report template (the template used for printing injection results) Spectral library (a group of spectra used for identifying unknown substances)

Sequence Is a collection of injections that are analyzed and processed together in series. Unknown: A sample for which the quantity, presence, or absence of components is to be determined during the analysis. Calibration Standard: A sample with known concentration(s) of component(s). Calibration Standards are used in the construction of calibration curves. Check Standard: A sample with known component concentration(s). Check Standards are used to verify a calibration.

Cont. Blank: An injection used to characterize the background signal (baseline), and/or to ensure that unwanted components are not detected. Blank “injections” can be made without an actual injection taking place. Matrix: The sample matrix. The peak areas in the Matrix can be subtracted from the corresponding peak areas in all the other injections in the sequence. Unspiked: An Unknown sample to be analyzed with the Standard Addition method. Spiked: An Unknown sample to be analyzed with the Standard Addition method, with known amounts of components added.

Creating a Sequence To create a sequence using the Sequence Wizard within the Console: In the Instruments category of the Console, select the instrument from the Navigation Pane. 2. In the Console, on the Create menu, click Sequence.

Cont. 3. Complete the injection configuration settings for the injections 4. Click Next. Note: When you are creating a sequence using the wizard, you can only add injections with type Unknown. After the sequence has been created, you can modify the injection types and positions. 5. Select methods and reporting preferences: For each field use the button to navigate to and select the file you want to use. When all fields are completed click Next. 6. Enter a comment for the sequence (optional) and click Finish. 7. The Save dialog box opens. 8. Specify where to save the sequence, enter a file name, click Save.

New Sequence Wizard

4. Acquire Data 1- Starting an Analysis After the sequence has been created and the instrument is ready, you can start data acquisition. Checking that the Instrument is Ready Check the baseline, for example, select the detector’s ePanel and click the Monitor Baseline button. When you are satisfied that the instrument is ready for analysis, start the sequence. Starting the Sequence 1. Select the Data category in the Console. 2. In the Navigation Pane, select the sequence you want to run by clicking on it. Sequence then opens in the Work Area.

2- Monitoring an Ongoing Analysis During analysis it is useful to monitor the detector signal and other instrument parameters (such as pressure and temperature). To monitor an ongoing analysis: 1. In the Console, choose the Instruments category and click your instrument’s name in the Navigation Pane. 2. Select the Home ePanel in the Work Area to monitor the detector signal and audit trail. Note: The settings of other modules can be monitored on their respective ePanels.

5. Processing Data After chromatographic has been acquired, it can be processed. All processing steps are performed in the Studio and saved in a processing method.

Data Processing Home

Data Processing Steps Reviewing Data in the Chromatography Studio Working with Chromatograms Detecting and Integrating Peaks Identifying Peaks Calibration and Quantitation

Reviewing Data in the Studio After data for all samples in a sequence has been acquired, it is useful to review the chromatograms and peak data before reporting the results. Often, peak detection, integration and calibration settings need to be modified before results are reported.

View Options There are several views in Chromeleon which can be selected from the Presets group on the Data Processing Home tab. You can also create new views and store these to be used again.

Working With Chromatograms You can view the integrated chromatogram of the current injection in the chromatogram . If the evaluation of data is not what you want, you can adapt the layout of the chromatogram to your needs.

Layout Options

Detecting and Integrating Peaks For correct quantification or qualification of a chromatogram, all peaks of interest must be detected and correctly integrated. To achieve this you can either: Create a new set of detection parameters. or Modify an existing processing method.

Steps Creating a New Set of Cobra Detection Parameters Modifying an existing Processing Method Insert a New Detection Parameter Modify and Delete Detection Parameters Integrate Unresolved Peaks

Smart peaks The SmartPeaks™ assistant helps you to quickly calculate the baseline of unresolved peaks. All you need to do is drag a window over the peaks of interest in your chromatogram. Cobra + Smart peaks together are enough to integrate 99% of chromatograms.

Identifying Peaks After peaks have been detected and satisfactorily integrated, they can be used for reporting or results calculations. When reporting, it is useful to name components in a chromatogram. Creating a Component Table Modifying Retention Times and Windows

Component Table The Name variable, is set to a generated name (Component 1, Component 2, etc.). The Window variable is set to an absolute value, which represents one-fourth of the distance from a peak to either the preceding peak or the next peak, depending on which peak is nearer. The Peak Type variable is set to AutoDetect, indicating that Chromeleon determined the peak type. The Comment variable is set to auto generated, indicating the component was created with the wizard. The component table is part of the Processing Method Editor and contains all parameters required to identify a peak and to determine the amounts of the substances serving as standards.

Create a Component Table There are three ways to create a component table: Via the Component Table Wizard Interactively in the chromatogram pane Via the component table (processing method)

Calibration and Quantitation In order to convert the area below a peak or the peak height into absolute amount or concentration values, calibration is required before the analysis. The calibration coefficients obtained during calibration can then be used to calculate unknown amounts.

Specifying the type. Creating and Assigning Calibration Levels. Entering Calibration Standard Amounts or Concentrations. Viewing Calibration Curves.

6. Reviewing and Reporting Results After data has been acquired and calibration performed you can review and report results. You can create report templates in any format and layout you require, or use one of Chromeleon's default templates.

To Start a Report Open the injection for which you want to view the report. On the Navigation Pane of the Chromatography Studio, click Report Designer. As an alternative, you can double-click a report template file in a sequence (under Associated Items). This will open the report showing the first injection in the injection list. Chromeleon opens the report with the default report template that is assigned to the sequence. If the sequence does not contain a report template yet, the Create a Report Template wizard is opened To create a new report template In the Chromeleon Console, on the Create menu, click Report Template.

Report Template

eWorkflow Routine Analysis

eWorkflow An eWorkflow is an electronic procedure for automating the laboratory processes related to a chromatographic analysis. It assists the user in creating an appropriate sequence with predefined associated files and a well-defined structure. An eWorkflow is typically created and configured by an administrator or lab manager in the eWorkflow Editor.

Creation Click eWorkflow in bars Create, create eWorkflow. Add the required field: Instrument, Methods, Attached files. Select the state Ready for Use.

Sequence General Select : The Report Template . The View Settings. The channel to be displayed during injection. Sequence name . Data Vault, Path - select the Storage Location for the Sequence.

Sequence layout Sequence layout Sequence header( Once) Sample Block (repeated) Bracket ( repeated) Sequence footer ( Once)

Sequence layout No. Option Description 1 Max. Samples per Bracket that is, the repetitions of the sample block allowed per bracket. (e g. 4 samples) 2 Max. Brackets per Sequence Define the maximum number of bracketed sample blocks allowed in a sequence. ( e g. 3 Brackets) ( 3 Brackets, 4 is Max Number of samples per Bracket) so this sequence can contains 12 samples max. No. of Alternate Brackets As complex sequences may require different types of brackets, Define the number of alternating brackets in the layout. Max 5 4 Use Bracket Block after Sequence Header Select this check box to insert a bracket block directly after the header block and before the first sample block. 5 Layout template The layout template is divided into several blocks, each in a different color. To add a new injection to a block, click the bottom line of the block. 6 Sequence Preview Type or select a number in the Number of Samples box to see what the injection list will look like. The preview will be refreshed as soon as you change the above settings or layout.

Sequence layout Sequence layout- preview Header 12 Samples,3 Samples per Brackets,4 Brackets Footer

Run eWorkflow click the category eWorkflows Select which eWorkflow Click Launch Set the number of samples to 12 Set the start position to 1. Click Finish.

Start

Getting started

Getting Started Steps 1- Switch on the instrument (open each module) 2- Switch on the PC . 3- Make sure the dongle is inserted at USB port. 4- Make Sure server is ON if not follow the following a- click on server icon b- click "start Instrument controller“ c- close service manager 5- Double Click on the Chromeleon icon 6- The "Home page" will open, make sure all modules are connected.

7- Open purge valve from Pump Module 7- Open purge valve from Pump Module. 8- Open "Pump" page, Press the purge button. 9- Make sure to get all air bubble out of the lines then close the purge. 10- Open the "Sampler" page. 11- Press the "Prime syringe" & "Wash buffer loop" & "Wash needle" button respectively .

12- Open the "Detector" page 12- Open the "Detector" page. 13- Switch on the Lamps and enter the wavelength 14- Go to "Data" Page 15- Create New Folder and name it. 16- Press "create" and create sequence 17- Follow the wizard to create your sequence. 18- Press "create" and create your inst. Method. 19- Follow the wizard to create your method. 20- "Start" your sequence.

21- Create your processing Method Using "Cobra" wizard 22- Create & print Report using "Report Page“

Using Calibration 1- From sequence need to choose standards Using Calibration 1- From sequence need to choose standards. 2- Choose level (create levels equal to no. of different concentration) 3- Save Sequence 4- double click on any sample to open processing method 5- Enter the concentration of each point at Levels box 6- To View Calibration curve click on "Calibration Plot" 7- To view result you will find Amount, Tab active NOW

Shutdown

Smart Shutdown The instrument is automatically shut down. The pump flow is stopped at the end of the method. Certain system components are turned off. Shutdown procedures are launched from the Console. You can specify whether the procedure starts immediately or automatically, as part of a queue. Before launching Smart Shutdown, make sure the mobile phase in the flow path does not contain dissolved salts (such as those in buffer solutions). Salt crystals that can form after the flow stops will shorten the lifetime of piston seals and may cause damage to columns. To avoid such problems, flush the flow path with a non-ionic fluid that is compatible with your column, such as deionized water and/or an organic solvent.

To run Smart Shutdown Display the queue Click the down arrow next to After running the queue, and then click run Smart Shutdown or run Smart Standby.

Thanks gamal.abdelhamid@meslo.com.eg