The document discusses Chromeleon, a chromatography data system. It describes the main Chromeleon software components, including the instrument controller service, client, services manager, instrument configuration manager, and administration console. It also covers the Chromeleon client, which contains the Chromeleon console and chromatography studio. The simple steps of an analysis using Chromeleon are outlined as starting Chromeleon, starting the instrument, creating a sequence, acquiring data, processing data, and reviewing/reporting results.

1. Gamal A. Hamid

2. Gamal A. Hamid
Contents
2
 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

3. IsaChromatography
DataSystem that
allowsyoutocontrol
chromatography
instruments and
evaluate,process,
report,andbackup
data.

4. Gamal A. Hamid
Chromeleon Software Components:
4
I. Instrument Controller Service
II. Client
III. Services Manager
IV. Instrument Configuration Manager
V. Administration Console

5. Gamal A. Hamid
I. Instrument Controller Service
5
 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
Data
Run
Start / Stop
Services
Manager
Client

6. Gamal A. Hamid
II. Client
6
 The Chromeleon Client provides the
user interface for all tasks related to
instrument operation, data analysis,
and data management.

7. Gamal A. Hamid
III. Service manager
7
No. Icon Description
1 Stopped
2
Starting or
stopping
3 Running idle
4 Active
5 Error
 Monitor the status of the
Instrument Controller and
other services.
 Start/Stop the Instrument
Controller service.
 Launch the Instrument
Configuration Manager tool.

8. Gamal A. Hamid
IV. Instrument Configuration Manager
8
 The Instrument Configuration is the tool in Chromeleon to configure
chromatography Instruments before they can be controlled by Chromeleon.

9. Gamal A. Hamid
V. Administration Console
9
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

10. Client
10

11. Gamal A. Hamid
II. Chromeleon Client
11
 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

12. Gamal A. Hamid
Software Sequence Order
12
 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”.

13. Gamal A. Hamid
1. Chromeleon Console
13
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.

14. 14
Console Components

15. Gamal A. Hamid
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.15

16. Gamal A. Hamid
2. Chromatography Studio
16
 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.

17. Gamal A. Hamid
Studio Components
17

18. Gamal A. Hamid
Chromatography Studio
18
In the Chromatography Studio you can edit all
objects related to the selected sequence:
I. Injection List
II. Instrument Methods
III. Data Processing
IV. View Settings
V. Report Templates
VI. Electronic Reports
VII. Spectral Libraries

19. Gamal A. Hamid
I. Injection List
19
 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.

20. Gamal A. Hamid
II. Instrument Methods
20
 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.

21. Gamal A. Hamid
instrument method
21

22. Gamal A. Hamid
III. The Data Processing
22

23. Gamal A. Hamid
IV. View Settings
23
 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.

24. Gamal A. Hamid
Reports and libraries
24
V. Report Templates
VI. Electronic Reports
VII. Spectral Libraries
Will cover later.

25. Simple Analysis
25

26. Gamal A. Hamid
Simple Analysis
26
1. Start Chromeleon
2. Start the instrument
3. Create a sequence
4. Acquire data
5. Process data
6. Review and report results
 Every analysis using Chromeleon
follows the same 6 basic steps:

27. Gamal A. Hamid
1. Start the Chromeleon
27
 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.)

28. Gamal A. Hamid
Configure Instruments
28
 Configure instruments to open
the Instrument Configuration
Manager, where you can add new
instruments or change the current
instrument configuration.

29. Gamal A. Hamid
Modules Selection
29
 Retrieving the configuration from module
given the right setting of each module.
 Select the modules according to the
configuration of the system

30. Gamal A. Hamid
2. Start Instrument
30
 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

31. Gamal A. Hamid
Establishing a Connection
31
 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
(for example Pump).

32. Gamal A. Hamid
Controlling and Monitoring the Instrument
32
To issue instrument commands follow these steps:
1. 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
wavelength of a UV/VIS detector or starting
mobile phase flow on a pump).

33. Gamal A. Hamid
ePanel/ePanel Set
33
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.

34. Gamal A. Hamid
ePanels
ePanel For Pump ePanel For UV Detector
34

35. Gamal A. Hamid
Monitoring
35

36. Gamal A. Hamid
Other Commands
36
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

37. Gamal A. Hamid
3. Creating a Sequence
37
 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:
I. Instrument Method (Must)
II. Processing Method
III. Report Template
But first

38. Gamal A. Hamid
I. Instrument Method
38
 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.

39. Gamal A. Hamid
Creating an Instrument Method
39
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.

40. Gamal A. Hamid
Instrument Method Wizard
40
 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

41. Gamal A. Hamid
Cont.
41
 Column Oven Columns
 Column Oven Time Program
 DAD Channels Setting
 DAD Time Table
 FLD General Setting
 FLD General Setting page 2
 Completion
 Check Method.

42. Gamal A. Hamid
II. Processing Method
42
 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.).

43. Gamal A. Hamid
Creating a Processing Method
43
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.

44. Gamal A. Hamid
Processing Method Wizard
44
 Create
 Processing Method
 Processing Method Template
 Named the Method & Finish
 Processing Method in Studio

45. Gamal A. Hamid
Processing Method Components
45
 Detection
 Components Table
 Calibration
 Unidentified peak G. table
 Chromatogram
Subtraction
 Advance Setting
 SST/ IRC

46. Gamal A. Hamid
Detection Parameters
46
Cobra Wizard
 Integration area
 Baseline noise range
 Smoothing width
 Minimum Area
 Channels and Injection types

47. Gamal A. Hamid
III. Creating a Report Template
47
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.

48. Gamal A. Hamid
Report Pages
48

49. Gamal A. Hamid
Sequence
49
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)

50. Gamal A. Hamid
Sequence
50
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.

51. Gamal A. Hamid
Cont.
51
 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.

52. Gamal A. Hamid
Creating a Sequence
52
To create a sequence using the
Sequence Wizard within the Console:
1. In the Instruments category of
the Console, select the
instrument from the
Navigation Pane.
2. In the Console, on the Create
menu, click Sequence.

53. Gamal A. Hamid
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.
53
Cont.

54. Gamal A. Hamid
New Sequence Wizard
54

55. Gamal A. Hamid
4. Acquire Data
55
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.

56. Gamal A. Hamid
56
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.

57. Gamal A. Hamid
5. Processing Data
57
 After chromatographic has been
acquired, it can be processed.
 All processing steps are performed in
the Studio and saved in a processing
method.

58. Gamal A. Hamid
Data Processing Home
58

59. Gamal A. Hamid
Data Processing Steps
59
I. Reviewing Data in the
Chromatography Studio
II. Working with Chromatograms
III. Detecting and Integrating Peaks
IV. Identifying Peaks
V. Calibration and Quantitation

60. Gamal A. Hamid
I. Reviewing Data in the Studio
60
 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.

61. Gamal A. Hamid
View Options
61
 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.

62. Gamal A. Hamid
II. Working With Chromatograms
62
 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.

63. Gamal A. Hamid
Layout Options
63

64. Gamal A. Hamid
III. Detecting and Integrating Peaks
64
 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.

65. Gamal A. Hamid
 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
65
Steps

66. Gamal A. Hamid
Smart peaks
66
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.

67. Gamal A. Hamid
IV. Identifying Peaks
67
 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

68. Gamal A. Hamid
Component Table
68
 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.
 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.

69. Gamal A. Hamid
Create a Component Table
69
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)

70. Gamal A. Hamid
V. Calibration and Quantitation
70
 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.

71. Gamal A. Hamid
71
 Specifying the type.
 Creating and Assigning Calibration Levels.
 Entering Calibration Standard Amounts
or Concentrations.
 Viewing Calibration
Curves.

72. Gamal A. Hamid
6. Reviewing and Reporting Results
72
 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.

73. Gamal A. Hamid
To Start a Report
73
 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.

74. Gamal A. Hamid
Report Template
74

75. eWorkflow
Routine Analysis
75

76. Gamal A. Hamid
eWorkflow
76
 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.

77. Gamal A. Hamid
Creation
77
1. Click eWorkflow in bars
2. Create, create eWorkflow.
3. Add the required field:
 Instrument,
 Methods,
 Attached files.
4. Select the state Ready for
Use.

78. Gamal A. Hamid
Sequence General
78
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.

79. 79
Sequence layout
1. Sequence header( Once)
2. Sample Block (repeated)
3. Bracket ( repeated)
4. Sequence footer ( Once)
Sequence layout

80. 80
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

81. Gamal A. Hamid
81
Sequence layout
- preview
1. Header
2. 12 Samples,3 Samples
per Brackets,4
Brackets
3. Footer
Sequence layout

82. Gamal A. Hamid
Run eWorkflow
82
 click the category eWorkflows Select which eWorkflow
 Click Launch Set the number of samples to 12
 Set the start position to 1. Click Finish.

83. Gamal A. Hamid
Start
83

84. Getting started A. Tarek
84

85. Gamal A. Hamid
Getting Started Steps
85
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.

86. Gamal A. Hamid
86
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 .

87. Gamal A. Hamid
87
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.

88. Gamal A. Hamid
88
21- Create your processing Method Using
"Cobra" wizard
22- Create & print Report using "Report Page“

89. Gamal A. Hamid
89
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

90. Shutdown
90

91. Gamal A. Hamid
 The instrument is automatically shut down.
 The pump flow is stopped at the end of the method.
 Certain system components (for example, detector lamps and temperature-
controlled modules) 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. 91
Smart Shutdown

92. Gamal A. Hamid
To run Smart Shutdown
92
 Display the queue
 Click the down arrow next to After
running the queue, and then click
run Smart Shutdown or run Smart
Standby.

93. Thanks
gamal.abdelhamid@meslo.com.eg
93