Guia Ezcrhome Elite

Agilent EZChrom Elite
Users Guide
Notices
Copyright Scientific Software,
Inc 1997-2005 Agilent
Technologies, Inc. 2006-2008.
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Manual Part Number

G4650-90008
Edition
January, 2008
Document Revision 3.3
Printed in USA
Agilent Technologies, Inc.
6612 Owens Dr.
Pleasanton, CA 94588-3334
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Contents
1
Using This Guide ................................................................................. 8

Introduction ............................................................................................................8
Who Should Read This Guide? ...........................................................................8
Basics of Operation ............................................................................ 9
Instrument Wizard .............................................................................. 9

Offline Instrument Wizard .................................................................................10
Client/Server Operation................................................................... 11
About the Navigation Pane.............................................................. 11
Navigate the Instrument Window .................................................. 13
Data Acquisition Using Agilent Instrument Controllers .............. 14

User access to runs in progress...............................................................14
Closing a Server Instrument .....................................................................15
Program Architecture and Data Structure .................................... 15

About Method Files ....................................................................................15
About Data File Structure..........................................................................16
Turn on Extended Security ................................................................................17
Extended Security .......................................................................................17
View the Method Audit Trail.............................................................................17
Opening and Saving Files ................................................................ 19

Open Data Files....................................................................................................19
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iii
Open Data File Options.............................................................................. 20

Open Method and Sequence Files................................................................... 22
Save Data Files............................................................................................ 23
10 Reading CDF Files ............................................................................. 25

11 The Instrument Window................................................................... 25
Start an Instrument............................................................................................. 25
Instrument Login................................................................................................. 25
View the Instrument Activity Log .................................................................... 27
About the Instrument Window......................................................................... 28
Change View Preferences ................................................................................. 29
Preferences - General ................................................................................ 30
Change File View Preferences ................................................................. 30
Locking your screen ................................................................................... 31
12 The Chromatogram Window............................................................ 32

About The Chromatogram Window ........................................................ 32
View Tiled or Overlay Data ....................................................................... 33
Zooming........................................................................................................ 34
Scroll the chromatogram ................................................................................... 34
Add a Trace (Viewing Multiple Chromatograms) ......................................... 35
Add Multiple Traces to a Chromatogram Window....................................... 38
Annotate a Chromatogram................................................................................ 40
Change the Chromatogram Appearance ........................................................ 42
Change the Axis Properties .............................................................................. 47
Change Data Graph Properties......................................................................... 49
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Users Guide
Set up a trace.......................................................................................................50
Remove a Trace ...................................................................................................54
Set Limits for X-Axis and Y-Axis.......................................................................54
13 Chromatogram Operations............................................................... 57
About Chromatogram Operations ....................................................................57
Move a Trace ...............................................................................................59
Stack Traces ................................................................................................59
Align two traces ..........................................................................................61
Stretch a chromatogram............................................................................62
Normalize Traces ........................................................................................63
Perform Mathematical Operations on Traces................................................65
Smoothing ....................................................................................................65
Calculate Derivatives..................................................................................66
Add two traces ............................................................................................68
Subtract two chromatograms ...................................................................68
Multiply Traces............................................................................................69
Divide chromatograms or traces ..............................................................69
Utilities ..................................................................................................................70
About Chromatogram Utilities..................................................................70
Print a trace..................................................................................................71
Copy to clipboard ........................................................................................71
Save a trace .................................................................................................71
14 Graphical Programming................................................................... 71
About Graphical Method Programming ..........................................................71
Users Guide
15 Data Acquisition and Control........................................................... 74

Data Acquisition and Control............................................................................ 74
Single Run Acquisition....................................................................................... 74
Run a Sequence .................................................................................................. 79
Stop a Run in Progress .............................................................................. 82
Extend a Run................................................................................................ 83
16 Turn Off GPIB Instruments ............................................................... 84

17 Tutorial................................................................................................ 85
Tutorial Overview ................................................................................................ 85
18 Tutorial - Acquiring and Analyzing Data........................................ 86

Instrument and Method Wizards ..................................................................... 86
Create a Data Acquisition Method .................................................................. 88
Acquisition Setup ....................................................................................... 88
Save Your Method ...................................................................................... 90
Run a Preliminary Sample......................................................................... 91
Set Integration Parameters Graphically ................................................. 92
Create a Calibration.................................................................................... 95
Calibrate Using a Stored Data File........................................................... 99
Create and Run a Sample Sequence..................................................... 100
Run a Sequence ........................................................................................ 105
19 Using the Tutorial Files .................................................................. 106

Review Multi-level Calibration Curves .......................................................... 106
Explore a Peak Table ........................................................................................ 108
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Examine a Custom Report ...............................................................................109

Changing Integration Parameters ..................................................................111
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vii
1 Using This Guide

Introduction
This Users Guide provides a basic operating overview and
Tutorial for the Agilent EZChrom Elite data system
Who Should Read This Guide?

This document is designed for new users who will be doing
acquisition of data and processing of results.
Users Guide
2 Basics of Operation
This section describes the basic operation of EZChrom Elite,
its file structure, features of the application windows and
chromatogram windows.
3 Instrument Wizard
Each time you start an instrument application (by doubleclicking the instrument icon from the Main window), an
Instrument Wizard will appear. This wizard is designed to
direct you to the basic functions of the instrument window.
Create or modify a method

This button starts the Method Wizard that will enable
you to step through creating or modifying a method.
Users Guide
Create a sequence
This button starts the Sequence Wizard that steps
you through creation of an acquisition or
reprocessing sequence.
Run one sample
This button opens a dialog where you can use a
stored method to run a single sample.
Run sequence of samples
This button opens the Run Sequence dialog where you
can start data acquisition using a stored sequence.
Show at instrument startup
If this box is selected, the Instrument Wizard will
appear each time this instrument is started.
Offline Instrument Wizard

If you are using an instrument offline, the Instrument Wizard
will display the following buttons, for creating methods,
sequences, or processing a stored sequence.
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4 Client/Server Operation
When operating in a Client/Server mode, you will have one or
more Client Workstations along with one or more Agilent
Instrument Controllers, configured on a network. All
instruments are physically attached to the Agilent Instrument
Controllers (AICs), and the Agilent Instrument Controllers
are the machines where the actual data acquisition and
control of instruments occur. The client workstations,
running the Client/Server software, are where the users of
the systems develop methods and sequences, and perform all
operations of the system, including submitting data
acquisition runs and sequences to the Agilent Instrument
Controllers.
5 About the Navigation Pane

By default, a Navigation pane is displayed at the left side of
the instrument window. This view enables you to quickly
switch between the major functions of the instrument
window. A functional area can also be accessed by clicking
on one of the function bars located at the bottom of the
navigation pane.
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Users Guide
To turn the Navigation pane on

1.
Select View followed by the Navigation pane

command.
To turn the Navigation pane off

1.
Click the x button at the top of the Navigation pane.
You can also "park" the Navigation pane at the left of the
Instrument window, which provides additional work space.
Once the Navigation pane is parked, you can view it again by
simply moving your mouse over the Navigation tab that
appears at the left. The pane will disappear when you move
your mouse back into the work space.
To "park" the Navigation pane
1.
Click the push-pin button at the top of the Navigation

pane.
6 Navigate the Instrument Window

The navigation pane of the instrument window gives you
single-click access to method, sequence, report, control, and
viewing options. The navigation buttons at the bottom of the
navigation pane open command trees that give you access to
commands that are also available from the menu bar of the
instrument window.
Navigation button
Displays
Method
Method commands, Data manual integration

fixes, and Tiled Display to display current data
tiled with selected Integration or Calibration
(Peak Table) information.
Sequence
Edit
Reports
Reports, Report template properties
Control
Instrument Setup, Run Queue, Instrument

Status
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13
Views
Data Display options, Manual Integration Fixes,

Baseline Check Status
7 Data Acquisition Using Agilent Instrument

Controllers
When you start a run or a sequence from a client workstation,
you are actually submitting that run or sequence to the
Agilent Instrument Controller (AIC) or EZServer where the
instrument is attached. Once you have submitted a run or
sequence, the AIC assumes control over the acquisition and
control functions. All methods and sequences are copied to
the AIC when a run queue item is submitted to the server. If
the network goes down, the Agilent Instrument Controller
will continue to run with the files it has on its hard disk.
User access to runs in progress

As the user who submitted the run or sequence, you will have
access to the Stop Run, Extend Run, or Stop Sequence
functions. If you are not the user who submitted the run or
sequence, you can view the run (if you have instrument
rights), but you cannot stop a run or sequence that has been
started by another user. Users with System Administration
or Instrument Administration rights have full access to the
run and sequence functions.
Once you have submitted a run or sequence to an AIC from a
client workstation, you can modify the method. You must save
the file (File>Method>Save) in order for the changes to be
used for subsequent sequence runs that use this method. If
more than one client changes and saves the method, the last
clients changes are saved and all others are lost. If the
method is not saved before the start of the next sequence run
using this method, the changes on a client will be lost when
the next sequence run starts.
The user who submitted a sequence to the AIC may add or
remove runs from the submitted sequence from a client
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Users Guide
workstation (if the user has appropriate privilege

assignment). In order for sequence changes to take effect, the
sequence must be saved (File>Sequence>Save). When the
sequence is saved, all other clients will be notified of the
change, and the next run of the sequence will be executed
from the modified sequence.
Closing a Server Instrument

Once an instrument application is started on an Agilent
Instrument Controller, it will remain open after all runs are
completed. Occasionally, it may be necessary to close a server
instrument (for example, to re-configure). Users with
Instrument Administration privileges can close a server
instrument by doing a right-hand mouse click on the
instrument icon in the CS Main window, then selecting the
Close Server command. You will be prompted to confirm
your choice.
If you select Yes, the command will force the server
instrument to close after it finishes the runs and all clients
have been disconnected.
8 Program Architecture and Data Structure

About Method Files
A method is used whenever you acquire and/or reprocess a
data file. It contains instructions for data acquisition (run
time, sampling rate, etc.), integration, calibration and peak
information, and reports, as well as optional functions such
as data export and user programs. Each method is capable of
acquiring multiple independent channels of data from a single
chromatograph. Each channel can have its own complete
independent parameters, including sampling rate, run time,
integration events, external events, calibration, and reporting.
Although the method file is a separate file, the information
contained in the method is saved in the raw data file at time
of acquisition. This way, the original method can be
reproduced, even if the method file was subsequently
modified.
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15
About Data File Structure

A data file is created on the designated drive whenever you
acquire a sample, or when you save a data file using the Save
As 32-bit command. The file contains the following
information:
File Information Header. This contains information such as
the date and time of acquisition.
Complete method parameters used to acquire and process
the data (this is the "original" method saved only when the
data is acquired). Because you can acquire multiple channels
of data simultaneously on a given chromatograph, the method
section may contain complete parameters for more than one
channel.
Raw data points for the run saved. Multiple chromatograms
may be present in a single data file, each of which represents
a detector channel acquired for the run. The raw data points
are saved in binary format.
Results. The original integration results are saved in the file
and can be recalled later when the file is opened. In addition,
the most recent analysis results and method are also saved in
the data file and updated whenever you analyze. The Sample
ID for the results is also saved, as are manual integration
fixes.
File Description. If you entered a description for the file, this
text information is stored with the file, and can be viewed
under the Data File Properties or from the Open Data File
dialog.
Instrument Configuration. The configuration of the
instrument used to acquire the data file is saved.
Data File Audit Trail. An audit trail log is always saved in
the data file that tracks analysis of the data.
Data files are saved using the file name and extension you
specify when you initiate the data acquisition. The limit on
file name length is 255 characters, including path.
Data File Checksum. If Extended Security is enabled, a
checksum is calculated for the entire file whenever the data
file is closed. When the file is opened, its checksum is verified
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Users Guide
first. If the check fails, the file cannot be opened and an error
message will appear in the instrument activity log. Checksum
verification, when enabled, is enterprise-wide. The checksum
feature is enabled from the Enterprise Options dialog in the
Main menu, and is labeled Extended Security. GLP and
Extended Security
Turn on Extended Security

In order to adhere to good laboratory practices, the software
does not let you over-write a data file. If you try to over-write
an existing data file name, the system will either give you an
error message, or trigger a failure action if encountered
during a Sequence operation.
If, for some reason, you wish to ignore GLP and have access
to over-writing of data files, your files must be located in a
directory whose path contains the term "public". For example,
if your data files are saved in a folder entitled "\Public\Data",
the software files saved in this folder can be overwritten.
Extended Security
To turn ON Extended Security,
1. From the Main Menu, click Tools followed by
Options... and then select the General tab.
2.
Click Extended Security if the box is not selected

already.
This selection is ON by default. When this option is selected,

causes a checksum to be calculated whenever a data file is
closed. When the file is subsequently opened, its checksum is
verified first. If the check fails (the calculated checksum for
the file does not match the one previously calculated for the
file) the file cannot be opened, and an error is posted in the
instrument activity log. Checksum verification is enterprisewide.
View the Method Audit Trail

Each Method file can have an Audit Trail enabled. When this
is enabled, changes to the method will be logged in the file
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17
and cannot be removed or overwritten. To view the changes

logged in the Audit Trail for a method,
1.
From the File menu, select Method followed by Audit

Trail... This will display the Audit Trail listing for the
current method. If the audit trail option is turned on
for the current method, this box will display the
logged changes to the method.
User The user who was logged into the system at time
of the change.
Logged The time the change was logged into the
system.
Source The method location of the change i.e. peak
table.
Activity The change that was made.
Reason The reason for the change, if changes were
logged.
2.
18
To view the details of a given entry, click on the entry

to highlight it, then click the right-hand mouse button.
Select the Show Detail command. Details of the
highlighted entry will appear.
Users Guide
9 Opening and Saving Files

Open Data Files
Whenever you open a file using the data system, you will be
presented with a dialog box that allows you to not only open
the file, but specify parameters for searching, as well as
on the
previewing file contents. The Open File button
command ribbon gives you access to the Open File menu.
When you select one of the types of files to open, a dialog will
appear where you can select the file from those on your hard
disk.
The Open Data File dialog contains the most options for how
you want to open and search for files. The list of files of the
type selected (Files of type) are shown. As with most
Windows applications, you can view these as a list, and show
details by clicking the appropriate button at the upper right
corner of the window. In addition, you can see a preview of
the chromatogram in the data file by pressing the Preview
Chromatogram button, or view the file description by
clicking the Description button. You can also use the *
"wildcard" character to view a list of certain file types. The
dialog appearance and behavior will be slightly different for
Users Guide
19
systems with advanced file security enabled. Users will be

limited to storing files within the current project folder and
the Enterprise Common folder. A folder bar will be included
in the dialog to facilitate navigation.
Open Data File Options

The Options box allows you to save time by loading additional
information at the time the data file is opened.
Method
If you select Current, the current method will not
change when you open the data file. When one of the
other Method options is selected, the method selected
will be loaded at the time the data file is opened.
From Results Loads the method used to create the
selected results. Original/Acquisition loads the
method used for the original acquisition of the data
file. This method will replace your current active
method.
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Users Guide
Results
When one of the Results options is selected, the data
file will be opened along with the selected results.
When a data file is opened with results, the
integration and baselines that generated those results
will be displayed automatically when the
chromatogram is drawn on the screen. If Most Recent
is selected, the data file will be opened with the
results from the last time the chromatogram was
analyzed. If the Save all analysis results option is
turned on (Enterprise Options/General tab), a list of
all analysis results will be available for you to open
with the file.
Open with Pretreatment
When this box is selected, the pretreatment file (if
applicable) used at the time the data was acquired
will be opened when the data file is opened.
Searching for Data Files
If you are interested in specific data files, there are
options that allow display of only the files of interest.
Using the area titled "Find files that match these
criteria", you can search for files that contain specific
information. You can specify all or part of a Sample
ID. You can search for files acquired by a designated
Analyst. You can find files that were acquired during
a specific time frame such as Yesterday, Last 7 Days,
Today. You can also search for files that were
modified during a specific time frame. These criteria
can be used one at a time or combined.
You can also include wildcards as part of the file
name to search. To do the search, fill in the field of
interest for files you want to search, then click Find
Now. For example, if you enter Tester* in the Sample
ID field and click Find Now, all the files where the
Sample ID is "Tester" followed by anything will be
displayed. Click the New Search button if you want to
clear the search settings and use new criteria for
searching.
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21
Note:
When using the Search feature, make sure the Windows Hide
File Extensions for Known File Types option is turned OFF. To
turn this off, from My Computer, click Tools followed by Folder
Options... and then click the View tab.
Open Method and Sequence Files

To open a method or sequence file,
1. From the File menu, select Method or Sequence
followed by Open.
2.
22
The Open dialog boxes for Method and Sequence files

are identical. The dialog appearance and behavior
will be slightly different for systems with advanced
file security enabled. Users will be limited to storing
files within the current project folder and the
Enterprise Common folder. A folder bar will be
included in the dialog to facilitate navigation.
Users Guide
Searching for Method and Sequence Files

The criteria you can use to search for specific method
and sequence files include selection of specific text
found in the file description (Text in Desc.), Analyst
name, and date Created or last Modified.
Note:
When using the Search feature, make sure the Windows Hide
File Extensions for Known File Types option is turned OFF. To
turn this off, from My Computer, click Tools followed by Folder
Options... and then click the View tab.
Save Data Files

To save a data file,
1. From the File menu, select Data followed by Save as
32-bit...
2.
A dialog opens where you can browse to a location

and type the filename to be used to save the file.
This command will save the current data file along with the
current method in a single file. This command is only enabled
when the current data file is not in 32-bit Elite data format
(such as 16-bit or converted files). In order to comply with
good laboratory practices, you will not be allowed to Save As
32-bit using the same name as an existing data file, unless
the file is located in a "Public" directory. A Public folder is a
folder where the path contains the term "public". Data files in
all other data system folders are protected from being overwritten. The dialog appearance and behavior will be slightly
different for systems with advanced file security enabled.
Users will be limited to storing files within the current project
folder and the Enterprise Common folder. A folder bar will be
included in the dialog to facilitate navigation.
Users Guide
23
To save the current data in a new data file, type the name of
the new data file in the File name field, then click Save. Use
the buttons at the upper right of the dialog box to view details
of a highlighted file, or to view the description of a
highlighted file. An entry "Saved from <FILENAME>" will be
logged into the saved file as the first entry.
If the Compress Data box is selected, the file will be saved in
a compressed format. Once saved in compressed format, it
will automatically be "decompressed" whenever the file is
opened. However, once a file is saved in compressed format,
you must do a "save as" command to save it in decompressed
format again.
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Users Guide
10 Reading CDF Files

When opening a CDF file, the software looks for one of the
following Y-axis labels:
"microvolts", "uvolts", "uv", "uau} or "millivolts", "mvolts", "mv",
"mau"
If one of these labels is not found, the software will try to
read it from an AIA.ini file, which is used to get multipliers
for non-standard file types. If there is no AIA.ini file
available, the software will try to make an estimate based on
the range of values.
If the CDF file being read is non-standard, you need to make
an AIA.ini file and put it in the data system program folder.
The file should contain the y-axis label and multiplier.
11 The Instrument Window

Start an Instrument
To access the Instrument Window where you can develop
methods and sequences, create custom reports, and acquire
data, double-click on the instrument icon you wish to start in
the main menu. You may be required to log-in before you can
access the instrument window functions. See Instrument
Login for details.
Instrument Login
Whenever the instrument login and project management is
enabled, you will be required to log-in whenever you attempt
to start an instrument application.
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25
Enter the information as prompted, and then click the Login

button.
User name:
Enter the user name which has been assigned to you
on the network.
Password:
Enter your assigned network password.
Save Password:
If the "save password" option is enabled by your
system administrator, a Save password checkbox will
appear.
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Users Guide
If you select this box, the password you type at login

will be saved when you click the Login button. Once
the password has been saved, whenever you login to
the instrument, the saved password will be used.
Note:
The password will be saved when the Login button is clicked,

whether or not the login is successful.
Domain:
Select the domain you have privileges on from the
drop-down list, or type in the correct domain. (Not
shown unless you are using a domain controller.)
Project:
Select a project to log into. This project will become
the default project path for methods, data, and
sequences in the instrument. You can, however,
create and save files in other locations even though
you have logged into a designated project.
Once you have logged into an instrument and selected
a project, that projects paths for methods, data,
sequences, and templates will be used unless you
designate a new project. To change the selected
project, use the File/Select Project command.
View the Instrument Activity Log

As you use a method to acquire data, a log of activity from the
current instrument is kept. To view this log, from the File
menu, click Instrument Activity Log and then click Display
Log. A window with the Instrument Activity Log appears. The
window displays the User who used the instrument, the time
the activity was logged into the Instrument Activity Log, and
a description of the activity.
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27
To view details of any line in the instrument activity log, click

on the line to highlight it, then do a right mouse click within
the spreadsheet. From this pop-up menu you can view details
of the highlighted line, print it, or print the entire activity log.
In addition, you can export, archive, or purge the activity log
from this menu.
Note:
Over time, the instrument activity log file may become large,
so periodically you should archive the file to a floppy or
another location and then purge it.
About the Instrument Window

When you open an instrument, the Instrument Window will
appear. From this window, all aspects of using the
instrument are performed, including
Method Development
Calibration
Sequence development
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Users Guide
Instrument control and data acquisition

Analysis and review of data
Reporting
Data export
You can customize the appearance of the application window
if you choose, adding or removing the Toolbars and Status
information. However, these features are designed to make
the system easier to use, and most users will prefer to have
these turned ON.
Change View Preferences

To change the appearance of the instrument window,
Users Guide
1.
From the View menu, click Preferences.
2.
Click General to change the general view preferences

for the instrument window.
29
Preferences - General
This tab is used to set up general preferences in the
instrument window.
Toolbar options
For each area of the window listed, you can turn on
or off the Toolbar and Tooltips if available. Click on
the toolbar area, then check the Show toolbar and
Tooltips boxes to enable your choices for that area.
Status bar options

Select the checkbox to turn on the status bar. The
status bar provides brief information at the bottom of
the instrument window, if enabled.
Time units
Select the time units for display of chromatographic
information.
Change File View Preferences

To change the appearance of the instrument window,
1.
30
From the View menu, click Preferences.

Users Guide
2.
3.
4.
5.
Click Files to change the file view preferences for the

instrument window.
Select the file type, then enter the number of files you
wish to display in the Max files box. This determines
the number of recent files displayed in the File menu.
Click Clear Files to clear the current recent files list
for the selected file type.
Click Clear All Files to clear the recent files for all
the file types.
Locking your screen

To lock the window from unauthorized use, from the Window
menu choose Lock. When you choose this command, all
menu items will be "Locked" except for the Window and Help
menu. Locked commands will not be accessible until you
unlock them again. This command is useful for multiple user
labs, where you may want to lock your current work while
you are temporarily away from the computer.
To unlock the screen, click the Lock Command again. You will
be required to log in your user name and password (if
instrument login and project management is enabled) to
unlock the screen.
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31
12 The Chromatogram Window

About The Chromatogram Window
Whenever there is data to be viewed, it is shown in a
chromatogram window. Normally, one chromatogram will
appear in each window, and multiple channel data files will
display multiple chromatogram windows - one for each
channel. However, it is possible to add multiple traces to a
single chromatogram window and perform comparison and
mathematical operations on them. To access specialized
commands for the chromatogram window, click the righthand mouse button somewhere within the chromatogram
window area. These commands allow you to add graphs or
chromatograms to the window, change the appearance,
annotations, and axes, perform mathematical operations on
chromatograms, and view or change the properties of existing
traces in the window.
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Users Guide
As data is being acquired, it is also displayed in a

chromatogram window. At the end of a run the data becomes
the "current data". You can change the appearance of the
chromatogram and select annotations, fonts, and labeling.
Utilities are available to print the current window view, copy
it to a clipboard, or save it in a file.
View Tiled or Overlay Data

When viewing data from multiple channel methods, you can
choose to view each channel in a separate window
(View>Tile Data), or you can overlay all channels in a single
window (View/Overlay Data). When all channels are overlaid
in a single window, you can still zoom, and change the
individual channel appearances, as described below.
When in Tiled mode, you can arrange how the windows are
tiled on your screen by using the Window>Cascade,
Window>Tile Horizontally, or Window>Tile Vertically
command.
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Zooming
You may want to examine a chromatogram in more detail, or
zoom in on a portion of the chromatogram. To do this, drag a
box around the area of interest by holding down the left
mouse button and dragging the box until it highlights the
section of interest. Then release the mouse button. To move
quickly to the previous level of zoom, double-click on the
chromatogram. To zoom to the full chromatogram again after
multiple zooming operations, click the right-hand mouse
button anywhere in the chromatogram window, then select
Full Unzoom from the menu displayed. You can also execute
a full unzoom of your chromatogram with Ctrl-Z or shiftdouble click in the chromatogram window. Once the
chromatogram is in a "zoomed" view, you can scroll it. See
Scrolling the chromatogram.
At the top of the chromatogram window is a display of Time
and Amplitude. These values change as you move the cursor
and reflect the time and amplitude of the trace where the
cursor is located. If you have more than one trace, you can
change the display to another trace by clicking on the
chromatogram trace with the mouse. If the traces are
displayed in different colors, the color of the Time and
Amplitude display will reflect the color of the trace displayed.
Scroll the chromatogram

Once you have zoomed in on a chromatogram, you can scroll
the chromatogram to the right or left without losing the zoom.
This is done by pressing the CTRL SHIFT keys down and
moving the mouse until the cursor changes to a "hand" and
dragging it to the left or right.
You can also scroll the X- or Y- axis to view features which
may be out of the range. To do this, press the CRTL SHIFT
keys down while the mouse cursor is outside the graph area,
yet near the axis of interest. The cursor will change to an
up/down arrow near the Y-axis, or a left/right arrow near the
X-axis. Moving the mouse in this mode will scroll the graph
up/down or left/right on the axis.
To restore the original view, in the chromatogram window,
click the right mouse button and then click Full Unzoom.
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Users Guide
Add a Trace (Viewing Multiple Chromatograms)

The chromatogram window is used to view data, either
current data (real-time) in the instrument window, or data
recalled from the disk. You can view multiple chromatograms
in a single chromatogram window if you wish. This is
convenient if, for example, you want to compare a past run
with your current data or overlay an oven or pump profile.
To add a new trace to the chromatogram window,
Users Guide
1.
Click the right mouse anywhere in the chromatogram

window. A menu will appear.
2.
Select the Add Trace command. When you select

this command, a dialog box will appear.
35
3.
Select the New Trace tab. Fill in the fields to add a

trace to the chromatogram window and set its
properties. These properties apply only to the trace
selected and are not saved as part of the method.
When a new trace is opened, the properties will be
set to default values. Added traces are normalized by
default.
Data Source
Enter the name of the file from which to get the trace.
You can also click the File button adjacent to the field
and select a data source.
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Current Data
This selection allows you to select a trace from the
current chromatography data.
Current Method
This selection enables you to select a trace from your
current method (if available). For example, you could
load an oven temperature program from an HP5890
instrument method.
Open Data
This allows you to select a stored data file from which
you can select a trace for display.
Trace
Select the trace to be displayed. Click the button to
display available traces.
Scale to
Select one of the scaling options.
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Trace x
Scales to
another trace in
the window.
Autoscale to largest peak
Scales such that

the largest peak
is on scale.
Autoscale to 2nd largest peak
Scales such that

the 2nd largest
peak is on scale.
Autoscale to 3rd largest peak
Scales such that

the 3rd largest
peak is on scale.
User Defined
Allows you to
enter a value for
Y max and min.
Normalized
Allows you to
normalize one
trace to fit on
the graph.
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Y min
If you have selected a User Defined scale, enter a
minimum value for the Y-axis.
Y max
maximum value for the Y-axis.
Units
Select the units for display.
X Offset
Enter a value in units for offset of the X-axis.
Y Offset
Enter a value in units for offset of the Y-axis.
Y Scale
If desired, enter a multiplier that will be applied to
the entire trace here.
Add Multiple Traces to a Chromatogram Window

If you want to quickly add more than one chromatogram to
your view,
1.
2.
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In the chromatogram window click the right hand

mouse button, followed by Add Multiple Traces
The Open File dialog box will appear where you can
select the traces to be displayed by selecting them
from the file list.
To add a file, either click on the file name, then click
the Add button, or simply double-click on the
filename from the list.
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3.
4.
5.
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Once you have added a data file to the list, you can
select the channel by clicking on the Trace field, then
click the down-arrow button. If multiple channels for
that file are available, select the desired channel by
clicking on it with the mouse.
To delete a trace from the display list, click on its
name or on its number, then click the Delete button.
When you are ready to open the multiple traces, click
Open. The selected files/channels will appear in your
chromatogram window.
39
Annotate a Chromatogram
To change the annotations on the chromatogram,
40
1.
From the chromatogram window, do a right mouse

click and then select Annotations.
2.
Click the Annotation tab in the Properties box. This

brings forward a dialog where you can designate how
you want the trace you are adding to be annotated.
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3.
4.
5.
6.
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Select the trace from the drop-down list. Then select

what features you wish to annotate. Normal choice is
Peaks. However, if you have the SEC option installed,
you can select SEC to annotate specific SEC features
on your chromatogram.
For the selected trace, click Peaks or Groups to
select what kind of annotation to use.
Click on an Available Annotation. When an
annotation is highlighted, you can add it to the
annotations to be shown by clicking the Green arrow
key (pointing to the right). This can also be done by
double-clicking the selection.
For certain annotations, you can also designate the
number of places to be displayed to the right of the
decimal point. Enter this value in the Decimals box
for the highlighted item.
41
7.
Note:
Click the check box(s) to display Baseline, USP

Width, or Retention Time Windows, Show
undetected named peaks, and Group ranges on the
trace. With the SEC option installed, you will have
access to additional SEC annotation features.
The Reference Peak window annotation displays the window
set in the Peak Table. This window is not adjusted for relative
retention time.
8.
Continue to select as many annotations as you wish

for this trace. When you have finished, click OK.
9.
You can select or change annotation for an existing

trace by doing a right-mouse click in the
chromatogram window, then select the Annotation
command. The selections you make will apply to all
traces you open for this channel or until you change
them (the OK or Apply button). If you want to apply
the annotation changes to all open channels, click the
Apply to All button. Annotations are not saved as
part of the method and are considered a function of
the instrument application. If you close a method and
re-open it, the current settings will apply.
Change the Chromatogram Appearance

You can change the appearance of the trace (line type, color,
etc.) from the Appearance tab in the Properties box. Click on
this tab to display the Appearance tab dialog.
To change the appearance of a chromatogram or trace,
42
1.
In the Chromatogram Window, do a right mouse click

and select Properties.
2.
Click the Appearance tab.
Users Guide
Scheme
If you have previously saved an appearance scheme
on disk, you can select it from this box. The Save As
button allows you to save the existing appearance
scheme on disk by giving it a name. The Delete button
allows you to delete a scheme and start again.
Item
This drop-down list lets you select which part of the
chromatogram window for which you wish to change
the appearance. The choices will include the graph
itself (including background and legends), and the
available traces.
Sub-item
Select the sub-item you wish to modify. The choices
for this will change based on the item you have
selected. For example, if the Item selected is the
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43
Graph, you will have access to setting up appearances

of sub-items including the background, axes and
labels for the graph. If the item selected is a
chromatogram data channel, you will have access to
setting appearances of sub-items such as baselines,
start and stop tic marks, and annotation. If the item
selected is text, you will have access to the Font
formatting commands as well.
When a sub-item is selected, you will have access to
fields appropriate to that item. For example, if you
have chosen the baseline sub-item, you can choose
the color and line type. If you have chosen the
annotation sub-item, you can choose the font
appearance and color.
You can change the appearance of any trace without adding a

new trace, by doing a right-mouse click in the chromatogram
window, then selecting the Appearance command. When
you select this command, you will see an identical dialog to
that shown above for the Appearance Tab.
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Users Guide
Sub-items available in the Appearance tab are as follows.

Item
Sub-Item
Description
Graph
Background
Select the color of the graph background. Default is

black.
Graph
Title
Select a color and font for the Title of the graph.

There must be a Graph Title defined in the Axis
Setup tab in order for it to appear in the window.
Graph
Left Y-Axis
Select a color for the left Y-Axis of the graph.
Graph
Left Y-Axis Major Ticks
Select a color for display of major unit marks on

the Left Y-Axis.
Graph
Left Y-Axis Minor Ticks
Select a color for display of minor unit marks on

the Left Y-Axis.
Graph
Left Y-Axis On/Off
Turns On or Off the Left Y-Axis
Graph
Right Y-Axis
Select a color for display of a right hand Y-Axis.
Graph
Right Y-Axis Major Ticks Select a color for display of right Y-Axis major
ticks.
Graph
Right Y-Axis Minor Ticks Select a color for display of right Y-Axis minor
ticks.
Graph
Right Y-Axis On/Off
Turns On or Off the right Y-Axis.
Graph
X-Axis
Select a color for the X-Axis display.
Graph
X-Axis Major Ticks
Select a color for display of major unit marks on

the X-Axis.
Graph
X-Axis Minor Ticks
Select a color for display of minor unit marks on

the X-Axis.
Graph
X-Axis On/Off
Turns On or Off the X-Axis.
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45
Graph
Legend
Select a color and/or font for display of the graph

legend. The legend indicates what traces are
currently displayed in the window. The Legend is
turned On or Off from the Axis Setup tab.
Graph
Grid
Select a color for display of the grid lines. Grid

lines are turned On and Off from the Axis Setup
tab.
Data
Trace
Select a color and/or line type for display of the

selected trace.
Data
Annotation
Select a color and font for display of the trace

Annotation(s). The items to be annotated for a
trace are selected in the Annotations tab.
Data
Baseline

baseline.
Data
Baseline Start Tick
Select a color and/or line type for display of

baseline start ticks.
Data
Baseline Stop Tick

baseline stop ticks.
Data
USP Width

USP Width, if calculated.
Data
RT Window

expected retention time windows for named peaks.
Data
RT Window (undet.)
Select a color for display of RT Window for

expected peaks that were not detected.
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Users Guide
Change the Axis Properties

The Axis Setup tab allows you to configure the appearance of
the axis on your chromatogram. These settings apply to active
traces. To change the Axis properties,
1.

and then select Axis Setup.
Graph Title
Enter a title for the graph, if desired. This appears at
the top of the graph.
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47
Axis
Using the drop-down list, select the axis of interest:
Left Y-Axis, Right Y-Axis, or X-Axis. Then for your
selection, you can choose the limits for the axis.
For Y-Axis selections, you may choose Use limits of
trace to get the limits from one of the traces in the
window, or you can select the Manually set trace's
limits to box and set the Y-Axis limits to your desired
range. If you choose None, no Y-Axis values will be
displayed.
For the X-Axis, you may either choose to Autoscale,
where the X-Axis is set to the longest trace. Or, you
may set an absolute range for the X-Axis by clicking
the Use This Range button, then enter a minimum
and maximum X-Axis value for the trace. Click the
Get Limits button to retrieve the X-Axis range from
the current trace.
Margins
Enter a value for the trace margins, in percent, for
top and bottom of the graph.
General Options
Select the check boxes to turn these graph
annotations on and off. If the legend box is selected,
the legend for a trace can be turned on or off from the
Trace Properties spreadsheet.
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Users Guide
Chromatogram Window with Legend and Grid displayed
Chromatogram Window with no Legend or Grid displayed

Orientation
Select portrait or landscape orientation for your
graph by clicking the appropriate button.
Change Data Graph Properties

Whenever a chromatogram or trace is displayed in the
Chromatogram Window, it uses the display settings contained
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49
in the Data Graph Properties. To change the Data Graph

Properties,
1. In the Chromatogram Window, do a right mouse click
and select Properties.
2.
Select the tab for the properties you wish to view or

change, as shown below
Properties tab
Used to
Trace Setup
Add or remove traces, set legends, set scaling.
Axis Setup
Add a graph title, change data range, set

margins and orientation, turn on and off
legends.
Appearance
Set color schemes, line styles, and fonts.
Set up a trace
This tab gives you access to adding/removing traces, and
setting scaling options for the traces. Each row in the
spreadsheet represents one of the traces currently in the
chromatogram window. The details of the highlighted trace
appear in the trace properties boxes in the bottom of the
dialog box where you can view or change them.
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Users Guide
Show
Click this box to show the trace in the chromatogram
window. De-select this box to remove the trace from
the display (but leaving it open). This is a convenient
way to temporarily remove a trace from the viewing
window.
Lgnd
Click this box to show the legend for the trace. The
legend appears in the upper right corner of the
window and displays the name of the trace. De-select
this box to remove the legend for this trace from the
chromatogram window. Setup for the appearance of
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51
the legend (color, etc.) is done in the Appearance tab

for the Graph item. Note: If you have not turned on
the Legend in the Axis Setup dialog, this box will
have no effect.
Data Source
Enter the name of the file from which to get the trace.
You can also click the File button adjacent to the field
and select a data source. The data source can be a
chromatogram or it can be a stored profile such as
temperature or flow program.
Current Data
This selection allows you to select a trace from the
current chromatography data.
Open Data
This allows you to select a stored data file from which
you can select a trace for display.
Current Method
This allows you to select a trace from the current
method (if available). Examples of traces from a
method include temperature profiles for instrument
control, for example.
Trace
Select the channel to be displayed.
Scale to
Select one of the scaling options.
52
Trace x
Scales to another
trace in the window.
Autoscale to largest peak
Scales such that the

largest peak is on
scale.
Autoscale to 2nd largest peak

2nd largest peak is
on scale.
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Autoscale to 3rd largest peak

3rd largest peak is on
scale.
User Defined
Allows you to enter

a value for Y max
and min.
Normalized
Allows you to
normalize one trace
to fit on the graph.
Y min
minimum value for the Y-axis.
Y max
maximum value for the Y-axis.
Units
Select the units for display.
X Offset
Enter a value in units for offset of the X-axis.
Y Offset
Enter a value in units for offset of the Y-axis.
Y Scale
If desired, enter a multiplier that will be applied to
the entire trace here.
Note:
You can set the X-axis range from the Rt-mouse click/Axis
Setup menu selection.
Annotations
Click this button to display the trace annotations
dialog.
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53
Hide Details
Click this button to hide the current trace details and
display only the spreadsheet.
Reset Scaling
Click this button to reset the scaling values to their
original values.
Remove a Trace
If you have multiple traces in your chromatogram window,
and you want to remove one or more of them from the
chromatogram window, click the right-hand mouse button
anywhere within the window, and select the Properties
command. A spreadsheet will appear where the currently
displayed traces are listed.
To completely remove a trace from the chromatogram
window, select the row by clicking on the # number, then
press the Delete key on your keyboard, or select the
Edit/Delete command. To temporarily remove the trace from
the window, de-select the checkbox in the Show column.
Click OK to return to the chromatogram window.
Set Limits for X-Axis and Y-Axis

Occasionally, you may want to set an absolute range for either
the X-Axis or Y-Axis, or both. To set limits for the X- and Yaxis,
54
1.

click and then select Properties.
2.
Click the Trace Setup tab to set Y-Axis minimum and

maximum values for the trace. To set an absolute
voltage range for all chromatograms, use the UserDefined option for the Scale To field. You must then
enter a Y-Min (minimum Y-Axis value) and Y-Max
(maximum Y-Axis value) for each chromatogram. If
you want all chromatograms to be displayed using
this same voltage scale, enter the same values for all
chromatograms.
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3.
Click the Axis Setup tab to set absolute ranges for the
trace. Select X-Axis, to set the range for the X-Axis.
Click Autoscale to set the X-Axis range automatically
to the range of the longest chromatogram (the default
selection), or click Use this range to enter an absolute
range in minutes. The Get Current Limits button
brings in the X-Axis range from the current
chromatogram window. This is useful because it
allows you to use the zoom function to identify the
desired region of the chromatogram and
automatically enter the range values.
4. Once you have set an absolute range for one or both
of these axes, the designated chromatogram(s) will
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55
5.
56
always be displayed in the chromatogram window

using these ranges until you change or reset them.
To reset the scaling of all chromatograms to default
values, click the Reset Scaling button.
Users Guide
13 Chromatogram Operations
About Chromatogram Operations
There are a number of chromatogram comparison and
mathematical operations that are available from the
chromatogram window. These are accessed by doing a right
mouse click in the chromatogram window and then selecting
Operations.
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58
Operation
Action
Move Trace
Lets you "grab" and move a trace within the

Stack Traces
Positions multiple traces with an offset.
Align
Adjusts a second chromatogram such that a

peak (or point) on one chromatogram will be
aligned with a peak (or point) on the first
chromatogram.
Stretch
Performs a two-point contraction or expansion

of chromatogram relative to another.
Nomalize
Normalizes one or more chromatograms to the

first chromatogram, adjusting the heights such
that the apex height of a selected peak
matches that of the peak selected on the first
trace.
Smooth
Performs a 9-point Savitsky-Golay smoothing

operation on a selected trace.
1st Derivative
Calculates and displays a 1st derivative of a

selected trace.
2nd Derivative
Calculates and displays a 2nd derivative of a

selected trace.
Add
Adds two traces and displays the result.
Subtract
Subtracts two traces and displays the result.
Multiply
Multiplies one trace by another and displays

the result.
Divide
Divides one trace by another and displays the

result.
Users Guide
Move a Trace
To "grab" a trace and move it with your mouse
1.
In the chromatogram window, do a right mouse click

and select Operations followed by Move Trace.
2.
Move your cursor over a trace until the cursor

changes to a "move" icon.
"Grab" the trace by clicking the left mouse button and
dragging the trace to a new location. When you
release the mouse button, the trace will be placed
where your cursor was located when you released the
button.
"Move Trace" will appear at the upper right corner of
the window. You can continue to move traces. When
finished, do a right mouse click and select Operations
followed by the Move Trace command again to turn
off the move trace operation.
3.
4.
Stack Traces
To quickly change the X-axis and Y-Axis offset for a trace
Users Guide
1.

and then select Operations followed by Stack
Traces...
2.
Enter a new X-axis and y-axis offset, and click OK.

The offset will be applied to additional traces
displayed in the chromatogram window.
59
Chromatograms before stacking
Chromatograms after stacking

To remove these offsets,
1.
In the chromatogram window, click the right mouse

button and then select Properties.
2.
Click the Trace Setup tab, then scroll to the right to

the X-axis and Y-axis offset columns where you can
delete or change these settings.
Click the Reset Scaling button to restore ALL settings
to their original values. Or, you can use the Stack
command again, entering "0" for both stack
parameters.
3.
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Users Guide
Align two traces

To Align one chromatogram to another,
1.
2.
In the chromatogram window, do a right mouse click,

and then select Operations followed by Align. Click
first on the point of the first chromatogram to which
you wish to align, then click on the peak (or point) of
the second chromatogram which you wish to align to
the first point. The second chromatogram will be
adjusted such that the peak (or point) you clicked
second will be aligned with the first point you clicked.
To remove the alignment, use the right-hand mouse
button/ Properties command to view the trace
spreadsheet. Click the Trace Setup tab, then scroll to
the right to the X-axis and Y-axis offset columns
where you can delete or change these settings. Click
the Reset Scaling button to restore ALL settings to
their original values.
Chromatograms before alignment.
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First peak of top chromatogram aligned to first peak on bottom

chromatogram.
Stretch a chromatogram
The stretch function allows you to perform a two-point
contraction or expansion of chromatograms relative to
another. To stretch a chromatogram,
1. In the chromatogram window, do a right mouse click
and then select Operations followed by Stretch.
2.
3.
Select points (or peaks) on the first chromatogram to

which the second will be stretched (or contracted).
Select two points on the second chromatogram. The
chromatogram between these two points will be
stretched or contracted to fit the two points specified
on the original chromatogram.
To un-do the stretch,

1.
62

and then select Properties. Click the Trace Setup
tab, then scroll to the right to the X-axis and Y-axis
offset columns where you can delete or change these
settings. Click the Reset Scaling button to restore
ALL settings to their original values.
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Chromatograms before stretching.
Bottom chromatogram stretched relative to top

chromatogram.
Normalize Traces
This function allows you to normalize one or more
chromatograms to the first chromatogram, adjusting the
heights such that the apex height of a selected peak matches
that of the peak selected on the first trace. Once you have
selected this command, you will be prompted to select the
start and then the apex of a peak in the first trace. Then you
will be prompted to click on the start and apex of a peak in
the second trace for normalization.
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To un-do the normalization, use the right-hand mouse button/

Properties command to view the trace spreadsheet. Click the
Trace Setup tab, then scroll to the right to the X-axis and Yaxis offset columns where you can delete or change these
settings. Click the Reset Scaling button to restore ALL
settings to their original values.
Chromatograms before normalization.
After Normalization.
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Users Guide
Perform Mathematical Operations on Traces

Performing mathematical operations on traces can be done
from within the chromatogram window. To perform a
mathematical operation on a trace,
1.

and select Operations, then select the operation you
wish to perform.
2.
Follow the instructions displayed to perform the

operation. The result of the operation will appear in
the window.
For a list of available operations, see Chromatogram

Operations.
Smoothing
To perform a 9-point Savitsky-Golay smoothing operation on
a selected data file,
1.

and then select Operations followed by Smooth. A
prompt will appear in the window instructing you to
Click on trace.
2.
Click on the chromatogram to be smoothed. The

result trace will appear in the window.
Chromatogram before smoothing.

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Smoothed result trace is displayed with original trace.
Calculate Derivatives
To calculate and display the 1st or 2nd derivative of a
chromatogram,
66
1.
Do a right mouse click on the chromatogram, and

then select Operations followed by 1st Derivative or
2nd Derivative. A prompt will appear in the window
Click on trace.
2.
Click on the chromatogram for which you wish to

perform the operation. The result trace will appear in
the window.
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Trace before 1st derivative.
1st derivative trace displayed with original trace.
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67
2nd Derivative displayed with original trace
Add two traces

To add two traces to a chromatogram window,
1.
In the chromatogram window, do a right mouse click,

and select Operations followed by Add.
2.
Click on 1st trace to select the first file by clicking the

mouse on the chromatogram.
Click on the 2nd trace to select the trace to be added to
the first by clicking on the trace with the mouse. The
result trace will appear in the window. Note that in
order for this operation to be valid, both traces must
have the same sampling frequency.
3.
Subtract two chromatograms

To subtract two traces,
1.

and then select Operations followed by Subtract.
2.
At the prompt, click on the 1st trace. Select the first

trace by clicking the mouse on the chromatogram.
Select the trace to be subtracted from the first by
clicking on the trace with the mouse. The result trace
will appear in the window.
3.
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Note:
In order for this operation to be valid, both traces must have

the same sampling frequency.
Multiply Traces
To multiply two traces,
1.

and select Operations followed by Multiply.
2.
Select the first trace by clicking the mouse on the

chromatogram or trace.
Select the trace to be multiplied by the first by
clicking on the 2nd trace with the mouse. The result
trace will appear in the window. For the multiply
operation, the units of the resulting trace are <trace 1
units> x <trace 2 units>.
3.
Divide chromatograms or traces

To divide two traces,
1.

and then select Operations followed by Divide.
2.
A prompt will appear in the window Click on 1st

trace. Select the first trace by clicking the mouse on
the chromatogram.
A second prompt Click on 2nd trace will appear.
Select the trace to be divided into the first by clicking
on the trace with the mouse. The result trace will
appear in the window. The equation used to calculate
the result trace is as follows.
3.
Where
p = the calculated point for the result trace at time t
y1 = a point from the first trace at time t
y2 = a point from the second trace at time t
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69
ymult = the y multiplier for the trace that converts it from

microvolts to the trace's displayed units
Utilities
About Chromatogram Utilities
The Utilities menu in the chromatogram window gives you
access to commands for saving, copying, or printing the
current chromatogram window. To access the Utilities, in the
Chromatogram Window do a right mouse click and then select
Utilities.
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Utility
Action
Print
Sends the current chromatogram view to the

printer.
Copy to Clipboard
Copies the contents of the chromatogram

window to the clipboard.
Save Trace...
Prompts you to click on a trace then opens the

save data file dialog.
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Print a trace
This command sends the current chromatogram window view
to the printer.
Copy to clipboard
To copy the contents of the window to the clipboard,
1.

click and select Utilities followed by Copy to
clipboard.
This command copies the current chromatogram window to

the clipboard as a metafile. From here, you can paste the view
into a word processing document or other application that
supports the clipboard. Note: To paste into Microsoft Word,
you need to use the Edit/Paste Special/Picture command.
Save a trace
Use this utility to save a trace as a data file.
1.
From the Utilities menu, select Save Trace.
2.
3.
Click on the trace you wish to save.

In the Save Data File As dialog, browse to the location
for saving the file and type the name for the file.
14 Graphical Programming
About Graphical Method Programming
The Graphical Programming menu enables you to add timed
events and set up other method parameters graphically by
clicking on the displayed chromatogram. These commands are
also available from the Graphical Programming Toolbar,
which is displayed by default at the bottom of the Instrument
Window. To turn on the Graphical Programming Toolbar,
1. From the menu, select View followed by Preferences.
2.
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Select Int Events and then select Toolbar.
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Parameters that can be set using graphical programming

include:
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Command
Action
Width
Inserts a Width event at the point on the

chromatogram.
Threshold
Inserts a Threshold event at the point on the

chromatogram.
Shoulder Sensitivity
Inserts a Shoulder Sensitivity event at the point

on the chromatogram.
Integration Off
Turns off integration at the point on the

chromatogram.
Valley to Valley
Turns on valley to valley baseline detection.
Horizontal Baseline
Forces a horizontal baseline from the point on

the chromatogram.
Backward Horizontal Baseline
Forces a backward horizontal baseline from the

point on the chromatogram.
Lowest Point Horizontal Baseline
Forces a horizontal baseline at the next lowest

point.
Tangent Skim
Forces a tangent skim.
Front Tangent Skim
Forces a front tangent skim.
Minimum Area
Set a minimum area for peak detection.
Negative Peak
Turn on negative peak detection.
Disable Peak End Detection
Disables the end of peak detection.
Reassign Peak
Designates a different peak as the calibrated

peak.
Manual Baseline
Manually define a baseline.
Manual Peak
Manually define the beginning and end of a

peak.
Split Peak
Force a perpendicular to split a peak.
Force Peak Start
Force the start of a peak.
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Force Peak Stop
Force the end of a peak.
Move Baseline
Manually move a baseline.
Reset Baseline
Force a baseline to the point.
Reset Baseline at Valley
Reset the baseline to the next valley.
Adjust Retention Time Window
Adjusts the retention time window.
Adjust Group Range
Adjust the group range.
Define Single Peak
Define a single peak and add it to the peak

calibration table.
Define Peaks
Define multiple peaks and add them to the peak

calibration table.
Define Groups
Define groups and add them to the group

calibration table.
Suggest Sampling Frequency
Suggest a sampling frequency for the

chromatogram.
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15 Data Acquisition and Control

Data Acquisition and Control
Commands that are available from the Control menu are
related to data acquisition and control of the instrument. In
general, there are two ways to acquire data: 1) single run
acquisition, where you acquire data for a single injection and
2) sequence acquisition, where you acquire data
automatically for a series of runs using a pre-programmed
sequence that defines the number of injections, methods, file
names, and calibration. Additional control menu items will
appear depending on the features supported by the
instrument configured.
Single Run Acquisition

There are two ways you can acquire data. One way is with a
sequence (for multiple runs), and the other way is to make a
single run. To make a single data acquisition run, you need to
specify the method to be used for analysis, and a file name for
data storage.
Note: In order to use a method for data acquisition, its
Instrument Setup should have the acquisition channel turned
On, and a sampling rate and run time designated.
, or
To make a single run, click the Single Run button
select the Control>Single Run command from the menu. A
dialog will appear.
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Run Information
This section allows you to specify files for the run.
Sample ID
Enter a Sample ID for the run. This can contain text
and numbers, and is saved with the data file. You can
also click the arrow and select from a number of predefined IDs.
Method
Enter the name of the method to be used for data
acquisition and processing. Include the entire path
name if the method is not in your default method
directory. You can select the method from a list of
methods available on your disk by clicking the File
button adjacent to the field.
Data Path
Enter a path name where the data acquired for this
run will be stored. Click the File button to select a
path from a list of those on your disk.
Data File
Enter a file name to be used to save the data on disk.
You can select from one of the pre-defined name
types by clicking the arrow button adjacent to the
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field. It is not possible to use an existing file name,

unless the file exists in located in a directory whose
path contains the term "public". For example, if you
data files are saved in a directory entitled
"C:\Public\Data", the files saved in this directory can
be overwritten. The software automatically appends a
.dat file extension.
Number of runs
Enter the number of runs you wish to make. The runs
will automatically proceed without review until
completed, incrementing each file name as
designated. If the sequence of single runs is aborted,
and the user then repeats the single acquisition
without changing any parameter, the run number will
start with the next number as if the sequence not
been aborted. For example, setting 4 runs with
starting run number of 101, then abort during run
102. When restarting, the next run number will be
105. If the Sample ID is also incremented, it will
increment in parallel.
Print Method Report
When this box is checked, the method report (or
reports) will be printed at the end of the run.
Amount Values
In this section, you can enter values that affect how
the concentrations are calculated. If you are making a
single data acquisition prior to calibrating your
method, simply leave these values at the default level.
Sample Amount
The Sample Amount value is used as a divisor during
calculation of concentrations. It is intended to
compensate for differences between samples due to
weighing and when percentages of the total sample
are being calculated rather than the amount detected
in an injection.
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Internal Standard Amount

For calibration runs, the Internal Standard Amount is
taken from the method Peak Table. For unknown
runs, enter the amount of the Internal Standard in
your unknown sample.
Multiplication Factors
Enter one to three multiplication factors to be used
for this run. All quantitated peaks will be multiplied
by these factors.
Dilution factors
Enter one to three dilution factors to be used for this
run. All quantitated peaks will be divided by these
factors.
Calibrate
Select this box if the sample is to be a calibration
sample. Once this box is clicked, the following fields
and options will be available.
Calibration Level
Enter the number of the calibration level represented
by this calibration standard. If this is a single level
calibration, enter 1.
Clear all calibration
Click this box if you want to clear all existing
calibration factors from your method before running
the sample.
Clear calibration for level
Click this box if you want to clear the existing
response factors for this level only before running the
sample.
Print calibration report
Click this box if you want to print a calibration report
after running the sample.
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Clear replicates
Click this box if you want to clear all existing
replicates from the existing calibration level before
running the sample.
Average replicates
Click this box if you want to average the replicates for
this calibration level.
Baseline Check
This box will appear if you have the Baseline Check
option implemented in the instrument configuration.
When this box is checked, it will trigger a baseline
check prior to the start of the run.
Begin run
By default, run will start immediately. If you want to
schedule the start of the sequence for a later time or
button to open the Schedule Run
date, click the
dialog where you can enter or select the time to start
the sequence.
Startup/Shutdown
For instruments that support it, boxes for Startup
and Shutdown will appear in the dialog. These boxes
enable you to designate the run as either a Startup or
Shutdown sample. When one of these boxes is
checked, it will trigger the Startup or Shutdown
routine on your instrument. For details, see the
control documentation for your instrument.
When you have completed the Single Acquisition Run dialog
box, click Start to begin the acquisition. The current data will
appear in the chromatogram window as it is acquired and
stored on disk. At the end of the run, the chromatogram will
be analyzed according to the method parameters, and a report
generated if specified. If the sample is not analyzed at the end
of the acquisition, click the Analyze button if you wish to
view the results.
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Run a Sequence
Once you have created and saved a sequence, you can use it
to acquire and process data. To start a sequence acquisition,
1.
From the Instrument Window, click the Sequence

, or from the Control menu, click
Run button
Sequence Run....
2.
Enter or select a sequence to use, set a run range,

mode, printing options and review options, then click
Start.
Sequence Information
Enter the Sequence Name to be used, or select the
sequence file from a list of available sequence files by
clicking the File button.
Run Range
Select the range of the sequence to be run.
All
Click this to execute all runs in the sequence.
Selection
If you have currently selected a series of runs in your
sequence spreadsheet by highlighting them, click this
to run only the highlighted runs.
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Range
Enter a range of runs to be executed. For example, an
entry of 4 - 6 will execute runs 4, 5, and 6 of the
sequence. An entry of 4- designates the 4th run
through the end of the sequence.
Mode
Select the manner by which you want to handle
autosampler dual towers (if any), processing mode,
and bracketed calibration (if used).
Tower
If your instrument is configured for Dual Tower, you
can select the tower mode to be used for the sequence
run. Selections include Dual, Front, and Rear.
Processing Mode
Select a mode for reprocessing the data. Options here
will vary depending on the instrument configured. If
the instrument does not support this feature, this
option will be grayed out. For certain instruments,
Overlap Sample Prep mode will be available. See
About Overlap Sample Prep for information and
restrictions for using this mode.
Bracketing
Select the type of bracketing you wish to perform.
(See Bracketed Calibrations for details.)
None Select this if you do not wish to bracket
calibrations.
Standard Select this if you wish to perform the
standard mode of bracketing calibrations.
Std. w/Clear Calib Select this if you wish to perform
the standard mode of bracketing calibrations, clearing
the calibration before the start of each calibration set.
Sequence Select this if you want to perform the
sequence mode of bracketing calibrations.
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Seq. w/ Back Calc Select this if you want to perform

the sequence mode of bracketing calibrations and
back-calculate calibration runs.
Review
Results Review
Click this box if you want the sequence to pause
between runs for you to review results.
Calibration Review
Click this box if you want the sequence to pause after
each calibration set, where a calibration set is defined
as one or more calibration runs that occur in a
sequence.
Printing
Print Method Reports
Click this box if you want the custom report defined
in the method to be printed for each run of the
sequence.
Print Sequence Reports
Click this box if you want sequence reports to be
printed.
Begin run
By default, run will start immediately. If you want to
schedule the start of the sequence for a later time or
button to open the Schedule Run
date, click the
dialog where you can enter or select the time to start
the sequence.
Email Recipient(s)
Use this field to enable email notification to be sent to
a designated address (entered in the To: field).
Select the On Start box to send email notification
when the sequence starts.
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Select the On Stop or Error box to send email

notification when the sequence stops or if an error
occurs.
When you have completed the dialog box, click Start to
initiate the sequence acquisition. You may see the data
displayed in real time in the chromatogram window(s), if the
"current data" is selected for viewing.
Stop a Run in Progress

When you want to stop data acquisition during a run,
1.
Click the STOP button that appears on the command

ribbon when the run is in progress, or from the
Control menu, click Stop Run.
2.
Select how you want to stop the run. If you are

running an instrument connected to an Agilent
Instrument Controller, you will not be able to stop the
run or sequence unless you are the user that
submitted it.
Note:
When using the STOP button, make sure to hold the mouse
button down until the STOP button icon changes to the
"depressed" appearance before releasing.
Stop current run only

Select this to end the run currently in progress. If the
run is a part of a currently-queued sequence, the
sequence will continue with the next run.
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Stop current run and sequence run

This selection stops the run currently in progress, and
terminates the sequence it is a part of. Other queued
items will proceed.
Stop sequence after current run completes
This selection will abort the sequence after the
current run in progress is completed.
Stop all run queue items you submitted
terminates all the items in the queue that were
submitted by you. Queue items submitted by other
users will be unaffected.
Stop all run queue items
terminates all items in the run queue.
Note:
When a run is stopped, the data up to that point is saved in

the data file. However, no analysis of the data will be
performed. If you want to produce a report or view results
from a run that was stopped, you must Analyze the data file.
Note:
If you are not the user that submitted the run or sequence or
are using an instrument offline, you do not have access to the
Stop command.
Extend a Run
While a run is in progress, you can extend the data
acquisition beyond the designated run time by
1.
From the menu, click Control followed by Extend

Run.
2.
A dialog will appear where you can enter the amount

of time by which you wish to extend the run.
Enter the number of minutes you wish to extend the
run, and then click the OK button.
3.
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Note:
If you are not the user that submitted the run or sequence or
are using an instrument offline, you do not have access to the
Stop or Extend Run command.
16 Turn Off GPIB Instruments

If you are using two instruments attached to a GPIB board, it
is important to close the instrument application (or close the
instrument window and then close the server) prior to
turning off the power to the instrument or instrument
modules, otherwise the other instrument attached to the
GPIB board may freeze.
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17 Tutorial
This section walks you through the basics of using EZChrom
Elite. Follow the steps to set up a method and acquire a data
file, then optimize the method for integration and set up
calibration. Use the Tutorial files provided with the software
to "play" with the software and become comfortable with its
use. Details on data file structure, application window
features, how to open and save files are located in Basics of
Operation.
Note:
This Tutorial assumes that EZChrom Elite is installed with all

an analog instrument using an SS420x or other supported
A/D converter installed and properly configured. If you have a
digital instrument configured, refer to the online help to
complete the instrument setup for data acquisition.
Tutorial Overview
The following list gives you a quick view of what the Tutorial
section contains. If you are just starting to use EZChrom
Elite, you should perform all steps in the Tutorial, in the
order presented.
Step 1: Create a Data Acquisition Method
Set up acquisition run time and
sampling rate
Save the method
Run a preliminary sample
Set Integration parameters
graphically
Step 2: Create a Single-Level Calibration
Name Calibrated Peaks
Run a a Single-Level Calibration
Step 3: Create and Run a Sample Sequence
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Step 4: Using Tutorial Files

Review a Multi-level Calibration
Explore a Peak Table
Examine a Custom Report
Change integration parameters
18 Tutorial - Acquiring and Analyzing Data

In this section of the Tutorial you will use the data system to
acquire data and optimize the integration, set up and run a
calibration standard, and create and run a sample sequence.
Details for advanced operation are located in later sections of
this manual.
Instrument and Method Wizards

To make using the system easy, you can use the built-in
Instrument and Method Wizards. These Wizards make it easy
to locate and step through the dialogs necessary to create or
modify methods. If you use the Method Wizard to create your
Tutorial methods, use the wizard buttons to move you to the
dialog associated with the Tutorial step you are on.
The Method Wizard is started from the Instrument Wizard
box by clicking the button labeled Create or modify a
method.
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When you click this button, the Method Wizard will appear,
allowing you to select how you want to use the wizard.
Select the Create a new method button to start creating your

tutorial method.
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When you select this button, the Method Wizard sets up a

bank of buttons in your application window that allow you to
"step" through all dialogs of method generation. A save button
is also provided.
Create a Data Acquisition Method

The first step toward acquiring a data file is to create a data
acquisition method. At this point, you merely need to make
sure that the method will acquire the data for a long enough
run time for your last peak to elute, using the default data
acquisition sampling rate (which is adequate for most
samples except for fast capillary runs.)
Note:
You can skip this step and use data and method files provided
if you do not currently have access to an instrument.
Acquisition Setup
To set your acquisition run time and sampling rate, go to the
Instrument Setup dialog. This is the first dialog displayed if
you are using the Method Wizard. Or, click on
Method/Instrument Setup, or click the Instrument Setup
button on the command ribbon. Select the detector tab for the
detector you will be using. Be sure to click the box adjacent to
Acquisition Channel On to turn on data acquisition for this
channel.
Note:
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If you are using an instrument control option, one or more

tabs will appear in Instrument Setup that provide instrumentspecific options. See the online help for that instrument for
details.
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The default Sampling Frequency should be adequate for most

types of chromatography. For Frequency data sampling, the
data rate is selected in Hz (samples per second). For Period
sampling, you can select the number of seconds (or
milliseconds) between data points. The default is Frequency
and this is how most chromatography applications are set up.
Make sure that the Run Time is long enough for your last
expected peak to elute. If you do not know how long it will
take to elute, set the run time to a high number, such as 100
minutes. (You can stop the run manually after the last peak
has eluted.) After your first run you can then adjust the run
time to a more appropriate number.
Click the Trigger tab and select the Trigger Type for the type
of remote start (if any) you have installed for the instrument
you will be using. (If no trigger is configured, this tab will not
appear.) The trigger for each instrument is set up during
configuration.
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None
Sampling of data starts immediately when Start

is clicked.
Manual
User must start the data sampling.
External Data sampling starts when externally triggered.

When you have completed the acquisition setup information,
click the X box in the upper right hand corner of the tab
window to exit the dialog.
Save Your Method

Once you have set the acquisition parameters, save your
method using a name you will recognize. Click on
File>Method/Save As A dialog box will appear.
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Select the folder in which you want to save your file. In the
Filename field, type Test.met as the filename for saving the
method.
Run a Preliminary Sample

You will now use the data acquisition method you just saved
to make your first data acquisition run. To aid in later steps
of the Tutorial, it is best to run a standard sample for your
first acquisition run.
1.
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To start the run, select Control>Single Run or

click the Single Run button.
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2.
At this point, enter Test in the Sample ID field.
3.
In the Method field, either type your method

name, along with its path, or select the Test.met
file from a file list on your disk by clicking on the
open file button adjacent to the field.
Enter a path for storage of data files in the Data
Path field, or select a path from a list presented
by clicking the open file button adjacent to the
field.
Enter Test.dat as the name for storing your data
in the Data File field. You must enter a unique
file name in this field. Therefore, if you have
performed this tutorial before, you must first
delete this file from your disk, or move it to a
different directory before proceeding.
Since you are not doing calibration at this point,
simply click Start and inject your standard
sample. You will see the data as it is acquired in
the chromatogram window on your screen.
4.
5.
6.
Set Integration Parameters Graphically

EZChrom Elite uses default integration parameters that are
appropriate for most simple chromatography. However, you
may have certain peaks that require special integration
treatment. Such special integration treatments are entered
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into your method as Integration Timed Events. These events

can be placed at the beginning of the run to apply to all peaks,
or they can be inserted at a certain place in the
chromatogram such that only some peaks are affected. Follow
the steps below to add the timed event to turn off integration
to your method.
Note:
You can perform this step using one of the multi calibration
level.dat files provided with the software.
1.
2.
Note:
If you dont know what a buttons function is, simply move

the cursor over the button (dont click) and a Tooltip box will
appear showing the buttons name or function.
3.
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At this point, your recently acquired

chromatogram should be displayed in your
chromatogram window. If it is not, click the Open
File button, select Open Data, and then select
your data file from the list displayed.
Alternatively, you can select one of the files
supplied with Elite.
Click the Analyze button to integrate the
chromatogram and display the baselines.
To add the Integration Off timed event, click the

Int Off button on the Toolbar. As instructed in the
status bar at the bottom of the window, click your
mouse once prior to a part of the chromatogram
where you want to turn integration off. (Select a
section of chromatogram where one or more
peaks elute.) Then click the mouse again at the
point on the chromatogram where you want to
turn integration on again. A dialog will appear.
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The points where you clicked your mouse are shown as

Start Time and Stop Time. The integration will be turned
off between these points on your chromatogram. The
Value is set at zero, as no numeric value is required for
this event. Click Analyze Now to add the event to the
method and re-integrate the chromatogram. (Add to
Table will simply add the event to the integration timed
events table without re-integration.)
Select the button next to Insert into Integration Events
table and the event will be added to the Integration
Events Table of your method (where it will be used on all
chromatograms analyzed using this method). Select the
button next to Insert into Manual Integration Fixes
table and the event will be added to the Manual
Integration Fixes Table of the present chromatogram
(where it will be applied only to this chromatogram).
Your chromatogram will be re-drawn using the new
integration event. Notice that the area you selected has no
baselines drawn because the integration has been turned
off for these peaks.
4.
5.
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The integration event is put into the Integration

Timed Events table. To view this table, click the
Integration Events button on the command ribbon.
Your integration timed events table will appear.
Notice the Integration Off timed event has been added
to the table.
To remove the Integration Off event from your
method, click on the Integration Off event name or
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the row number, then press the Delete key on your

keyboard. You can also delete the event using the
Edit/Cut command. Using this command, you could
re-insert the event using the Edit/Paste command if
you wished. To temporarily view the effect of
removing an event without actually removing it from
the table, click the check box adjacent to the event to
de-select it. To re-select the event, click the check box
once again.
6. When you are finished with the Integration Events
table, click the X box to close it and return to your
chromatogram.
Create a Calibration
If you are interested in peak quantitation (calculation of
results based on the running of standards, you must set up
your method for calibration. Further details on how to set up
multiple level calibrations are given in the Method
Development section of this manual. For this tutorial,
however, you will set up a single level of calibration.
Setting up any type of calibration involves the following steps.
Identify the Calibrated Peaks and enter standard
amounts in the method
Run the standard sample(s)
Review the calibration curve
The easiest way to enter calibration peak data is to actually
run the standard sample first, then use the stored data file to
graphically define your calibration peaks. If you have been
following the Tutorial, you should already have a standard
sample saved on your disk. If you do not, you can either run a
standard sample using the steps shown above in the Run a
Preliminary Sample section of this Tutorial, or you may
select one of the data files provided with the data system.
1.
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Open your stored data file by clicking the Open File

button and select Open Data Select your standard
data file from the list, or select one of the data files.
Once the file is displayed in your current data
chromatogram window, click the Analyze button to
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2.
integration the chromatogram and show the

baselines.
Click the Define Single Peak button on the Toolbar.
A dialog box will appear for the first detected peak in
the chromatogram.
The retention time of the first detected peak will

appear. If you want to add this peak to the peak table,
complete the dialog for this peak. If you do not wish
to add this peak to the peak table, click the Next
button. If you want to move to a specific peak in the
chromatogram, click on that peak with your mouse.
The retention time shown in the dialog will change to
reflect the selected peak.
Peak Name
Enter the name of the compound in this field.
Conc Level
Concentration Level 1 is shown. Enter the amount of
this compound for this concentration level. (Note: For
setting up more than one level for this compound, you
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would enter Concentration Level 2 and the amount

for that level. Continue to enter level concentrations
until you have completed the number of calibration
levels desired.)
Units
Enter the units to be used for display of results.
ISTD ID #
If you are doing internal standard calibration, enter
the ID # for the internal standard peak for this
compound. This is the peak ID number from the peak
table. If you dont know it, you can add it in the peak
table later.
Ref ID #
Enter a retention time reference peak ID # to be used
for this peak. This is the peak ID number from the
peak table. If you dont know it, you can add it later
in the peak table. Reference peaks are used to locate
calibrated peaks when chromatographic conditions
change such that retention times shift.
Retention Time Window
Select how you want to enter the retention time
window for this peak. The window is used for peak
identification in case of slight deviations from the
expected retention time.
Relative
Click this if you want the system to calculate the
retention time window based on a % of the expected
retention time of the peak. Enter the % you want to
use for calculation of the window.
Absolute
Click this if you want to enter an absolute window for
the peak. Enter the value you want to use for the
retention time window, in minutes.
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Click Next to move to the next detected peak. Click

Back to move to the previous detected peak in the
chromatogram. The current peak and total peaks in
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the chromatogram is displayed on the right of the

dialog box. When you are finished adding peaks to
your peak table, click Done. Each peak you defined
will become a row in your peak table. Note that if you
already had peaks in your peak table, the peaks you
just defined will be added to those already present.
To view the peak table, click the Peak/Group Tables
button from the command ribbon.
4.
Once you have defined your peaks, click the Peak

Table button and the calibration peak table will
appear. Make sure the Named Peaks tab is selected.
Each peak you defined will appear as a row in the
Peak Table spreadsheet, along with its retention time
and other parameters you entered.
Information in the spreadsheet can be edited or

changed by scrolling through the rows and columns.
Details on contents of the Peak Table are described in
the calibration section of this manual.
5.
Do not enter information in the other columns at this

time. Close the Peak Table by clicking the X box in
the upper right corner of the spreadsheet window.
Your method is now ready to be calibrated. Before you

proceed, save the method on your disk. To do this, click the
Save button followed by Save Method, or select
File/Method/Save from the menu. (If you wish to save the
method using a different name, use the File/Method/Save As
command.)
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Calibrate Using a Stored Data File

In order for the software to calculate amounts for unknown
samples, your method must contain the areas generated for
each component in your standard sample. In order to get
these areas into your method, you can either run the standard
sample again, designated as a calibration run, or you can
calibrate the method using the stored run from before, using
the Analysis>Single Level Calibration command. To use the
stored data file to calibrate the method, follow the steps
outlined below.
1.
Select Analysis>Analysis Single Level Calibration

from the menu bar. A dialog box will appear where
you must designate file information for your
calibration.
2.
Enter the sample identification in the first field. If

you are following the tutorial exactly, this will be
Test.
3.
Enter the name of the method you want to calibrate,

including full path name. If you arent sure of the
method name, select it from a list by clicking the
Open File button adjacent to the field. The Tutorial
method is Test.met.
Enter the data path name, or select it from the list
using the open file button.
Enter the name of the calibration data file in the Data
File field. The open file button lets you select the file
name from the disk. The name used in the Tutorial is
Test.dat.
4.
5.
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99
6.
Leave the Amount Values set to "1". For details on

how these values are used, see Method
Development.
7.
Click on the Calibration checkbox, then enter a "1"

for Calibration Level. Since this method is currently
uncalibrated, it is unnecessary to select any of the
boxes dealing with calibrations or replicates.
However, if you are unsure of the method contents,
click the Clear all calibration box before starting.
8.
When you have completed the dialog, click Start.

When the analysis is complete, the chromatogram will
be integrated, and the areas for the peaks identified
as calibration compounds will be entered into the
method. The calibration curves will be generated
using these areas. At this point, the method is
calibrated for a single level, and it can now be used to
run and analyze samples with the calibration
compounds in unknown amounts.
Create and Run a Sample Sequence

If you are using an autosampler to inject samples, you must
define the samples to be injected and how they are to be
acquired and analyzed. This is done using a sample
Sequence. A sample Sequence can be used to acquire both
calibration and unknown samples. It can also be used to
automatically re-analyze stored data files. Details on creating
and using a Sequence are located in the Sequence section. In
this part of the Tutorial you will create and use a simple
sequence to acquire a calibration sample and two or three
unknown samples.
1. To create a new sequence, click the
File>Sequence>Sequence Wizard command. A
Sequence Wizard dialog box will appear.
100
Users Guide
2. Type the method to be used for the acquisition, or

select the name from a list of available methods by
clicking the File Open button.
3. For Method, enter the method name (including path)
for the method you have been using for this Tutorial.
If you dont know the entire path name, you can
select it by clicking the file button next to the field,
and selecting your method name from the list
displayed. If you are following the Tutorial, enter
Test.met as your method name. Leave the Amount
values at their default values.
4. Click the For Acquisition button. This will cause the
Sequence Wizard to prompt you for information
required for data acquisition. Then click Next.
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101
5.
6.
7.
8.
9.
102
The Sample ID field is for an identification for the

samples. Click the blue right arrow and select the
Line number and Method name. This will cause each
sample to be identified with the sequence line number
and current method name.
In the Data Path field, enter the path where you want
the data to be stored, or select an existing path by
clicking the File Open button.
For Data File, click the blue right arrow, and select
Sample ID. This will cause the data files to be named
by the sample ID you selected above. Using a
numbered identification ensures the data file name
for each run is a unique name, preventing errors that
will occur if you try to acquire data using an existing
data file name.
For number of unknown runs in sequence, enter 3.
Leave the other fields at default values.
Click Next to continue.
Users Guide
10. In this dialog, the calibration ID and calibration file

names are automatically set to the identifications
from the previous dialog. Set the number of
calibration levels to "1", and leave the calibration
repetitions per level at "1" also. Leave all other boxes
unchecked, then click Next.
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103
11. Select the check boxes to cause the samples to be

included in a summary report and calibration
summary report. Do not select the other boxes.
12. Click Finish. A sequence spreadsheet will appear,
with the file and method names you specified shown.
13. At this point, the sequence is set up to run 1

calibration sample and 3 unknown runs. Notice the
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Users Guide
Sample IDs and Data File names are numbered

automatically to prevent duplication. In order to run
a calibration standard as the first run, you must
designate that run to be a calibration run. This has
been done automatically by the Sequence Wizard.
Unknown runs always have a Level of "0". The
information in the Run Type field may be abbreviated
if there is more than one run type designation. To
view the possible Run Types, click the arrow next to
the run type. For details on each of these run types,
see the Sequence section. Since the method we have
been creating in this Tutorial is a single level
calibration, only one calibration standard run is
necessary.
14. To save the sample sequence file, click the Save\Save
Sequence button to go to the Save Sequence dialog
box, or use the File/Sequence/Save As command
from the menu bar. Select the
C:\datasystem\Sequence folder (where datasystem
is your program installation folder), then enter the
name Test or Test.seq for your sequence file name.
Note:
By default, sequence files are saved with the .seq extension.
Run a Sequence
To acquire data using the sequence file you just created, click
the Sequence Run button on the command ribbon, or do a
right-hand mouse click in the sequence spreadsheet, and
select Run Sequence. A dialog box will appear.
Users Guide
105
Enter the name of your sequence file by typing the name,

along with path, in the Sequence Name field. You can also
select it from a list of sequence files on your disk by clicking
the file button next to the field. Leave the other parameters as
their defaults.
Prepare your autosampler to inject your standard sample,
followed by 3 unknown samples. When you are ready to inject
your first sample, click Start. When the sequence is
completed, you will have acquired and saved the data files for
one standard and three unknown runs, and generated a
simple result report for each unknown sample and a
summary report for the sequence.
Because you have not yet defined a sequence summary
report, do not check the Print sequence reports box.
19 Using the Tutorial Files

In this section of the Tutorial, you will use the tutorial files
provided to become familiar with additional features of the
Data System.
Review Multi-level Calibration Curves

Once you have fully calibrated a method, the calibration
curves and associated data can be viewed using the Review
Calibration function. In order to see a fully calibrated multi106
Users Guide
level calibration, use the multilevel calibration.met file

provided with the data system.
1.
2.
Open the multilevel calibration.met method file by

clicking the Open button followed by Open Method.
Select the multilevel calibration.met file from your
disk. It will be located in the \datasystem\Methods
folder. (Where datasystem = your installation
program folder.)
Once you have opened the multilevel calibration.met
method, click the Review Calibration button, or
select the Method/Review Calibration command.
The following window will appear.
The calibrated peaks in the method are listed in the

peak list at the top right corner of the window. The
calibration curve shown is for the peak that is
highlighted. You can view the other curves by
highlighting their peak name. At the top of the screen
is a spreadsheet that displays all the calibration
information, including areas used to create the
current calibration curve.
3.
Users Guide
The calibration curve fit type by default is Point-toPoint. To overlay a different fit type, click the right
mouse button anywhere in the calibration curve box.
Select Fit Type and then select Linear. Notice the
new linear calibration curve is overlaid on the Pointto-Point curve. In the box at the right, the equations
107
for the different fit types displayed are shown, along

with the goodness of fit calculation, r2, which is not
calculated for the Point-to-Point curve since it is by
definition a perfect fit to the data.
For additional details on using Review Calibration, see
Method Development. To close the window, click the X box
at the upper right corner of the Review Calibration window.
Explore a Peak Table

The Peak Table is where method calibration information is
located. In this section, you will use a method provided with
the software to examine a Peak Table and become familiar
with what a completed peak table looks like.
1.
2.
3.
108
Open the multilevel calibration.met method which is

located in the c:\datasystem\Methods folder (where
datasystem is your program folder), by clicking the
File button, followed by Method, then selecting the
c:\datasystem\Methods\multilevel calibration.met
method from the list of methods on your disk.
Once the multilevel calibration.met method is open,
view the Peak Table by clicking the Peak Table button
on the command ribbon. A peak table will appear.
On the Named Peaks tab, you will find a table

containing all of the calibration information for the
calibrated peaks in this method. If you scroll to the
right, you will see many different columns, each of
which represent a parameter for the calibration,
Users Guide
including the Levels, which contain the calibration

amounts for each compound at each level of
calibration. Note that it is possible to customize the
Peak Table such that only parameters needed for a
given calibration are displayed. Details on what each
column represents, along with how to customize the
Peak Table, are given in the Method Development
chapter of this manual.
Examine a Custom Report

A complete suite of report templates are provided that can be
used without modification to generate reports. To see an
example of one of these reports, use the
Reports>View>External Standard Report command from
the menu bar. (Make sure your current chromatogram has
been analyzed first.) The standard report will appear in a
window on your screen.
If your method contains no defined custom report, the system

will use the standard report formats to print reports when
required.
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109
If you wish, you can modify the standard report templates, or

create entirely new reports using the Custom Report feature.
You can create custom method reports and / or custom
Sequence reports. These are described in detail in the Custom
Reports section.
To view the custom report in the multilevel calibration.met
file, first open the file if it is not already open. (Use the File
Open button, followed by Method, then select it from the file
list.) Click the Edit Custom Report button on the command
toolbar to access the method custom report editor. The
current method custom report will appear.
Examine the custom report template by scrolling through it

using the scroll bars that appear on the bottom and side of
the window. Before you attempt to edit or create your own
custom report, you should thoroughly review the Custom
Report section. To return to the method, click the x box in the
upper right corner of the custom report window.
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Users Guide
Changing Integration Parameters

Another important aspect of using a computerized data
system is the ability to customize the integration using
Integration Timed Events. In this part of the Tutorial, you will
use the multi calibration level 3.dat data file provided to
become familiar with how to enter integration timed events
into your method, and to view the effects of some of these
events. Complete details on how each integration timed event
works are given in the Integration section.
1.
2.
Note:
Users Guide
Open the multi calibration level 3.dat data file by

clicking the File button, followed by Data Files, and
then select the Multical3.dat file from the \Data folder
on your disk. Select the Open with Method option to
open the multilevel calibration.met method file that
was used to acquire the data file.
Click the Analyze button to analyze the
chromatogram and display the baselines.
The vertical line cursor moves with your mouse. The retention
time where the cursor is located is shown at the top of the
111
3.
Add the Valley-to-Valley timed event to integrate the

cluster of 4 large peaks with valley-to-valley baselines.
To do this, click the Valley button on the integration
toolbar. Then, click the mouse once before the first
large peak, then again just after the last peak.
When the dialog box appears displaying the start and stop
points for the event, click the Analyze Now button and view
the chromatogram. Notice the peaks within the region of the
event are now integrated using the valley-to-valley event, and
baselines are adjusted accordingly.
112
Users Guide
4.
Click the Integration Events Table button from the

command ribbon. Note the addition of the Valley to
Valley event in the table.
5.
Remove the Valley to Valley event by clicking its

number with the mouse, then select Edit/Delete from
the menu bar. You can also test integration without
the event, yet leave it in the timed event table, by deselecting the check box next to the Valley to Valley
event and then re-integrating the chromatogram.
Close the Integration Events Table by clicking the x
box at the top right corner of the table.
6.
Practice adding and deleting integration timed events

using the multi calibration level 3.dat data file until
you feel comfortable with adding and deleting
integration events.
You have now completed the Tutorial. For detailed
explanations on how to create multi-level calibrations, create
custom reports, and create and use sample sequences are
given in later sections. And dont forget to use the extensive
on-line Help as you work with the software.
Users Guide
113
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Agilent EZChrom Elite

Manual Part Number

including but not limited to the

Restricted Rights Legend

subject to Agilent Technologies

Using This Guide ................................................................................. 8

Basics of Operation ............................................................................ 9

Instrument Wizard .............................................................................. 9

About the Navigation Pane.............................................................. 11

Navigate the Instrument Window .................................................. 13

Data Acquisition Using Agilent Instrument Controllers .............. 14

Program Architecture and Data Structure .................................... 15

Opening and Saving Files ................................................................ 19

Open Data File Options.............................................................................. 20

10 Reading CDF Files ............................................................................. 25

12 The Chromatogram Window............................................................ 32

15 Data Acquisition and Control........................................................... 74

16 Turn Off GPIB Instruments ............................................................... 84

18 Tutorial - Acquiring and Analyzing Data........................................ 86

19 Using the Tutorial Files .................................................................. 106

Examine a Custom Report ...............................................................................109

1 Using This Guide

Who Should Read This Guide?

Create or modify a method

Offline Instrument Wizard

5 About the Navigation Pane

To turn the Navigation pane on

Select View followed by the Navigation pane

To turn the Navigation pane off

Click the x button at the top of the Navigation pane.

Click the push-pin button at the top of the Navigation

6 Navigate the Instrument Window

Method commands, Data manual integration

Reports, Report template properties

Instrument Setup, Run Queue, Instrument

Data Display options, Manual Integration Fixes,

7 Data Acquisition Using Agilent Instrument

User access to runs in progress

workstation (if the user has appropriate privilege

Closing a Server Instrument

8 Program Architecture and Data Structure

About Data File Structure

Turn on Extended Security

Click Extended Security if the box is not selected

This selection is ON by default. When this option is selected,

View the Method Audit Trail

and cannot be removed or overwritten. To view the changes

From the File menu, select Method followed by Audit

To view the details of a given entry, click on the entry

9 Opening and Saving Files

systems with advanced file security enabled. Users will be

Open Data File Options

Open Method and Sequence Files

The Open dialog boxes for Method and Sequence files

Searching for Method and Sequence Files

Save Data Files

A dialog opens where you can browse to a location

10 Reading CDF Files

11 The Instrument Window