Agilent 32-Bit ChemStation for GC, LC, LC/MSD, and A/D Systems

Agilent 32-Bit ChemStation for GC, LC, LC/MSD, and A/D Systems
Agilent 32-Bit ChemStation for
GC, LC, LC/MSD, and A/D Systems
- Rev. B.01.01
October 2004
What’s New in Rev. B.01.01
Revision B.01.01 is the first release
of ChemStation on 32-Bit software
architecture. Customers currently
operating an Agilent ChemStation
with a GC, LC, LC/MSD, or A/D
instrument can take the advantage
of the new features by upgrading
their software.
The following new features are
included in Revision B.01.01:
• Support for Microsoft Windows®
XP Professional with Service
Pack 1a
• Support for Microsoft Windows®
2000 Professional with Service
Pack 4
• Software conversion to 32-Bit
architecture provides increased
system performance and
• Support for long file names for
data files, methods, sequences,
logbook entries and reports.
• Extension of the automatic file
naming function which names
raw data files with a prefix and
counter to allow for generation
of filenames with a total of
17 characters.
• Support for long file names in
user interfaces and dialog
• Optimization of screens and
windows to use 1024 x 768
• New Chem32 integrator provides improved integration
result accuracy.
• New Baseline Correction
integration event allows treatment of noisy or drifting
• Four new integration events
allow selection of skimming
mode for tailing or fronting
• New Sequence Editor dialog
allows the user to define the
columns to be displayed in the
Sequence Table and define the
width (in characters) of each
column shown.
• Support for 6850 Series II
• Support for the new G1888A
• Support for the new 7683B ALS
• Support for the 1100 Series dual
loop autosampler (G2258A) high
throughput overlapped injection
• Support for the use of hyperthreading on Pentium IV or higher PC's running Windows XP.
• Support for a color HP LaserJet
printer (LJ2500TN).
• Support for the new 1100 Series
HPLC Maintenance & Repair
• Automatic installation of
Companion software with GC
ChemStation installation.
• New CHEM32 default directory
used for installation and operation.
• New Common Agilent
ChemStation Program Group
allows access to all installed
ChemStation Plus applications
via a single program group in
the Windows Start panel.
• New ChemStation specific
parameter file called
• Faster software installation.
• Simplified ChemStation software deinstallation using the
Windows Add/Remove Programs
feature in Control Panel.
• Conversion of ChemStation Help
to HTML format.
• Quality and defect fixes.
New features related to ChemStation Plus systems that include
the ChemStore add-on module
(these features will only be seen if
ChemStore is installed):
• Improved integration with
• Two new ChemStore related
icons in Method and Run
Control and Data Analysis
- ChemStore Lock Session, and
- Launch ChemStore Review
• Display of ChemStore Study
name in status bar in Method
and Run Control view.
• Inclusion of new ChemStore
Study column in the Sequence
• New ChemStore custom field
set-up dialog which can be
opened via a button and is automatically called whenever a
new line is appended in the
Sequence Table.
• Incorporation of ChemStore
transfer settings in the
Sequence Parameters dialog.
Table of Contents
What’s new in B.01.01 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
General Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4
Computer Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Minimum PC Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Recommended PC Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
LC/MS ChemStation Computer Hardware . . . . . . . . . . . . . . . . . . . . .7
Maximum Instrument Configurations . . . . . . . . . . . . . . . . . . . . . . . . .7
IEEE-488 GP-IB Support Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
LAN-MIO Support Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
LAN Configuration Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Printers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Operating System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Methods and Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
System Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Data Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Software User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Data Analysis - Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Data Analysis - Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Data Analysis - Quantification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Data Analysis - Standard Reporting . . . . . . . . . . . . . . . . . . . . . . . . . .16
Data Analysis - Specialized Reporting . . . . . . . . . . . . . . . . . . . . . . . .17
Utilies, Compatibilities and Interlacing . . . . . . . . . . . . . . . . . . . . . . .18
XML Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Customization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Automation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Good Laboratory Practice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Instrument Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Agilent ChemStation for GC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
Agilent ChemStation for LC Systems . . . . . . . . . . . . . . . . . . . . . . . .25
Agilent ChemStation for LC/MSD Systems . . . . . . . . . . . . . . . . . . . .29
Agilent ChemStation for A/D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32
Additional Data Evaluation Modules . . . . . . . . . . . . . . . . . . . . . . . . .33
High Throughput Purification Software Module . . . . . . . . . . . . . . .30
Agilent ChemStore C/S Database Client Software . . . . . . . . . . . . . .37
Agilent ChemStation Plus Security Pack . . . . . . . . . . . . . . . . . . . . .37
Agilent ChemStation Plus Method Validation Pack . . . . . . . . . . . . .37
Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
General Description
The Agilent 32-Bit ChemStations
for GC, LC, LC/MSD, and A/D systems are instrument control, data
acquisition and data evaluation
systems for:
• Agilent 6890N, 6890 Plus and
6890A gas chromatographs,
• Agilent 6850 Series II and 6850
gas chromatographs,
• Agilent 5890 Series II and 4890D
gas chromatographs,
• Agilent 1100 Series modules
and systems for HPLC, including the Agilent 1100 Series
• HP 1090 Series liquid chromatographs, and
• Agilent 35900E dual channel
analog-to-digital interfaces.
The software is designed to run on
IBM compatible personal computers with a PCI interface under
Microsoft Windows operating
Core ChemStation 2D
Four core 32-Bit ChemStation 2D
software products are available.
Each core software product provides data acquisition, instrument
control, data analysis (integration,
quantification and reporting),
automation and customization for
a single analytical instrument. A
single instrument may collect data
from a number of different detectors simultaneously. The four
core 2D software products are:
• Agilent 32-Bit ChemStation for
2D Liquid Chromatography (LC)
systems (G2170BA)
• Agilent 32-Bit ChemStation for
Gas Chromatography (GC)
systems (G2070BA)
• Agilent 32-Bit ChemStation for
Liquid Chromatography / Mass
Selective Detector (LC/MSD)
systems (G2710BA)
• Agilent 32-Bit ChemStation for
35900E Analog to Digital
Converter (A/D) systems,
ChemStation 3D Software
The capabilities of the core 2D LC
software may be expanded to
allow for 3D data through the purchase of the additional LC 3D
Spectral Module, Product Number
ChemStation Additional
Instrument Control Software
The instrument control capabilities of the core Agilent
ChemStation software may be
extended to allow for multiple
instrument systems by purchasing
additional instrument control software. It is possible to configure
up to four chromatography instruments per ChemStation PC. The
four additional instrument control
software products are:
• Additional LC Instrument
Control and Data Acquisition
software (G2171BA)
• Additional GC Instrument
Control and Data Acquisition
software (G2071BA)
• Additional LC/MS Instrument
Control, Data Acquisition and
data evaluation software,
• Additional 35900E Analog to
Digital Converter (A/D)
Instrument Control and Data
Acquisition software (G2073BA)
ChemStation License to Use
Software on another PC
Once an initial core ChemStation
software product has been purchased it is possible to purchase
licenses to use that software on
another PC. The available license
products are:
• License to use 2D LC
ChemStation software on
another PC (G2175BA)
• License to use 3D LC
ChemStation software on
another PC (G2185BA)
• License to use GC ChemStation
software on another PC,
• License to use A/D ChemStation
software on another PC
ChemStation Data Analysis
Only Software
There are three data analysis only
ChemStation software products.
These products are designed for
data evaluation only purposes, for
example in an office environment,
and should not have instruments
configured. The three data analysis only software products are:
• ChemStation Data Analysis
software for LC (G2190BA)
• ChemStation Data Analysis
software for GC (G2090BA)
• ChemStation Data Analysis
software for LC/MSD
ChemStation Plus Add-On
Software Modules
Agilent provides a range of add-on
software modules which extend
the capabilities of the ChemStation base software. The modular architecture ensures that you
can control your enhanced system
from the same, familiar user interface. ChemStation Plus is a fully
scaleable solution that enables
you to expand your data system
from single PC to instrument configurations right through to distributed, multi-technique configurations and client-server functionality. Users, instruments and
applications can be added without
• Agilent Method Validation Pack,
(G2184AA) provides automated
validation of analytical
Dedicated Solutions for
Specific Applications
• High Throughput Purification
(Purify) software modules
Advanced, high-capacity preparative LC for large numbers of
• Agilent ChemStation
Companion – provides a simple
single-screen user interface for
GC routine analysis.
Automatically installed with GC
ChemStation software.
• Agilent ChemStore,
• Retention Time Locking,
Standalone/Client (G2181BA)
(G2080BA) – requires 32-Bit GC
• ChemStore Server (G1410A)
ChemStation software.
ChemStore provides centralized
data organization and storage,
• Integrated HeadSpace control
custom calculations, review
software (G2924AA) – requires
and approval as well as power32-Bit GC ChemStation softful report generation capabiliware. Support for Agilent
ties such as control charting. It
G1888A, G1289B/G1290B
is available as either a
HeadSpace sampler.
Standalone or Client/Server
• Analyst software (G2731AA) for
LC/MSD data analysis – requires
• Agilent ChemStation Plus
Security Pack (G2183AA)
LC/MSD ChemStation software.
Compliance with regulatory
guidelines such as the FDA's 21
CFR Part 11.
Computer Hardware
The 32-Bit ChemStation consists
of Hewlett-Packard personal computer hardware and ChemStation
software. The hardware is an IBM
compatible personal computer
with an ISA or PCI interface bus.
The personal computer is interfaced to the analytical instruments
through a LAN card, GP-IB internal card, or a combination of one
GP-IB card and a LAN card. All
cards plug directly into the computer’s PCI or interface. ThirdParty instruments can be connected via the Agilent 35900E A/DConverter interface. The separate
hardware components that comprise a particular instrument configuration, including third party
instrumentation, may need to be
coordinated through a remote
cabling system for time critical
events such as injection.
Non HP / Compaq Computers
The Agilent ChemStation has
been designed to successfully run
on a wide range of compatible
personal computers equipped
with accessories and peripherals
that adhere to the programming
standards for the Intel PC platform and Microsoft Windows
operating systems.
Agilent Technologies has tested
the Agilent ChemStation software
mainly on HewlettPackard/Compaq equipment. All
configuration information listed in
this manual applies to HewlettPackard/Compaq Kayak, Vectra
and EVO computers and may not
be optimized for other vendor's
PCs. The standard configuration
of the GPIB interface, for
instance, may conflict with the
Minimum PC Configuration
Windows XP and Windows
2000 based systems:
• Hewlett-Packard / Compaq PC
with Pentium III*, 600 MHz
• XGA display (1024x768
• 8 GB hard disk
• MS Windows compatible
pointing device
• 10/100 baseT LAN interface
Minimum Memory
• 256 MB RAM for 2D or 3D,
single or multiple instrument
• 256 MB RAM for configurations
running additional applications
e.g. ChemStore
* Agilent supports the use of hyperthreading on Pentium IV or higher PC's running
Windows XP.
memory configuration of a
non-HP /Compaq computer.
Additional accessory interface
boards may cause conflicts of
hardware related resources
(I/O ports, interrupt settings,
DMA channels). For a non-HP/
Compaq computer, use the setup
utility program supplied by the
manufacturer to configure your
computer and check the supplied
documentation to eliminate
resource conflicts in your PC's
setup, especially regarding the
configuration of the GPIB interface. Although the software is
also designed to be run on other
compatible hardware Agilent
Technologies will not necessarily
accept responsibility for defects
solely observed and reported on
third party hardware.
Recommended PC Configuration
Windows XP and Windows
2000 based systems:
• Hewlett-Packard / Compaq
Vectra VL420 or Evo D510 or
comparable Intel based PC
model Pentium IV or higher*,
1.5 GHz or higher
• XGA display (1024 x 768
• 256 MB RAM or higher
• 20 GB hard disk or higher
• MS Windows compatible
pointing device
• 10/100 baseT LAN interface
* Agilent supports the use of hyperthreading on Pentium IV or higher PC's running Windows XP.
LC/MSD ChemStation Minimum PC Configuration
A distinct set of hardware specifcations and requirements exists
for LC/MS ChemStation systems
running an SL MSD and using the
fast scanning feature. The software requires data system components with the following minimal
specifications for Windows XP or
Windows 2000 based systems:
• Hewlett-Packard / Compaq PC
with Pentium III*, 800MHz
• XGA display (1024x768
• 15 GB hard disk
• MS Windows compatible
pointing device
drive (minimum 4x speed)
• A 10/100 baseT LAN interface
• 256 MB RAM
• A PCI interface bus for the data
acquisition interface
• A 10/100 baseT LAN interface
• Audio card or integrated audio
* Agilent supports the use of hyperthreading on Pentium IV or higher PC's running
Windows XP.
Maximum Instrument Configurations
A maximum of four instruments
may be configured per Agilent
• A maximum of two diode array
detector instruments may be
configured per PC. If two
diode array detector instruments are configured in addition to ChemStore the configuration requires a PC with at
least 512 MB RAM and a 1 GHz
Pentium processor.
• A maximum of one VWD
module, one pump module and
one autosampler module are
allowed per instrument on a PC
with four instruments configured.
• A maximum of three instruments are supported per PC
when ChemStore is installed.
• No additional instruments are
supported beyond one Agilent
1100 or one 1090 Series II
HPLC when an Agilent 1100
Series LC/MSD module is configured.
modules are counted as 2 modules: Agilent 1100 DAD, Agilent
1100 FLD, Agilent 1100 VWD and
the Agilent 6890 GC. Please contact your Agilent Technologies
representative to determine
whether configurations approaching this 12 module limit are possible.
There is also a limitation on the
total number of analytical modules that can be connected to an
Agilent ChemStation PC.
Generally a maximum of 12 instrument modules can be configured
but this is dependant upon the
exact configuration. The following
For correct configuration of specific instruments and modules
please contact your Agilent
Technologies representative.
IEEE-488 GP-IB Support Matrix
Instruments Supported on
Agilent 6890 Gas Chromatograph
Agilent 5890 Gas Chromatograph
Agilent 1090 Series LC systems
82350A/B GP-IB Interface
Analytical instruments that communicate with the Agilent
ChemStation via GPIB require a
GPIB board to be installed in the
computer. Agilent 82350A or
82350B PCI high-performance
GPIB interface cards can be used
on Windows 2000 and Windows
XP Professional systems. For
both cards a PCI slot is required
on the PC. The Agilent 82350 is a
PCI GPIB interface card and no
additional settings such as changing the I/O base address are
required. Please note that GPIB
communication requires installation of the SICL I/O library version
L.02.01 or higher. Please ask your
local Agilent Technologies representative for additional details.
LAN-MIO Support Matrix
G1369A Agilent LAN Interface
The firmware of the card has to
be revision A.01.05 or higher. For
use only with LC systems.
J2552B/C JetDirect Internal
Printer Servers (MIO)
The firmware of the JetDirect
card has to be revision A.08.32 or
J4100A JetDirect N Internal
Printer Servers (MIO)
The firmware of the JetDirect
card has to be revision K.08.32 or
• LAN communication with the
Agilent 6890A requires
firmware revision A.03.08 or
higher. This is available in an
electronic chip format from
Agilent Technologies (Please
ask your local Agilent
Technologies representative for
details). The 6890N requires
firmware revision N.05.04 or
higher and LAN board
firmware revision 04.7B3.
• LAN communication with the
Agilent 1100 Series requires
firmware revision A.05.11 or
greater. This is available on
the Agilent ChemStation CDROM and can be updated
quickly and easily. Please ask
your local Agilent Technologies
representative for details.
Instruments Supported on
Agilent 1100 Series LC systems
Agilent 6890 Gas Chromatograph
Agilent 6850 Gas Chromatograph
Agilent 1100 Series LC/MS
Agilent 35900E A/D systems
G1369A LAN Interface Card
LAN interface cards are used to
connect analytical instruments to
the LAN. Jet Direct or G1369A
LAN cards are required. The minimum firmware required for the
G1369A LAN card is A.01.05.
Additional details are available in
the Agilent G1369A LAN Interface
LAN Configuration Requirements
Communication Protocols
Instruments are controlled over
LAN using industry standard
TCP/IP (Transmission Control
Protocol / Internet Protocol). It is
necessary to verify correct communication between the PC and analytical instruments connected over
the LAN. The Microsoft TCP/IP protocol needs to be installed and configured as a network protocol on
the PC.
The boot strap protocol is used to
configure the JetDirect or G1369A
LAN card. The Boot strap protocol
requires a BootP service. The
Agilent BootP Service uses the LAN
communication parameters specified in the Configuration Editor to
establish communication. The
Agilent BootP Service can be used
for central administration and distribution of IP addresses and settings.
Fixed IP Addresses for
IP addresses can be stored in the
non-volatile RAM of the modules.
It is possible to assign fixed IP
address to the Agilent 1100 modules, using either a handheld
Control Module or Telnet to
assign IP addresses.
Additional Hardware Required
for LAN Instrument Control
An industry standard LAN PC
card is shipped with all Agilent
ChemStation 32-Bit PC bundles.
An instrument LAN card can also
be ordered from Agilent
Technoligies as an option to the
instrument or as an individual
part. Please ask your Agilent
Technologies representative for
Twisted pair
• 10/100 baseT twisted pair
cabling with RJ45 connectors
can be used together with an
Agilent G2402A 8-port 10/100
auto sensing switch for the
ability to connect one or more
instrument to a PC.
A twisted pair 'crossover' cable
can be used to make a single connection from one PC to one
instrument. This configuration is
only suitable for single instrument
configurations. This configuration is not supported on Agilent
1100 Series LC/MSD systems.
LAN Transmission Rates
Traffic on the LAN from each
instrument is approximately
100KB per second for a 2D instrument at maximum data rate.
Industry standard LAN cabling
using twisted pair or coaxial
The Agilent ChemStation has
been designed to work with printers that are compatible with the
operating system. The software
operates with any Microsoft
Windows compatible printer
capable of interpreting an escape
code language (e.g. PCL) or page
description language (e.g.
PostScript). The printer may be
directly connected to the computer through a parallel or serial
interface or connected through a
Local Area Network. Serial port
printers are supported by the
operating system but may exhibit
speed performance limitations.
Networked printers must be
shared by a network server running a network protocol supported by the Microsoft operating system.
Recommended black and white
printers are the HP LaserJet
family using PCL 5e or 6. For
lower performance applications it
is possible to use the HP DeskJet
family. Please note that the HP
DeskJet printer family is not recommended for high throughput
Recommended color printers are
the HP LaserJet 2500TN or an HP
DeskJet family printer.
Agilent Technologies has not tested all printer and printer driver
combinations that are supported
in the Windows environment.
Print performance and results
may vary on other manufacturer's
printers and appropriate drivers.
Please note that host-based printers (e.g. GDI or PPA printers)
impose more processing tasks on
the CPU and are not recommended for use with the Agilent
ChemStation on-line sessions.
Operating System
The Agilent 32-Bit ChemStation
requires Microsoft Windows 2000
Professional with Service Pack 4
or Windows XP Professional with
Service Pack 1a.
Methods and Sequences
The Agilent ChemStation analytical method fully describes how a
particular separation is performed.
It contains all the parameters for
instrument control, data acquisition and evaluation, including
integration, quantification and
reporting. The system may be set
up to acquire data from a number
of samples by different methods.
The control file for this operation
is called a sequence and holds the
individual sample information,
references to the appropriate
methods and automatic recalibration specifications.
It allows users to define their
instruments,GP-IB addresses, IP
LAN addresses, the directories for
data, sequences and methods, and
the color definition for the
ChemStation software.
System Configuration
The configuration of the instrument system is done through the
configuration editor program.
Data Model
The ChemStation software is
designed around a data model
based on a memory structure
called a register. Registers are
multi-purpose structures that can
hold analytical data and information for both two dimensional
(e.g., time/intensity) and three
dimensional (e.g.
time/intensity/wavelength) analyses.
The ChemStation provides, commands and functions to construct,
expand, extract and, where it
does not alter primary data, edit
Registers hold information about
their contents in register headers.
The registers are further subdivided into one or more objects.
Typically an object holds data
that describes an analytical measurement, such as a chromatogra10
phy signal. Each of these objects
have their own header with information about the analytical measurement such as the data file
name, injection date and time,
sample name, and tables. Tables
are used to hold different types of
data as one block of information.
For example, the quantification
process in a calibrated method
constructs a quantification table
that contains peak numbers, compound names, compound amounts
and retention times.
Like other parts of the registers,
tables may be user-defined and
have the functionality of database
tables with the additional benefit
of being directly associated with
the base piece of analytical information from which they were
Each register may hold information for different purposes. As
well as analytical data, the register data model is used for holding
configuration information and
analytical methods. They may be
saved as files on non-volatile storage and reloaded into the
ChemStation memory, printed and
plotted to the screen or a hardcopy device. Their binary format
means they are not editable outside the ChemStation and each
data item may also be protected
by assigning access attributes to it
when it is created.
Their design fits extremely well to
modern database technology
enabling systems to be developed
to map analytical results or data
directly to a relational database
Software User Interface
The Agilent ChemStation user
interface is designed into Views
that group software functionality
according to typical analytical
tasks. Three standard views are
present in all software configurations:
• The Method and Run Control
view for controlling and acquiing data from the instrument.
• The Data Analysis view for
reviewing and re-evaluating
data that has been acquired.
• The Report Layout view for
designing specific report layouts.
Additional views are present if
additional data evaluation modules have been installed or for certain instrument configurations
that support instrument diagnostics and verification procedures.
The ChemStation Companion view
offers an easy to use interface
specifically designed for the production operator and routine labs.
Instrument operators can run samples from an easy to use, preconfigured table.
Each view consists of a set of
standard user elements including
menus and toolbars.
The standard toolbar provides
rapid access to the common system specification information
such as methods and sequences.
view additionally incorporates a
system status bar, a sample information area, that may be configured for single runs or automated
runs, and a schematic instrument
interface diagram for GC, LC,
LC/MSD configurations. The
schematic instrument interface
diagram uses hot spots to allow
rapid access to instrument parameters and an animated graphical
overview of the status of each
analysis as it proceeds. The
schematic instrument diagram
may be turned off if it is not
required, to save memory and
other Windows resources.
The Data Analysis view extends
the standard toolbar to specific
data analysis modes including
integration, calibration, reporting,
annotation, signal comparison and
additional specialized modes if the
appropriate modules are installed.
Each of these separate data analysis modes are supported with a
mode-specific toolset.
The Report Layout view allows
the user to graphically define the
layout of a specific report style in
a graphical object orientated fashion. It too uses a set of toolbars
specific to this task.
The Method and Run Control
Data Acquisition
The status of the instrument is
continually monitored and updated on the display, along with
the elapsed run time of the analysis, both when the software is a
visible window and when it is
iconized. The transactions that
occur during the analysis, including any errors and the instrument
conditions at the start and the end
of the analysis, are recorded in
the system's logbook, an extract
of which is stored with every data
The instrument conditions, such
as flow, temperature, pressure and
solvent composition for liquid
chromatographs may be recorded
and stored with each data file.
These instrument parameters can
be displayed and plotted to testify
to the quality of each analysis.
The exact nature of the parameters recorded depends both on the
technique and the capabilities of
the configured instrument.
One or more display windows
may be used to monitor the data
being acquired by the instrument
in real time. The data are displayed in real measurement units
such as mAU, Volts, degrees or
bar. The windows may each show
multiple overlaid chromatographic signals or instrument parameters, such as pressure. The display
default settings may be adjusted
and are remembered by the system so users can set their own
preferred settings as the instrument default. The window has
zoom capability and the cursor
may be used to display a specific
signal’s response at any point in
The complete functionality of the
ChemStation can be used during
an analysis with an off-line copy
of the software.
A snapshot command is available
for users who wish to start processing data before the analysis is
The layout of the signal and status
information windows, including
the components of the schematic
instrument interface diagram, is
saved automatically.
Data Analysis - Display
The data analysis view extends
the standard tool bar with taskgrouped data analysis functions
including integration, calibration,
reporting, annotation and signal
comparison toolsets. The following key graphical operations are
• Single or multi-signal displays
selectable when loading the
• Overlays of chromatograms
from different samples.
• Subtraction of one chromatogram from another.
• Graphical vertical and horizontal alignment of signals to help
visual comparison.
• Signal inversion or mirroring to
help visual comparison.
• Graphical zoom and scrolling
• Adjustment of display attributes
including selection of tick
marks, baselines, axes, retention times and compound
names. The user can also select
the font for the RT and com-
pound labels, adjust the size
and orientation of the display,
select the display as overlaid or
separated and select scaling
The chromatogram display may
include graphical overlays of
instrument parameters depending on the capability of the configured instrument.
User defined annotations may
be interactively added to the
display, with the selection of
font, size, text rotation and
color. Once defined, the annotations may be graphically
moved, edited or deleted.
Copy the display to the
Windows clipboard in both
metafile and bitmap format.
A Pick Mode function to display
the values of individual data
points in detector units.
Export of time/intensity digitized points to the Microsoft
Windows clipboard.
Display of fraction results in
graphics and table format
Data Analysis - Integration
The Chem32 integration algorithm
used in the 32-Bit ChemStation is
the second revision of a new generation integrator offering
improved ruggedness, reliability
and ease-of-use.
Integrator Capabilities
The integrator algorithms include
the following key capabilities:
• an autointegrate capability used
to set up initial integrator parameters,
• the ability to define individual
integration event tables for
each chromatographic signal if
multiple signals or more than
one detector is used,
• interactive definition of integration events that allows users to
graphically select event times,
• graphical manual or rubberband integration of chro-
matograms requiring human
interpretation (these events
may also be recorded in the
method and used as part of the
automated operation),
display and printing of
integration results,
the ability to integrate at least
1000 peaks per chromatogram.
integrator parameter definitions
to set or modify the basic integrator settings for area rejection, height rejection, peak
width and slope sensitivity,
baseline control parameters,
such as force baseline, hold
baseline, baseline at all valleys,
baseline at the next valley, fit
baseline backwards from the
end of the current peak,
area summation control,
negative peak recognition,
tangent skim processing
including solvent peak definition commands,
the ability to define individual
front/tail tangent skim calculations event tables for all chromatographic signals,
the ability to use baseline correction parameters (non signal
integrator control commands
defining retention time ranges
for the integrator operation.
peak shoulder allocation
through the use of second
derivative or degree of curvature calculations, and
improved sampling of nonequidistant data points for better performance with DAD LC
data files that are reconstructed
from DAD spectra
Data Analysis - Quantification
The Agilent ChemStation’s calibration mode of the data analysis
view allows simultaneous display
• the signal or signals being calibrated with an indication of the
current compound’s retention
time window,
• the calibration table whose display may be configured from a
comprehensive selection of calibration parameters, and
• the calibration curve for the
compound being calibrated.
All the calibration mode windows
are linked so that changes in one
are automatically reflected in all
the others. This mode allows
graphical selection and modifications of the calibration data.
Quantification is based on %,
Normalized %, External standard,
External standard %, Internal
standard and Internal standard %
calculations calculated on either
peak area or height. Calibrations
may be multilevel and include
multiple internal standard definitions. Calibration histories are
automatically saved and can be
used to weight the recalibration
The following calibration point
weighting options are available:
Equal – All calibration points
have equal weight in the curve.
Linear (Amnt) – A calibration
point with the amount x has the
weighting 1/x normalized to the
smallest amount so that the
largest weight factor is 1.
Normalization is done by multiplying the weight with the smallest
amount. For example the weight
of a calibration point with the
amount x is (1/x) x a where a is
the smallest amount of the cali-
brated compound prepared in the
calibration standards. If the origin
is included it is assigned the mean
of the weightings of the other calibration points.
Linear (Resp) – A calibration
point with the response y has the
weighting 1/y normalized to the
smallest response so that the
largest weight factor is 1.
Normalization is done by multiplying the weight with the smallest
response. For example the weight
of a calibration point with the
amount y is (1/y) x b where b is
the response corresponding to the
smallest amount of the calibrated
compound prepared in the calibration standards. If the origin is
included it is assigned the mean of
the weightings of the other calibration points.
Quadratic (Amnt) – A calibration point with the amount x has
the weighting 1/x2 normalized to
the smallest amount so that the
largest weight factor is 1.
Normalization is done by multiplying the weight with the smallest
amount. For example the weight
of a calibration point with the
amount x is (1/x2) x a2 where a is
the smallest amount of the calibrated compound prepared in the
calibration standards.
Quadratic (Resp) — A calibration point with the response y has
the weighting 1/y2 normalized to
the smallest response so that the
largest weight factor is 1.
Normalization is done by multiplying the weight with the smallest
response. For example the weight
of a calibration point with the
response y is (1/y2) x b2 where b
is the response corresponding to
the smallest amount of the calibrated compound prepared in the
calibration standards.
# Calibrations – A calibration
point is weighted according to the
number of recalibrations of the
point. No normalization is done.
The origin of the calibration curve
may be specified as
• ignored — the origin (0,0) is not
used in the curve calculations,
• included — the origin is used as
one of the calibration points,
• forced — the curve is forced
through the origin, and
• connected — the linear segment
is constructed between the origin and lowest calibration point
on the curve.
are indicated on the appropriate
analysis report. They may be used
in conjunction with the control
samples that can be defined as
part of the automation setup, to
verify the performance of the system running automatically.
The ChemStation can calibrate
methods with up to 1000 peaks
and 2000 calibration points. This
means, for example, with 1000 calibrated peaks only two calibration
levels may be defined for each
peak. With fewer peaks more levels may be defined in proportion
to these limits (for example, 100
compounds could have 20 levels
The group calibration capability
allows the user to group calibrated peaks into a named group and
report quantitative results for both
the individual group members and
the group itself.
Compound identification may be
refined by defining individual
retention time windows’ parameter limits and qualifier peaks.
Qualifier peaks are usually the
same compound detected on a different signal with a predictable
response ratio. They are used as a
further check on peak identification rather than just relying on
retention times.
Each calibrated compound may
have individual absolute limits for
the amount, peak area, peak
height, symmetry, efficiency in
plates, resolution and k’. Results
lying outside any defined limits
Data Analysis - Standard Reporting
A standard set of user definable
report styles for sample reporting
are selectable from the report
specification screen. Every standard report type contains standard
information groups and a series of
optional information groups.
The standard groups include
• A header with the originating
data file and sample name.
• A footer with the instrument
name, operator name, print
time and page number in ‘page
x of y’ format.
• A sample information block that
includes sample name, vial
number, method and sequence
information, operator and
instrument name and sample
information text.
• A quantification results table
containing retention times and
the integration or quantification
table depending on the calculation scheme chosen. This table
can be formatted either by
retention time or by signal.
Users may select from a series of
optional information groups by
specifying a particular style for
the analytical report. These groups
• A front page that can include
user-defined text.
• Repetition of the sample information block on every page.
• Instrument conditions.
• The analytical column for LC
and LC/MSD systems.
• The run logbook.
• The chromatogram with annotation options that include selection from peak retention times,
compound names, tick marks,
baselines and axes. The user
may also select the annotation
fonts, graphical orientation, size
and whether the graphics are
overlaid or separated. If the
ChemStation is connected to
instruments that can record
instrument parameters as a signal, such as temperature, flow
and pressure, the user may also
select to include these graphics
in the report.
• Calibration table and calibration
Reports may be output to either
the screen, printer or to file.
If the screen is selected as the
report destination,, the report
together with graphics will be displayed in the Report Preview windown from which it can be printed.
Report File Formats
A report can be saved in four different formats. Each format has a
specific extension. It is possible to
select more than one format for a
.TXT – The report text is printed
as an ASCII text file.
.WMF – Each report graphic (signal or calibration curve) is saved
in a Microsoft Windows metafile
(WMF). Several .WMF files for one
report are possible. The generated
file format adheres to the
Microsoft standard metafile format as defined in the Windows
software development documentation. These files are compatible
with the Aldus Placeable Metafile
(APM) format used by a number
of proprietary software packages.
.DIF – The tabular report data is
saved in Data Interchange Format
(DIF). This format is accepted by
spreadsheet programs such as
Microsoft Excel. Independent
from the report style selected,
only the information contained in
the report style Short will be
.CSV – The report is in Comma
Separated Values (CSV) format.
This is a very simple format for
tabular data that is accepted by
many spreadsheet programs and
databases. Independent from the
report style selected, only the
information contained in the
report style "Short" will be saved.
There can be several .DIF and
.CSV files for a single report. For
each report block, the first file, for
example, REPORT00.CSV, contains the report header information. Subsequent files contain the
tabular results. If the results are
sorted by retention time, only one
file is required for the complete
table, for example,
REPORT01.CSV. If the results are
sorted by signal, a separate table
is required for each signal. In this
case, the files are named
Report01.CSV through
ReportNN.CSV, where NN is the
number of the signal.
.XLS – The report is exported to a
Microsoft Excel spreadsheet in
(XLS) format. The
data generally requires additional
.HTML – Results are saved in
Hypertext markup language for
viewing in web browsers.
Data Analysis - Specialized Reporting
Advanced reporting capabilities
are also included in the 32-Bit
ChemStation for users who
require a more specialized set of
reports. These include statistics
on separation quality, reports that
include trend analyses between
samples and user-defined report
from the performance report style.
The noise parameters are reported
as a signal-to-noise ratio for each
peak or calibrated compound and
a noise table for each signal. Each
noise table includes noise calculated by the six times standard
deviation, peak to peak and ASTM
methods as well as the wander
and drift.
System Suitability Reports
System suitability reports enable
users to report system performance parameters for individual
analyses. There are three variations, or styles of these reports.
The Standard Performance report
prints parameters for uncalibrated
methods that include
• retention time,
• capacity factor, k’,
• peak area,
• peak height,
• symmetry,
• true peak width at half height,
• efficiency in plates,
• resolution, and
• selectivity.
For calibrated methods the compound name and amount replace
the peak area, height and selectivity columns.
The report header includes the
standard header and footer, sample information block, the analytical column parameters and
optionally a plot of the chromatogram.
The Extended Performance style
adds plots of each individual peak
showing graphically the peak start
and stop times, half width and
baseline. This style includes the
following parameters in addition
to the ones reported by the standard performance reports:
• area, height and amount,
• skew,
• excess,
• USP tailing factor,
• time interval between data
points and number of data
points over the peak,
• statistical moments (M0 to M4),
• peak width at half height calculated by the true, five sigma,
tangent and tailing methods,
• plate/column and plates/meter
calculated by the peak width at
half height, five sigma, tangent
and statistical methods.
Users may define their own noise
evaluation ranges and acceptable
limits for these performance criteria. Values lying outside the userdefined acceptable limits are indicated on the report.
Sequence Summary Reports
The Performance and Noise style
adds an evaluation of the signal
noise, in up to seven user-defined
evaluation ranges, to the data
Sequence summary reports are
produced at the end of a series of
automated analyses. Their range
of application is from a brief summary of the samples analyzed to a
detailed graphical repeatability or
trend analysis of user-selectable
parameters between different
samples analyzed by the same
method. The reports are built up
from nine optional categories of
• a header page that may be user
• the instrument configuration
including revision numbers and
analytical column for LC and
LC/MSD systems,
• the list of samples scheduled for
analysis; the sequence,
• the logbook printout which
states what was analyzed and
documents the data acquisition
and processing steps as well as
any unexpected events,
• a printout of the analytical
• individual sample reports,
• statistics on calibration samples,
• statistics on unknown samples,
• a summary page that may be
either a sample summary, one
line of information per analysis,
or a compound summary with a
short compound summary table
in addition to the sample summary.
The statistical reports may be
selected as standard or extended
styles. The Standard Style is textbased and includes the mean,
standard deviation (SD), relative
standard deviation (RSD) and
standard error for the following
parameters tabulated by compound:
retention time,
peak width, and
peak symmetry.
The Extended Style includes
graphical trend analyses based on
a selection of parameters for statistical evaluation. The parameters
that can be selected include
• retention time,
• area,
• height,
• amount,
• peak width at half height, by the
sigma, tangent and tailing methods,
• peak symmetry,
• tailing factor,
• capacity factor, k’,
• theoretical plates by the peak
width at half height, sigma, tangent and statistic methods ,
• resolution by the peak width at
half height, sigma, tangent and
statistic methods,
• selectivity,
• skew, and
• excess.
Technique specific parameters for
liquid chromatography include:
• peak purity evaluation factors
(with the diode-array spectral
evaluation module only), and
• spectral library comparison factor (with the diode-array spectral evaluation module only).
The report includes a separate
graphical trend analysis for each
selected parameter. Sequence
summary reports may be output to
the printer, to file or both. The
user may select to either print or
suppress individual analysis
reports together with the
sequence summary.
Customized Reports
A customized reporting design
view is included in the ChemStation for users who want to
define the exact content of their
own reports. The user graphically
defines a report layout which may
include general sample information, signal, integration and quantitative analytical result information. The user may define individual elements, such as text, tables
and graphics, organize them in
sections and graphically adjust the
relative position, size and orientation of each defined element. The
individual sections may be added,
deleted, re-ordered and nested.
The user may define headers and
footers to appear on every page,
time stamps for the report and
page numbering in the ‘page x of
y’ format. The information included in the report may be any
ChemStation or user-defined parameter.
Once the report has been designed
it may be associated with a particular method to make it the default
report format for that particular
type of analysis.
Customized reports may be output
to the screen, a printer or a file.
Reports to the screen include
Control Chart Reports
A Control Chart feature is included with the ChemStation software.
Once this feature is installed and
selected, the user may automatically track a selected parameter of
a compound each time a method
is run. These parameters include:
Amount, Response Factor,
Utilities and Compatibilities
The ChemStation can import and
export data files in the ANDI
(Analytical Data Interchange)
chromatography format of the
Analytical Instrument Association
(AIA), revision 1.0, copyright 1992.
Data import is supported at com-
pliance level one (sample information and signal data) and data
export at compliance level two
(sample information, signal data
and integration results).
The ChemStation includes commands and functions to support
the Dynamic Data Exchange
(DDE) standard of the Microsoft
Windows platform as both a DDE
client and a DDE server. The command set includes commands to
establish and terminate connections, transfer information in both
directions and execute remote
Data Analysis - Integration
All files (data files, methods,
sequences, log files etc) created
on previous ChemStation Rev
A.xx.xx systems can be loaded
and used in the new 32-Bit Rev
B.01.0x ChemStation. The Rev
B.01.0x system converts Rev
A.xx.xx files to a new structure
during saving. The new structure
is not compatible for use with
older Rev A.xx.xx systems and the
system will warn users to save
files with a new name when performing the one-time conversion
in the new system. To maintain
backwards compatibility it is recommended to save converted files
with a different name to the original Rev A.xx.xx file. This pre-
serves the original Rev A.xx.xx
file which can continue to be used
with ChemStation Rev. A.xx.xx
systems if desired.
To connect the ChemStation to a
Laboratory Information
Management System (LIMS) or
Knowledge Management System
(KMS) the ChemStation offers an
interface based on the standardized XML format. The interface
allows manual import of sample
data into the ChemStation
sequence. This process can be
automated using the ChemStation
macro language. In addition the
interface allows manual or fully
automated export of sample and
result information. The XML
schema files provided with the
software allow an easy adaptation
of the interface for a specific LIMS
or knowledge Management system. More information is available
in the Agilent ChemStation XML
interface users guide (Agilent Part
Number G2170-90221).
XML Interface
XML (eXtensible Markup
Language) is a protocol for structuring data in pure text format; the
XML file contains data with
embedded structural information
and, being pure text, it can be edited with a simple editor like
Notepad. XML has become a very
flexible and portable format especially for exchanging data between
different systems.
The ChemStation can be customized using a powerful command
set . These commands may be
grouped to automatically execute
a specific function; such a group
is called a macro. Users writing
macros may define their own variables, build in conditional or looping constructs, perform physical
I/O including file handling and
user interaction, nest their
macros and schedule and
exchange data with other MSDOS or Microsoft Windows applications.
More information on customization is available in the Macro
Programming Guide within the
Agilent ChemStation online help.
The ChemStation can execute
multi-method sequences.
The sequence parameter set may
be defined to use automatically
generated files or sequentially
numbered files with a user-defined
prefix of up to fifteen characters.
The user may select to run full
analyses or data reprocessing only
sequences and can also select one
of a series of technique specific
shutdown commands or a userdefined shutdown macro that runs
when the sequence terminates
either by error or after all the
analyses are completed.
The sequence table, or list of
analyses to run, is built in a
spreadsheet-like user interface
that allows users to specify vial
numbers and sample names,
analysis methods, sample quantification parameters including sample amount, a multiplier and dilution factor, calibration specification, a data exchange parameter
(LIMSID) and the number of
repeat injections. Depending on
the configured instruments and
modules, additional fields will
accessible. For example if an
Agilent 1100 LC system includes a
fraction collector the "Fract. Start"
colum will appear in the sequence
table. The user can configure the
columns to be displayed in the
sequence table as well as the individual column widths. The user
can jump between individual cells
in the table and copy, cut or paste
individual cells or entire rows or
series of rows in order to build
sequences efficiently and quickly.
A sequence table can easily be
created or changed using the filldown wizard function. The
sequence import wizard allows the
import of sequences from any
kind of delimited text file.
Samples may be identified in the
sequence table as unknowns, calibration or control sample types.
The sample type determines any
special data evaluation treatment
of the sample:
• Unknown samples are evaluated and reported according to
the method specification,
• Calibration samples are used to
recalibrate the quantification
component of the method as
described below, and
• Control samples are evaluated
against the limits for each component defined in the method.
If the results lie outside any
specified parameter range the
execution of the sequence will
be halted.
Calibration samples may be
defined as simple, cyclic or bracketed. Simple recalibrations mean a
recalibration occurs each time a
calibration sample is defined in
the sequence. Cyclic recalibrations occur at defined intervals
during analysis of a series of
unknowns. In bracketing a series
of unknown samples are analyzed
between two calibration sets. The
quantitative reports for the
unknown samples are then calculated using a calibration table
averaged between the two calibration sets.
The partial sequence functionality
allows users to see the order of
execution of the sequence and
also select individual sample
entries to rerun or re-evaluate.
When re-evaluating data already
acquired users can specify
whether reprocessing uses the
original sample quantification data
or new data entered in the
sequence's sample table.
Sequences may be paused to run
single injection priority samples
by another method then restarted
without disrupting the automation.
Samples can be added to the
sequence table while the sequence
is executing.
Both the sequence and partial
sequence tables may be printed.
Batch Review is an additional
mode of data analysis that provides automation by allowing a
fast and easy first-pass review of a
batch of samples. The batch consists of all or a selection of runs
from a sequence. You can check
the calibration accuracy and the
individual integrations before
approving the results. All chromatogram-specific modified integration parameters can be saved
for data traceability. Once data is
accepted the entire batch can be
reprocessed to generate reports
with one keystroke.
Good Laboratory Practice
The 32-Bit ChemStation is developed to internationally recognized
design and development standards
and has a number of features
specifically to help users operating in a regulated environment.
These features help users validate
and specify methods, verify that
methods are fit for their intended
use, verify system performance
and operation and ensure the
traceability, integrity and security
of the data.
Development Process
The Agilent Certificate of
Validation shipped with each software package documents the software development and testing
steps executed as part of the
development cycle. The development process is registered to the
ISO 9001 quality standard. It is
documented together with on-site
revalidation protocols in the validation CD-ROM.
Method Specification and Use
• Global methods — the complete
instrument and data analysis
specification is stored in one
place. Methods include individual compound range specifications to check that quantification results are not applied outside the calibrated range.
• The method change history log
allows users of a validated
method to automatically record
how and when a method was
changed. Users may add a reason for the change to the
change history log. The change
history log is automatically
stored as part of the method. To
prevent unauthorized access to
the records it is protected by
the user access scheme,
described below. The change
history log may be viewed and
• Limits may be assigned on a
compound-by-compound basis
in each method for a number of
chromatographic and system
performance parameters, as
described in the data analysis
quantification section. Results
exceeding these parameter
ranges are used to control the
execution of automated
sequences as described in the
automation section. They are
indicated on the appropriate
analysis report.
• System performance or suitability reports (see ‘Reporting’ sections ) provide detailed analysis
of the separation quality.
• The ChemStation may be configured for restricted access
through two user access levels,
an operator and manager level.
The manager level may be password protected and allows
access to the complete ChemStation functionality. The operator level restricts the user to
key functionality and to executing defined analytical methods.
The operator level is intended
for use in routine laboratories
and specifically prevents users
from modifying and creating
new methods.
Method Robustness
Sequence summary reports (see
section “Data Analysis Specialized Reporting” provide a
means to test methods for robustness. The extended format reports
for user-selected criteria are
reported as trend charts and may
be used to determine the realistic
operation limits. These limits can
then be incorporated in the
method to ensure, through the
analysis of control samples, that
the method is operating within
System Operation
The ChemStation software verification kit, that is part of the standard software, automatically
checks for the correct operation
of the data evaluation parts of the
software by comparing results
generated when a test is executed
against pre-recorded known values. The verification test allows
users to define their own data files
and methods to be the basis of the
Data Traceability, Integrity and
• The run-time logbook provides a
transaction log of the complete
system. It also records any
unusual events (such as errors
or parameter changes made
during a run), as well as the
instrument conditions before
and after each analysis. A copy
of the relevant logbook extract
is saved with each data file.
• The actual instrument conditions, such as pressure, flow,
and temperature, that occurred
during each analysis are also
recorded if the configured
instrument supports this capability. This data can be subsequently displayed graphically
with the chromatogram to show
the actual instrument conditions during that particular
analysis. These graphics may be
included on each report.
• Methods saved with the data file
record the actual method at the
time of the analysis and allow
the complete reconstruction of
the reported data at a later
date. The method is saved at
the completion of all the analytical steps.
• All reports have time stamps
and traceable page numbering
(‘page x of y’ style). The user
may select the level of detail in
each report ranging from simple
summary reports to complete
system details (see Reporting
• GLP save register files, specified
as part of the method configuration, save all the original data
including sample information,
data analysis method, chromatographic signals, instrument
conditions, integration and
quantification results, report
data and the run logbook in one
checksum protected binary file.
This is an uneditable binary format that ensures the integrity of
the results. The file includes a
revisioning scheme that indicates if data has been
• Control sample types may be
defined in the sequence table
and used to automatically
check the instrument performance against quality control
sample results when the instrument is running unattended.
Results that are outside the
user-specified acceptable range
will stop the automatic execution of the instrument.
• Data security is achieved in the
PC environment through password protected PCs, software
locks built into both Microsoft
operating systems and secure
(password-protected) networks.
Instrument Control
The instrument control capabilities of the Agilent ChemStation
may be expanded through the purchase of additional instrument
modules to allow multiple instrument, mixed technique configurations.
The instrument control capabili-
ties are documented in the following sections, each relating to a
specific technique.
In addition to GC control the following features are noted:
• Graphical user interface for
easy access to all method areas
for all Agilent GCs
• Table driven system scheduler
which permits clock time programming for all Agilent GCs.
Quick Method allows the
Agilent Series 6890 and Agilent
6850 GC user to enter a limited
number of setpoints from
which the Agilent ChemStation
will create a method.
• Method resolution in the
Agilent ChemStation
(Agilent 6890 and Agilent 6850
Series only) will verify and alert
the operator of potential
problems if a method was
created on a different GC
system or if the configuration
has changed.
• Capillary columns can be
calibrated from the ChemStation
trol, through a timetable, a maximum of eight valves or relays.
Agilent ChemStation for GC
Instrument Control and Data
Acquisition with the Agilent
ChemStation for GC
(G2070BA) and the Additional
GC Instrument Module
The Agilent ChemStation for GC
combines instrument control, data
acquisition, and data analysis software for the Agilent 6890, 6850,
5890 Series II, and 4890D gas
chromatographs and the Agilent
35900E A/D converter.
The Agilent ChemStation is interfaced to the GC via GP-IB, or LAN
and collects full range digital data
from detectors. Depending on the
detector type, data can be
acquired at rates up to 20 Hz from
the Agilent 5890 and Agilent
4890D Series and up to 200 Hz
from the Agilent 6890 and Agilent
6850 Series.
When interfaced to an Agilent gas
chromatograph, the Agilent
ChemStation can control GC
parameters for heated zones,
oven temperatures, detectors,
inlets, cryogenic cooling, signals,
electronic pressure and flow control, and cool on-column temperature programming.
The Agilent ChemStation can display graphically the oven temperature, inlet temperature, inlet pressure, auxiliary channel pressure
and column flow programs. The
Agilent ChemStation also can con-
The Agilent 7673 and Agilent 7683
Series automatic samplers allow
for complete automation of sample introduction in single front,
single rear or dual-injector configurations.
Dual-injector configurations
(Agilent 6890 Series, 5890 II, and
4890D GCs) allow individual or
synchronous injections. Each
automatic sampler allows a 3-vial
turret, 8-vial turret, or 100-vial
access if a sample tray is fitted.
(6890 and 5890 Series only). The
6850 GC also supports the
G2880A 22/27 positions tray. The
Agilent ChemStation allows random sample access and priority
sample injection.
The following autosampler parameters may be controlled:
• number of syringe pumps
• number of syringe washes
• the injection volume
• the bottle number for each
a viscosity delay
on-column injection setup
syringe size
depth of needle penetration
multiple injections per run in
cooperation with PTV for large
volume injection
For the Agilent 7683 Series,
plunger speed may be
controlled from a maximum of
100 µl/sec to a minimum of
5 µl/sec when using a 10 µl
For the Agilent 7683B, larger
turret for 2x increase in solvent
and waste capacity (6890, 6850
For the Agilent 7683B, solvent
saver made for 4x increase in
solvent usage (6890, 6850 only).
For large volume injections a
100-µl syringe can be used with
the Agilent 7683 Series.
The Agilent ChemStation allows
the user to optionally display a
Sampling Diagram window containing a graphical display of the
one hundred vial tray, indicating
which samples have already run,
which sample is currently running,
and which samples will be run.
The G1926A bar code reader
attachment is supported in the
100-vial tray configuration of the
autosampler. The bar code reader
can be used to help build automation sequences and verify that the
identity of the injected sample
matches the name in the sequence
table at injection time.
The new G2615A bar code reader
is used with the 7683 automatic
liquid sampler tray.
The Agilent ChemStation can
acquire a third and fourth signal
from external detectors in a single
run by adding the 35900E A/D
Agilent GC ChemStation
The Agilent ChemStation
Companion provides the user with
a simple single-screen user interface for GC routine analysis. In
the Companion View, the user is
limited to selecting pre-programmed samples, methods, vial
numbers, and run control. Users
cannot modify or create any methods or run any methods or samples
not assigned to them by their lab
manager. The Agilent ChemStation
Companion is installed automatically during the GC ChemStation
Retention Time Locking
Retention Time Locking (RTL)
software, product number
G2080BA, is an add-on to the
Retention Time Locking (RTL), is
a useful technique developed by
Agilent Technologies to match
analyte retention times between
and among Agilent GC systems.
RTL is essentially based on voidtime matching through an empirically determined pressure-retention time calibration curve. RTL
calibration curves are specific to
the analyte chosen (pick one analyte in your standard, the best
choice is a peak well separated
from other peaks and in the mid-
dle portion of the chromatogram),
type of column used (stationary
phase type, phase ratio, and column dimensions), carrier gas type,
and oven temperature program
used in the method. Once the calibration has been done for an initial (“original”) method, the
method and its associated RTL
calibration can be transferred to
another instrument with the same
column type and carrier gas type.
RTL software in Agilent
ChemStations assists with the
process of determining and using
RTL calibrations.
To lock a new system to the original system, carrier gas head pressure is adjusted using the RTL calibration curve. The retention time
of a target compound (same one
used to generate the RTL calibration) can be locked onto the
desired retention time value. All
other analyte retention times will
then also match those of the
RTL software also provides the
capability to search retention
timetables. Searching unknowns is
based primarily on retention times
and may also include element
information (such as one might get
from selective detectors) to narrow search results further. Users
can create, edit, import and export
RTL libraries.
The RTL Pesticide Library, product number G2081AA, includes the
retention times for pesticides and
suspected endocrine disrupters.
To use this library, the RTL software product G2080BA must be
installed. Peak identification is
performed by comparing the retention time of the unknown peak
Agilent ChemStation for LC Systems
Instrument Control and Data
Acquisition with the Agilent
ChemStation for LC Systems
(G2170BA) and the Additional
LC Instrument Module
The Agilent ChemStation for LC
and additional LC instrument
module controls and acquires data
from the Agilent 1100 Series modules and systems for LC, the HP
1090 Series liquid chromatography
systems with either the filter photometric detector (FPD) or built-in
diode-array detector (DAD), the
stand-alone HP 1040 diode-array
detector (DAD) and the Agilent
35900E dual channel interfaces.
All the sampling, pumping and
detector options of the Agilent
1100 Series modules and systems
for LC, and the HP 1090 Series
liquid chromatographs can be
Sampling Systems
The injection systems may be
manual or automated with an
autosampler or well-plate autosampler. All automatic injectors
may be programmed for different
injection volumes, the speed of
injection and the injector wash
procedure. The user may also specify a complete injector program
for sample dilution, standard addition or sample derivatization. The
commands available for the injector program include draw, eject,
mix, wait, inject, sampler valve
and column switch control. These
can be defined in conjunction
with the sample, a vial/well-plate
offset from the sample, a numbered vial/well, waste and air.
The Agilent bar code reader is
available for selected autosampler
configurations. It can be used to
help build automation sequences
and verify the identity of the
injected sample matches the name
in the sequence table at injection
time. In LC configurations it can
also be used to mix liquid samples
as a step in an injection program.
The following Agilent 1100 injection systems are supported:
• Standard autosampler
(G1313A / G1329A)
• Thermostatted standard
autosampler ( G1327A)
• Well-plate autosampler (G1367A)
• Thermostatted well-plate
autosampler (G1368A)
• Thermostatted micro
autosampler (G1378A)
• Micro well-plate autosampler
• Thermostatted micro well-plate
autosampler (G1378A)
• Preparative autosampler
• Thermostatted preparative
autosampler (G2261A)
• Agilent sample capacity
extension (G2257A) for the 1100
Series well-plate sampler
G1367A and micro well-plate
sampler G1377A
• Agilent dual loop autosampler
• Agilent thermostat option
(G1330A / B)
• Agilent fraction collectors
(G1364A / B / C / D)
• Agilent 1100 Series barcode
reader (G2256A) for the sample
capacity extension G2257A
Solvent Delivery Systems
All the solvent delivery systems
have a set of initial parameters,
including pressure limits, initial
flow and composition, that are
complemented by a time-table for
programming changes in flow,
composition and pressure limits.
These parameters can be viewed
graphically. Users can define a
postrun time for column equilibration.
The following Agilent 1100 solvent delivery systems are supported:
• Isocratic pump (G1310A)
• Binary pump (G1312A)
• Quaternary pump
(G1354A / G1311A)
• Preparative pump (G1361A /
G1391A with gradient
• Capillary pump
(G1376A pump only / G1382A
with degasser)
• Agilent 1100 nanoflow pump
(G2226A pump only / G2225A
with degasser)
Column Compartments
The Agilent 1100 Series thermostatted column compartment
can be set between 10 °C below
ambient and 80 °C. The temperature is programmable during the
run through a timetable. The
HP 1090 column oven temperature can be set to a constant temperature (20 °C above ambient to
100 °C without external cooling).
Column switching valves are programmable from the software.
The Agilent ChemStation supports
external valves as well as thermostatted valves built into the column compartment.
Spectral data from all diode-array
detectors may be acquired in a peakcontrolled or full acquisition mode.
The following external Agilent
valves are supported:
• Agilent 1100 Series 2Pos/10Port
valve (G1157A)
• Agilent 1100 Series 2-positon/6port (standard) valve (G1158A)
• Agilent 1100 Series 6-position
selection valve (G1159A)
• Agilent 1100 Series 12-posi
tion/13-port selection valve
• Agilent 1100 Series 2-position/
6-port (micro) valve (G1162A)
• Agilent 1100 Series
2-position/10-port (micro) valve
The following thermostatted
valves built into the column compartment are supported:
• 2-position/6-port valve option
(G1316A# 055)
• 2-position/6-port micro valve
option (G1316A # 056)
• 2-position/10-port valve option
(G1316A # 057)
The maximum number of external
valves connected to one Agilent
1100 Series HPLC system is limited to 5 or less, depending on the
system configuration. For details
please contact your Agilent representative.
The ChemStation software can
simultaneously acquire five chromatographic and reference signals
each with an independent bandwidth from the Agilent 1100
Series diode-array detector.
The system can simultaneously
acquire up to a total of eight chromatographic and reference signals
from the HP 1090 with an independent bandwidth.
The detectors have a graphical test
for signal intensity and wavelength
calibration. All DADs may have the
initial parameters changed during
a run by a time-based program.
Users can program wavelength
and spectral acquisition mode
changes in the time table.
Initial parameters that may be
set for the DADs include signal
wavelengths and reference
wavelengths, spectral acquisition
mode, signal sampling rate and
The HP 1090 filter photometric
detector (FPD) may be programmed with parameters to set
the lamp current, response time
and the filter. The filter may be
changed during an analysis
through events in the detector's
time table. The ChemStation
includes a diagnosis screen for
testing the reference and sample
photo diode light paths in the
detector. The FPD is interfaced to
the ChemStation through the digital GP-IB interface for control and
through a dual channel A/D interface for the data acquisition (see
The Agilent 1100 Series variable
wavelength detector (VWD) may
be programmed with a single
detection wavelength. Data acquisition rates may be programmed
for peak widths from <0.12 up to
8.00 seconds. The VWD can be
programmed with a timetable to
change the wavelength and perform wavelength scans during the
course of an analysis.
The Agilent 1100 Series multiple
wavelength detector (MWD) can
simultaneously acquire up to five
chromatographic signals each
with independent reference wavelengths and bandwidths. The signal acquisition rate may be set for
peak widths between 0.1 and 16
seconds. During the course of an
analysis the MWD can be programmed with a timetable to
change wavelengths, bandwidths
and peak-widths for all five wavelengths.
The optical unit temperature of
the Agilent 1100 Series refractive
index detector (RID) can be set
between 20 and 55ºC. The signal
acquisition rate may be adjusted
for peak widths from <0.12 up to 8
seconds. During the course of an
analysis the RID can be programmed with a timetable to change
Polarity and Peakwidth of the
acquired chromatographic signal.
For diagnostic and troubleshooting
purposes, it is possible to store
Diode Signal 1, Diode Signal 2,
Optical Unit Temperature, Polarity
and the Balance Signal in addition
to the chromatographic signal.
The Agilent 1100 Series fluorescence detector (FLD) may be programmed for single wavelength or
simultaneous multiple wavelength
detection and spectra aquisition.
Up to four signals at different exitation or different emission wavelengths may be obained. Within a
timetable initial exitation or emission wavelengths, response time,
PMT Gain and baseline behaviour
as well as spectral parameters
may be changed. Exitation or
emission spectra can be watched
online and stored and analyzed as
described for DAD spectra. For a
single compound trapped in the
flow cell, complete information on
exitation and emission spectra is
available in a single task with the
fluorescence scan and can be
watched as an iso-plot or as 3Dgraphics.
The Agilent 35900E dual channel
interface allow the system to
acquire data from detectors that
are not interfaced for data acquisition through GP-IB or LAN, such
as the FPD, the HP 1047A refractive index detector or a third party
detector. One or two analog signals per instrument may be configured; if only one is used the other
is available for use with another
instrument. Data rates up to 100
Hz per signal may be defined. The
user may also define the units for
acquisition and their relationship
to the voltage signal (units/volt).
The Agilent 35900E interfaces
offer external event control
through digital TTL (transistortransistor logic) signals, each of
which are given specific state
(high and low) names, that may be
time-programmed before, during
and after an analysis. The Agilent
35900E can be configured for up
to eight signals for each independent channel.
Fraction collectors
All different versions of the
Agilent 1100 Series fraction collectors (G1364A, G1364B, G1364C,
G1364D) can be fully controlled
from Agilent ChemStation.
Fraction data can be reviewed in
the fraction task of the data analysis screen. The maximum number
of fraction collectors connected to
one Agilent 1100 Series Purification system is limited to 3 (with
the possibility for one additional
recovery fraction collector).
Depending on the system configuration up to two Purification systems can be controlled from single
ChemStation system (without
purification related software add
on). Optional add-on software, e.g.
High/Throughput Purification software (G2262AA, G2263AA,
G2265AA) or Easy Access
(G2725AA) provides advanced
Agilent 1100 Series Instrument
The Agilent ChemStation for LC
includes an instrument operational qualification and performance verification (OQ/PV) view
in which users of the Agilent 1100
Series of modules and systems
may select a series of semi or
fully-automated tests to test the
operational suitability of the LC
To perform instrument verification
it is first necessary to purchase
the relevant service from Agilent
Technologies. The required
method and sequence files will be
installed at the time of service
delivery by an authorised Agilent
service provider. Please contact
you local Agilent Technologies
representative for more details.
Agilent 1100 Series
The Agilent 1100 Series of systems
and modules for LC have an additional ChemStation diagnosis
The diagnosis view is designed to
help users identify instrument
malfunctions starting from a particular symptom. A failure of a
particular instrument verification
test will automatically identify the
appropriate symptom for the user
or the user may select the symptom interactively.
One or more possible causes is
listed for each symptom. Each
possible cause is associated with a
series of diagnostic measurements, with limits, and a series of
diagnostic tests. Users observe the
measurements and carry out the
tests in order to confirm or dismiss the possible cause of the
instrument malfunction.
Once identified, the cause of the
instrument malfunction may be
repaired by using the repair procedures given on the Agilent 1100
Series Maintenance and Repair
CD-ROM. The repair procedures
include parts and materials
breakdowns and clear animated
step-by-step graphics or video
with a sound track for each repair
procedure. The procedures are
called directly from the Agilent
ChemStation diagnostics view.
Agilent ChemStation for LC/MSD Systems
Instrument Control, Data
Acquisition, and Data
Evaluation with the Agilent
Chem-Station for LC/MSD
Systems (G2710AA) and the
LC/MSD ChemStation Add-on
Module (G2715AA)
The Agilent ChemStation for
LC/MSD systems (G2710AA) and
the LC/MSD ChemStation Add-on
module (G2715AA) provide control, data acquisition, and data
evaluation capabilities for Agilent
1100 Series LC/MSD systems. The
G2710AA and G2715AA LC/MS
software includes the G2170AA LC
ChemStation and G2180AA diodearray detector (DAD) spectral
evaluation module. Add-on module. Together, these software
components provide integrated
control with a common graphical
user interface for all of the Agilent
1100 Series LC modules and systems, including the Agilent 1100
Series DAD as well as the Agilent
1100 Series LC/MSD. In addition
to the Agilent 1100 Series family
of modules and systems, the HP
1090 Series II liquid chromatography system, as well as the Agilent
35900E A/D interface can be controlled by G2710AA as part of
LC/MSD systems. The Agilent
ChemStation for LC/MSD system
supports a single Agilent 1100
Series LC/MSD system.
LC/MSD System Control
The software provides digital control of the LC/MSD API ion source
and ion optics, dynamic ramping
of ion optics element voltages, and
control for spraying and drying
gases. Method-specific LC/MSD
parameters include spectral acquisition mode (scan/SIM), signal
sampling rate, LC/MSD tune file,
ionization mode (APCI, APPI or
API-ES mode) and polarity (positive or negative ion detection).
Within a LC/MSD method,
LC/MSD-timed events include
mass range, SIM ion groups, mass
analyzer stepsize, fragmentor voltage, electron multiplier gain, MS
on/off, and API ion source parameters. Fragmen-tor voltage settings may be dynamically ramped
within a scan to optimize response
for various m/z values. LC/MSD
operating parameters such as fragmentor voltage, drying gas temperature, and EMV gain can be
acquired and saved with a data
file. These instrument parameters
can be displayed and plotted as a
record of the exact values associated with the acquired data.
In addition to the standard
ChemStation automation capabilities for single run methods and
mutiple method sequences, an FIA
(Flow Injection Analysis) Series
automation mode is available
through software selection. In this
mode, which requires the Agilent
1100 Series LC autosampler, the
Agilent 1100 Series LC/MSD system can be programmed to make
multiple injections from a single
or multiple sample vials, storing
all data in a single datafile. Up to
two LC/MSD method parameters
can be programmatically varied
with each injection.
The system includes the ability to
do fast scanning of up to 5250
amu/sec and includes autotune for
fast scanning. Also included is
support of the Agilent Analog
Output Accessory which provides
up to 12 SIM signals directly to a
customer LIMS system.
LC/MSD Tuning
The Agilent ChemStation for
LC/MSD systems includes a
LC/MSD tune view in which users
of the Agilent 1100 Series LC/MSD
may select to either automatically,
or manually tune the instrument.
The Agilent 1100 Series LC/MSD
integrated calibrant delivery
system is software-controlled,
and together with the software
autotune provides fully automated
tuning of the Agilent 1100 Series
LC/MSD for API-electrospray
(API-ES), atmospheric pressure
chemical ionization (APCI) and
atmospheric pressure photo ionization (APPI) modes of operation.
An extensive set of manual tune
capabilities is also provided for
users who wish to manually tune
the Agilent 1100 Series LC/MSD.
Agilent 1100 Series LC/MSD
Instrument Verification
Computer-aided operational qualification and performance verification (OQ/PV) tests and procedures
can be used to verify that system
performance is acceptable on an
ongoing basis. Early maintenance
feedback (EMF) tracks the status
of system maintenance items and
provides notification when a preventive maintenance procedure is
due. On-line diagnostics enable
system troubleshooting using integrated tests. System logbooks provide date- and time-stamped
records of runs, errors, and maintenance events.
To perform instrument verification
it is first necessary to purchase
the relevant service from Agilent
Technologies. The required
method and sequence files will be
installed at the time of service
delivery by an authorised Agilent
service provider. Please contact
you local Agilent Technologies
representative for more details.
Diagnostics/Early Maintenance
The Agilent 1100 Series LC/MSD
software extends the diagnosis
view of the existing LC
ChemStation to include tests for
the Agilent 1100 Series LC/MSD.
The diagnosis view is designed to
help users identify instrument
malfunctions starting from a particular symptom. Maintenance and
repair procedures for the Agilent
1100 Series LC/MSD can be called
directly within the diagnosis view
from the Agilent 1100 Series
LC/MSD Maintenance and Repair
CD-ROM. The procedures include
parts and materials breakdowns
and clear animated step-by-step
graphics and multimedia clips for
each repair procedure.
Early Maintenance Feedback
(EMF) automatically notifies the
user when maintenance is
required for key system components such as rough pumps, calibrant delivery system, spray
chamber, and electron multiplier.
tral toolset. Reports can include
either UV-visible or mass spectral
data, or both.
LC/MS Technical Primer
The data from the mass selective
detector may be displayed in a
number of ways. The total ion
chromatogram (TIC) is the summation of all mass signals (m/z
values) over the entire acquired
data range. An extracted ion chromatogram (EIC) displays the signals of individual ions (m/z values) or a range of m/z values.
The Agilent ChemStation for
LC/MSD includes an on-line multimedia LC/MS technical primer.
The primer includes information
to assist users of the Agilent 1100
Series LC/MSD system with a variety of LC/MS technical topics,
including API-LC/MS theory,
method development and solution
chemistry for API-LC/MS, and CID
(collision induced dissociation).
LC/MSD Data Evaluation
The LC/MSD ChemStation
includes all of the data evaluation
capabilities of the Agilent 3D
Chem-Station for LC, including
data evaluation for UV-visible
spectra acquired from a supported
diode-array detector (DAD). In
addition, the LC/MSD ChemStation includes capabilities for
evaluation of mass spectral data
acquired from the Agilent 1100
Series LC/MSD module.
Both UV-visible and LC/MSD data
can be viewed, compared, and
printed. Chromatograms from the
separate detectors may be simultaneously displayed, aligned, and
resized to correlate peaks from
one chromatogram to the other.
Mass spectra and UV-visible
spectra can be simultaneously
reviewed using a common spec-
Interactive Data Processing
The mass selective detector signals (TIC and /or EICs) may be
displayed along with those from
other LC detectors. The software
permits peak alignment for chromatograms from different detectors connected in series. Full,
comparative mass and UV-visible
spectra manipulation are available
including selection of spectra by:
• individual spectrum,
• peak apex spectrum,
• average spectrum over a graphically defined retention time
• range of spectra, and
• all spectra over a peak.
The user may also select how the
spectra are processed when they
are displayed. The available
options include:
• background subtracted spectra,
• limiting the m/z range,
• smoothing,
• normalization, and
• continuous curves or histogram
All of the standard ChemStation
quantification capabilities are
available for use with mass spectral data. TIC or EIC signals can
be used for quantification. For target compound analysis, retention
time windows, quantification ion
signals, and qualifier ion signals/
ratios can be defined on a percompound basis.
Peak Purity
The LC/MSD ChemStation
includes all the UV-visible peak
purity data evaluation capabilities
of the Agilent diode-array detector
(DAD) spectral evaluation module.
Capability for peak purity determination using LC/MSD mass spectral data is also included. Peak
purity may be determined interactively on either a peak by peak
basis, for all the peaks from a certain data file, or automatically at
the end of an analysis as part of
the method.
The user can select to interactively evaluate peak purity for data
sets that include both DAD spectral data and LC/MSD spectral
data in either a single or dual
mode. In single mode, the software configures the purity user
interface for evaluation of data
from either one of the two data
types at a time. The user can
toggle between the data types if
desired. The dual mode user interface permits simultaneous evaluation of spectral purity using both
DAD and LC/MSD data.
In interactive operation, the
LC/MSD peak purity function
examines the most significant ions
across a user-selected chromatographic peak to determine if more
than one compound is present.
The software automatically overlays extracted ion chromatograms
for the selected peak, with each
extracted ion chromatogram displayed in a separate color. A table
of the number of components
located and the two most significant ions used to resolve each
component is displayed. The
next/previous peak or the next/
previous impure peak can be
selected by simple mouse actions.
A purity report that includes peak
purity assessment for all peaks in
a chromatogram can also be
specified and displayed/printed.
the position of cross-hairs on the
iso-abundance plot. In the isoabundance plot, a color scale is
used to represent signal intensity.
Users can define the contour color
schemes and retention time and
m/z ranges for the display.
Acquired mass spectra can also be
displayed as a three dimensional
plot of m/z against retention time
and abundance. The display can
be graphically adjusted by the
user in the time, m/z, and intensity
domains. The resolution of the
plot is selectable, and the orientation of the plot can be adjusted
graphically. The plot may be printed, and the color scheme adjusted.
Iso-abundance Plot and Three
Dimensional Plot
In addition to iso-absorbance and
three dimensional plots for UV-visible spectral data, the LC/MSD
ChemStation also provides equivalent capabilities for mass spectral
The MS iso-abundance plot displays acquired mass spectra as a
color-contoured map of m/z
against retention time together
with areas for display of m/z signals and mass spectra defined by
Agilent ChemStation for A/D
Acquisition with the Agilent
ChemStation for A/D
(G2072BA) and the Additional
A/D Instrument Module
The A/D ChemStation and additional A/D interface acquisition
module controls and acquires data
from Agilent 35900E dual channel
interface. These interfaces allow
the ChemStation to acquire data
from instruments that are not
capable of being interfaced for
data acquisition through the GP-IB
system or LAN. One or two analog
signals per instrument may be
configured; if only one is used the
other is available for use with
another instrument running on
another timebase. Data may be
acquired at up to 100 Hz per signal.
The user may also define the units
for acquisition and their relationship to the voltage signal
(units/volt). The Agilent 35900E
interfaces offer external event
control through digital TTL
(transistor-transistor logic) signals,
each of which are given specific
state (high and low) names, that
may be time-programmed before,
during and after an analysis. The
Agilent 35900E can be configured
for up to eight TTL signals for
each independent channel.
Additional Data Evaluation Modules
The data processing capability of
the ChemStation may also be
expanded through the purchase of
additional data processing modules for specific applications:
• LC diode-array detector (DAD)
spectral evaluation module
• Agilent ChemStore sample organization and results database
module (G2181BA)
LC Diode-Array Detector
(DAD) Spectral Evaluation
Module (G2180BA)
UV-visible spectra, acquired using
a diode-array detector, may be
graphically selected from a chromatogram signal for visual inspection and comparison or may be
used for peak purity determinations, wavelength optimization
and component identification
through spectral libraries. The
spectral library functionality can
be extended to automatic identification of components in up to
four user-defined spectral libraries
based on peak or target compound identification.
Interactive Spectral Processing
Users may graphically select spectra from a chromatographic signal
for visual inspection and printing.
The spectra are displayed in a separate spectral window and may be
overlaid for comparisons. The
user can select spectra in the following modes:
• individual spectrum,
• peak apex spectrum,
• average spectrum over a graphically defined retention time
• range of spectra, and
• all spectra over a peak
The user may also select how the
spectra are processed when they
are extracted. The available
options include:
• setting the subtracted reference
spectrum or spectra,
• limiting the extracted wavelength range,
• customizing the spectral and
reference display, and
• setting the spectral processing.
Options include setting a
smoothing and splining factor,
logarithmic processing and
derivative order.
Peak Purity Determinations
Peak purity may be determined
interactively on a peak by peak
basis, for all the peaks from a certain data file, or automatically at
the end of each analysis as part of
the method. Users may optimize
peak purity processing for accuracy or performance by setting preferences relating to:
• the number of spectra used over
a peak,
• the wavelength range used for
the purity determination,
• the reference spectra,
• the purity threshold,
• spectral processing including
logarithmic, smoothing and
splining factors and derivative
The purity components are calculated and displayed. These include
the spectra, the spectral differences, the signals, a signals-based
ratiogram, similarity and threshold
Similarity curves give the most
detailed information about a
peak’s purity. User selected or
average spectra are compared
with all the other spectra acquired
during the peak's elution and the
resulting spectral comparison factors are plotted as the similarity
curve. For a perfectly pure peak
the similarity curve will be a
straight line corresponding to a
theoretically pure compound.
Impurities will cause a deviation
from this ideal line. The similarity
curves are plotted with reference
to the theoretically pure line and
the user-defined purity threshold.
The similarity curve gives the best
indication of any impurities that
occurred in the peak as it eluted.
The deviation of the similarity
curve from the ideal theoretically
pure value is influenced by both
compound impurities and spectral
noise. The user-defined purity
threshold may be replaced by a
system calculated threshold curve
based on the signal-to-noise ratio
of the peak in question. The noise
sample may be user selected and,
if truly representative of the spectral noise when the peak eluted,
compensates for any deviation of
the similarity curve, from the theoretically pure value, attributable to
spectral noise.
Wavelength Optimization using
the Iso-absorbance Plot
UV-visible spectra, acquired continuously during an analysis, can
be used to determine the optimum
signal wavelengths and bandwidths for routine detection by a
signal-based method. The isoabsorbance plot displays the
acquired spectra as a color-contoured map of wavelength against
retention time together with areas
for the display of both signals and
spectra defined by the position of
the cross-hairs on the isoabsorbance plot.
The iso-absorbance map can be
used in four modes:
• Quick view mode allows users
to view and compare spectra
and signals by moving a crosshair over the area of the contour map. Spectra and signals
are continuously extracted and
updated in the display areas.
The extracted spectra and signals may be frozen in the display areas for comparison purposes.
• Zoom mode allows users to
zoom into areas of interest on
the iso-absorbance map.
• Signals mode allows users to
extract a particular signal, with
a graphically determined bandwidth, into the chromatographic window for routine data processing such as integration and
• Spectral mode allows users to
extract spectra into the spectral
window for further processing.
of spectral libraries each with up
to as many entries as there is
available system memory (typically hundreds of entries). Libraries
may be loaded and searched by
selecting individual spectra from a
chromatogram and searching the
library for the best matches. The
library search may be constrained
by specifying a search template
Users can define the contour color that allows the user to define a
retention time window and
schemes and retention time and
include the informational data
wavelength ranges for display.
associated with each library entry.
For example, the applicable retenThree Dimensional Plot
tion time can be constrained to ±
UV-visible spectra acquired contin- 5 % of the library retention time
and the entry names must start
uously during an analysis, can be
with the letter ‘B’. The search
displayed as a three-dimensional
results may be displayed on the
plot. The display may be graphiscreen and printed.
cally adjusted by the users in the
time, intensity and wavelength
Users may build their own
domains. The resolution of the
libraries by analyzing known subplot is selectable.
stances under defined analytical
• The orientation of the plot can
be adjusted graphically. The ori- conditions, creating a new library
and entering the individual spectra
entation of the display is not
and the information fields to
restricted in any dimension.
describe the entry into the library.
• The plot may be printed.
Library entries may be added,
• The color scheme used in the
deleted, edited, viewed or printed.
plot may be selected from a
Details of each spectrum in a
number of choices.
library including absorbance and
Spectral Libraries
wavelength data may be examined.
Spectral libraries allow users to
Automated Spectral Library
positively identify compounds by
Search Reports
comparing the spectra of peaks in
the sample to libraries of spectra
Automated spectral library search
derived from analytical standards. reports allow users to automatically identify and quantify
The ChemStation allows users to
unknown samples based on the
use libraries both interactively and positive identification from up to
automatically. The ChemStation
four separate spectral libraries.
can manage an unlimited number
Search criteria may be specified
The iso-absorbance plot is typically used during method development to explore the sample’s
response at different UV-visible
wavelengths in order to determine
the optimal detection wavelengths
and bandwidths through experimentation with the integration and
quantification processes.
for each library separately through
a library search template that
allows users to constrain the
search both in the retention time
and library entry identification
One of three search modes may be
selected :
• Standard search mode identifies
each integrated peak in the
chromatogram from the library.
• Target analysis from the calibration table limits the library
search to those library entries
identically named in the calibration table. Identification may be
further constrained through the
use of the library template to
restrict other search criteria
such as the retention time window. After positive identification, quantification proceeds
according to the data in the calibration table
• Target analysis from the library
uses the library entries to identify peaks in the chromatogram
that are within the RT window
specified for the particular
library entry. This mode differs
from the standard search mode
in that it excludes peaks whose
retention times are not covered
by library entry time windows.
Consequently it is typically faster
than the Standard search, especially if there are many more
peaks in the sample than there are
entries in the library. After positive identification, quantification
proceeds according to the data in
the calibration table.
The calculation of the peak purity
factor may be included as part of
the library search.
Report styles can be selected to
produce simple library search
reports or a combination of library
search and standard performance
reports described above.
Spectral Data Import and
The ChemStation spectral module
can import spectra stored in
Agilent’s .WAV format files, from
the HP 8452 and
Agilent 8453 spectrophotometers,
and industry standard JCAMP
spectrum files.
The ChemStation is data file compatible with Agilent’s ChemStation
for UV-visible spectroscopy running in the Windows environment.
Both DAD and UV-visible spectra
may be exchanged between the
two systems either as ChemStation register files or through
the Windows clipboard.
High Throughput Purification Software Module (Purify)
The High Throughput/Purification
software module (G2262AA) is
designed for the needs of preparative HPLC. It offers utmost flexibility for purification of large
numbers of samples. For efficient
data review the graphical user
interface provides an easy way for
sample and fraction tracking.
Sophisticated import and export
functionality allows smooth integration of the system in the purification workflow.
In addition, the MS-based fraction
collection add on software package G2263AA allows fraction triggering based on up to 16 masses.
And/Or fraction logic on UV and
MS or other signal offers highest
flexibility for complex purification
Agilent ChemStore C/S Database Client Software
The Agilent ChemStore C/S
database client software G2181BA
may be added to any Agilent
ChemStation configuration. The
specifications for this product
may be found in the dedicated
“Agilent ChemStation Plus
Specifications” document.
Agilent Chemstation Plus Security Pack
The ChemStation Plus Security
Pack (G2183AA) is a module of
the Agilent Plus Series designed
to support the requirements of 21
CFR Part 11. In the Agilent
ChemStation the ChemStation
Plus Security Pack modifies data
analysis and provides advanced
data management with regard to
supporting the requirements
for electronic records and electronic signature. The specifications for this product can be
found in the "Agilent ChemStation Plus Specifications"
Agilent ChemStation Plus Method Validation Pack
The Method Validation Pack
(G2184AA) is an add-on software
module for ChemStation Plus and
provides a fully validated, off-theshelf software solution that supports labs in performing the entire
method validation process from
planning through to presentation
of the final report – without the
problems associated with data
transfer. The specifications for
this product can be found in the
"Agilent ChemStation Plus
Specifications" document.
The software has been successfully tested for compatibility with the
standard networking components
of the Windows environment. The
software will run at the same time
as other network software and
computer applications written for,
and adhering to, the recommended programming practices of the
Microsoft Windows operating
These products enable the
ChemStation to share physical
devices such as plotters and
printers with other laboratory
computers as well as sharing
information such as data files
and methods.
The Agilent ChemStation
software may be installed on a
suitable network server and
downloaded onto the client PCs as
required. Each client specific configuration ensures a suitable environment for different techniques
and individual users while the centralized software installation
relieves the burden of managing
many copies of the same Agilent
ChemStation installation in one
work environment.
The documentation set has specific components designed for:
• installing the Agilent
ChemStation software,
• using the Agilent ChemStation
• understanding the principles of
how the software works, and
• customizing the Agilent
• interfacing teh Agilent
ChemStation with LIMS
Installing and Learning
Each Agilent ChemStation software product comes with an
installation manual that includes
details of the key steps in PC
hardware and software requirements, instrument interface installation, Agilent ChemStation installation and installation qualification. The installation manual is
specific to the purchased configuration and includes troubleshooting, system records and system
maintenance advice.
Each Agilent ChemStation
includes a task-based tutorial that
is built into the software. This
tutorial is the primary learning aid
and is designed to let users learn
what they want at their own pace.
Each analytical task is divided
into a number of clear, guided
steps each of which the users may
see executed automatically by the
software and then practice themselves.
The Understanding Your
ChemStation manual documents
the principals of the software
operation and the algorithms used
in the data manipulations.
Two additional categories of online information are designed for
the routine user.
The ChemStation includes comprehensive, Windows-style, context sensitive and indexed on-line
help. This system gives detailed
explanations of every screen and
the meaning of the parameters on
that screen. The detailed explanations are backed up by graphics
where appropriate, and may be
copied to the Windows clipboard
for incorporation in the users own
documentation, or printed.
The online help also includes
check lists of the more complex
technique-specific and common
chromatography tasks to help less
frequent users who want to be
sure they set up the system correctly. These checklists are directly linked to the detailed on-line
help information.
Sophisticated users who wish to
customize the operation of the
ChemStation, or who want to
build in additional features, may
do so by writing macros using the
command set.
The primary reference manual,
A Guide to Macro Programming
(available as online help), has a
comprehensive set of functional
examples backed up by a complete description of the internal
data types and structures.
The Commands Help file,
accessed directly from the
ChemStation’s Help menu or the
Show command dialog box, is the
programmer’s function reference.
It includes syntax and parameter
explanations with example
macros illustrating the use of
many of the commands. By virtue
of being on-line, the users can
copy the examples and command
syntax directly into their own
macro source files.
The Agilent ChemStation Plus
XML Connectivity Guide (Agilent
Publication Number: G2170-90221)
includes installation and reference
information for implementing an
XML interface between the Agilent
ChemStation and a LIMS
(Laboratory Information
Management System). The guide
contains examples of the XML
files and the schemas used to generate them. XML (eXtensible
Markup Language) is a protocol
for structuring data in pure text
format. XML is a highly flexible
and portable format for exchanging data between different systems.
Windows, Windows 2000 and Windows XP are
registered trademarks of Microsoft
The Information in this publication is subject to
change without prior notice.
Copyright © 1995-2004 Agilent Technologies
All Rights Reserved. Reproduction, adaptation
or translation without prior written permission
is prohibited, except as allowed under the
copyright laws.
Published October 1, 2004
Publication Number 5989-1600EN
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