Agilent Technologies 6100 Series LC/MS User manual

Agilent 6100 Series Quadrupole LC/MS
Systems
Quick Start Guide
Where to find more information 1
Configuration Diagrams 3
ChemStation Views 5
Basic Operation 18
Deconvolution 23
Operating Tips 25
Troubleshooting Tips 27
This manual applies to OpenLAB CDS ChemStation Edition Software (version
C.01.03 and later until superseded) and Agilent 6100 Series LC/MS
instruments.
Where to find more information
Online Help Use online Help for in-depth information beyond what is shown
in this Quick Start Guide. Display online Help in any of the following ways:
•Click the Help button in the toolbar.
•Select Help Topics from the Help menu.
•Click the Help button on most dialog boxes to show task-specific help.

What’s New in C.01.06?
2 Agilent 6100 Series LC/MS System Quick Start Guide
User Guides Besides this Quick Start Guide, the following guides are shipped
with your system and are also available in PDF format on the installation disk.
•Agilent 6100 Series Quadrupole LC/MS Systems Familiarization Guide
•Agilent 6100 Series Quadrupole LC/MS Systems Concepts Guide
•Agilent 6100 Series Quadrupole LC/MS Systems Installation Guide
•Agilent 6000 Series LC/MS Maintenance Guide
What’s New in C.01.06?
•5 kDa/sec and 10 kDa/sec Fast Scan speeds on G6120B and G6130B with
step size of 0.2 Da. Multiple Fast Scan speeds, such as 5k Da/sec and 10k
Da/sec., are now supported for Data Acquisition.
•5 kDa/sec, 8 kDa/sec, and 16 kDa/sec Ultrafast Scan speeds on G6150B
with step size of 0.2 Da. Multiple Ultrafast Scan speeds, such as 5 kDa/sec
and 8 kDa/sec or 8 kDa/sec, and 16 kDa/sec are now supported for Data
Acquisition.
What's New in C.01.03?
•Support for Windows 7 32-Bit and 64-Bit with Service Pack 1.
•Support for Fast Scan on G6120B.
•Support for Fast Polarity Switching on G6120B (hardware upgrade
required).
•Support for ESI with Agilent Jet Stream Technology on G6130B (hardware
upgrade required).
What's New in C.01.02?
•Support for Windows 7 32-Bit and 64-Bit.
•Support for 6100 Series LC/MS on OpenLAB CDS ChemStation Edition.

Configuration Diagrams
1100/1200/1260/1290 Series LC
Agilent 6100 Series LC/MS System Quick Start Guide 3
Configuration Diagrams
1100/1200/1260/1290 Series LC
Solvent bottles
LC Detector
(DAD or VWD)
Control module
(optional)
Vacuum degasser
Pump
Solvent cabinet
Column
compartment
Autosampler

Configuration Diagrams
LC Cabling
4 Agilent 6100 Series LC/MS System Quick Start Guide
LC Cabling
Remote cable
CAN bus cable
AC power
Shielded LAN cable
to network hub
CAN bus cable
Analog signal
to recorder

ChemStation Views
LC Cabling
Agilent 6100 Series LC/MS System Quick Start Guide 5
ChemStation Views
The LC/MS ChemStation software consists of several views. Click one of the
view buttons in the lower left corner of the screen, or from the View menu, to
change to a different view.
Method and Run Control View Allows you to set up methods and adjust
instrument parameters to inject samples and acquire data one sample at a
time or in automated sequences. See the next page for more information.
Data Analysis View Allows you to perform various data evaluation tasks on
chromatograms and spectra, such as integration, quantitation, checking peak
purity, deconvolution, and report generation. See page 9 for more information.
Report Layout View Allows you to design custom report templates to use with
the data generated by your ChemStation. See page 12 for more information.
Verification (OQ/PV) View For use by Agilent service engineers to determine
if your system is operating in a predictable manner. This view is useful to
show Good Laboratory Practice (GLP) compliance, which some government
agencies can require. See page 14 for more information.
Diagnosis View Allows you to run tests to diagnose instrument problems and
access information on how to resolve these problems. The early maintenance
feedback (EMF) feature can notify you when it is time to perform system
maintenance before a problem occurs. See page 16 for more information.
MSD Tune View In this view, you can calibrate your LC/MS automatically. You
can also set MS parameters manually for specific types of molecules. See
page 17 for more information.

ChemStation Views
Method and Run Control View
6 Agilent 6100 Series LC/MS System Quick Start Guide
Method and Run Control View
NOTE The user interface for Method and Run Control can be configured in two ways during
installation. See Agilent 6100 Series Single Quad LC/MS System Installation Guide for
information on installation and configuration.
If your instrument is configured with the Classic user interface, then see ChemStation
online Help and these manuals on the ChemStation disk:
•Agilent 6100 Series Single Quad LC/MS Systems Quick Start Guide
•Agilent 6100 Series Quadrupole LC/MS Systems Familiarization Guide
•Agilent 6100 Series Quadrupole LC/MS Systems Concepts Guide
Message Line
View
Selection
Tool Set Selection:
Sequence or Single
Sample
Run
Control
System
Diagram
Top Toolbar
Online Plot
Method Overview
File List
Method Sequence
Data
Analysis
Status Bar
MS, FIA Disk Space

ChemStation Views
Method and Run Control View
Agilent 6100 Series LC/MS System Quick Start Guide 7
Status and Run
Bars: Instrument
Control Tab
Right-click the Method icon to see the following commands:
Run Time Checklist, Method Information, Edit Entire Method, Method Audit
Trail, Print Method, and Help.
System Diagram Each icon of the system diagram represents one component or module of your
system. Click on an icon if you want to edit the method parameters or go to the
online Help for that particular component.
Start
Sequence
Stop
Sequence
Method
Pump & Solvents Column
Injector Detectors

ChemStation Views
Method and Run Control View
8 Agilent 6100 Series LC/MS System Quick Start Guide
Single Sample
Tool Set
This toolset allows you to work on methods and run an analysis for a single
sample. Move the cursor over a button to view a description of it.
Sequence
Tool Set
This toolset allows you to work on sequences and run automated analyses of
multiple samples. Move the cursor over a button to view a description of it.
Flow Injection
Analysis (FIA)
This toolset allows you to inject multiple samples directly into the detector,
which lets you bypass the chromatographic column. The results are sent to a
single data file. FIA can be used for method development or for applications
that do not require chromatography.
Click the Single Sample icon to display this toolset.
Click the Sequence icon to display this toolset.
To enable FIA from the system diagram:
• Click the FIA icon.
• Select Edit FIA Series.
• Mark the Enable FIA Series in Method option and edit the
FIA Table.

ChemStation Views
Data Analysis View
Agilent 6100 Series LC/MS System Quick Start Guide 9
Data Analysis View
The various tool sets available in Data Analysis View are shown on the
following pages. You can view a description of a button by moving the cursor
over it.
Display Graphics
Tools
Tool Set Selection
Cursor Tools
Signal View Selection
DAD Signal
LC/MS Signal
Message Line
Navigation Tools
File List

ChemStation Views
Data Analysis View
10 Agilent 6100 Series LC/MS System Quick Start Guide
Common Tool Set This toolset is always present in Data Analysis view.
Graphics Tool Set Allows you to manipulate the graphic display.
Integration Tool Set Allows you to perform integration and reporting tasks on
a chromatogram.