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C.01.03 and later until superseded) and Agilent 6100 Series LC/MS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.

ChemStation Views
Data Analysis View
Agilent 6100 Series LC/MS System Quick Start Guide 11
Calibration Tool Set Allows you to perform calibration tasks for quantitation.
Signal Tool Set Allows you to work graphically with the UV or MS signal.
Purify Tool Set Allows you to work graphically with your purification data.
Spectral Tool Set Allows you to perform spectral evaluation tasks.
Deconvolution Tool Set Allows you to transforms mass spectra from
multiply-charged ions into a calculated molecular weight.

ChemStation Views
Report Layout View
12 Agilent 6100 Series LC/MS System Quick Start Guide
Report Layout View
Report Layout
Tool Set This toolset is present in the Report Layout view. Move the cursor
over a button to view a description of it.
Tips •Edit or create a report layout as described in the online Help.
•To test your report layout, select a calculation technique from the
drop-down list box to define how the results are calculated.
•Load a data file. The results are loaded into the report template using the
selected calculation.
•Select File / Add to Report Styles to add your completed report template
to the list of available report styles. Now you can use your customized
report within a method.
New Section Menu
Message Line
Report Template Calculation Technique
Report Section
Insertion Triangle
Click a blue triangle to activate
the new section menu (triangle
turns red)
Toolbar

ChemStation Views
Report Layout View
Agilent 6100 Series LC/MS System Quick Start Guide 13
Sample Report Layouts (in \CHEM32\REPSTYLE)
Template Description
SIMPLE.FRP Includes a chromatogram and calibration curves per calibrated
compounds.
NESTED.FRP Shows how to nest subsections.
SPECTRA.FRP Shows how to include spectra.
PURITY.FRP Shows how to include peak purity data.
ESTD.FRP Uses the same elements as the standard ESTD reports so you can
customize your external standard reports.
AREAPCT.FRP Uses the same elements as the standard area percent report so you can
customize your area percent reports.
Print Preview button

ChemStation Views
Verification (OQ/PV) View
14 Agilent 6100 Series LC/MS System Quick Start Guide
Verification (OQ/PV) View
The Verification (OQ/PV) view lets Agilent service engineers test whether your
analytical instruments and the ChemStation software are operating correctly
according to predefined performance criteria.
Operation Qualification (OQ) Operation Qualification is the documented
verification that the equipment-related system or subsystem performs as
intended throughout representative or anticipated operating ranges.
Message
Line
Start/Stop Run
System
Diagram
Verification Toolbar
Task
Selection
Menu

ChemStation Views
Verification (OQ/PV) View
Agilent 6100 Series LC/MS System Quick Start Guide 15
Performance Verification (PV) Performance Verification is the documented
verification that the process and or the total process-related system performs
as intended throughout all anticipated operating ranges.
System Diagram Each icon of the system diagram represents one component
or module of your system.
Verification Toolbar The Verification toolbar is displayed when you select
Show Top Toolbar from the View menu. Move the cursor over a button to view
a description of it.
Available Tests The following verification tests are supplied with your
ChemStation software for use by an Agilent service engineer. Refer to the
online Help for more information on these tests.
•VWD Wavelength Accuracy
•Intensity
•Holmium
•Temperature Accuracy
•Noise, Flow, Temperature
•DAD Wavelength Accuracy
•Injector Precision
•Detector Linearity/Carry-over
•Injector Linearity
•Gradient Composition

ChemStation Views
Diagnosis View
16 Agilent 6100 Series LC/MS System Quick Start Guide
Diagnosis View
This view allows you to carry out diagnostic and maintenance activities on
your system.
Diagnosis Toolbar The Diagnosis toolbar is displayed when you select Show
Top Toolbar from the View menu. Move the cursor over button to view a
description of it.
Instrument
Panel
Symptoms Cause
Information Pad
Possible Causes
Variables Display
View
Selection
Message Line
Task
Selection
Menu

ChemStation Views
MSD Tune View
Agilent 6100 Series LC/MS System Quick Start Guide 17
MSD Tune View
MSD Tune Toolset
This toolset is present in MSD Tune view.
Title Bar
View Selection
Message Line
MSD Tune Toolbar Status Bar
File Selection
Load an LC/MS tune file. Calibrate the mass axis.
Save the current tune file. Change spray chamber
parameters.
Generate a profile and scan
report.
Edit LC/MS parameters for
manual tuning.
Autotune the LC/MS and print a
tune report.
Acquire multiple scans and send
results to data file.

Basic Operation
Start up and shut down the system
18 Agilent 6100 Series LC/MS System Quick Start Guide
Basic Operation
Start up and shut down the system
Task Instruction Comment
To start up the system 1 From the Method and Run Control
view, click the button on the
system status bar. When you move
mouse over the button, if system is
currently idle, it turns green.
2Set up the LC conditions (pump,
column heater, and detector).
3Set up the LC/MS spray chamber
conditions as described in the MSD
Spray Chamber dialog box topic in
the online Help.
Allow 15 minutes for the system to warm
up.
This procedure assumes that the
system is under vacuum and the LC
and LC/MS are properly connected. It
also assumes that the liquid flow path
is properly set up.
To put the system in Standby Mode 1 Flush the system with pure mobile
phase to ensure that the flow path is
clear of buffers. This prevents the
nebulizer from plugging. A plugged
nebulizer can cause a high back
pressure, which can damage the LC
flow cell.
It is good practice to flush the flow
path (including the column) for 5 to 10
minutes with a mobile phase without
buffers such as 50:50
water/acetonitrile.
2Click the button on the system
status bar. All modules are set to
standby mode (indicated by the gray
color in the system diagram).
Put the system in standby mode
overnight or whenever you are not
analyzing samples for an extended
time. The standby state for the LC/MS
leaves the nebulizer and drying gas on
at low flow.
Standby for the LC/MS is:
•20 psi for the nebulizer,
•3 L/min for drying gas,
•300 °C for drying gas temperature,
•325 °C for the APCI vaporizer, if
present
•the MS stream selection valve is
set LC to Waste.
For Agilent Jet Stream source:
•Sheath temp 100°C
•Sheath gas flow 2.2 L/minute

Basic Operation
Tune the LC/MS
Agilent 6100 Series LC/MS System Quick Start Guide 19
Tune the LC/MS
When the LC/MS is used as a detector for the LC, a mass spectrum is
associated with each data point in the LC chromatogram. To obtain high
quality, accurate mass spectra, optimize the LC/MS to:
•Maximize sensitivity
•Maintain acceptable resolution
•Ensure accurate mass assignment
Tuning is the process of adjusting LC/MS parameters to achieve these goals.
After the LC/MS parameters have been optimized, they must be saved in a
tune file (.tun). This tune file is then specified in the method that is used to
acquire data for your samples.
Frequent tuning, whether automated or manual, is not required. Once tuned,
the LC/MS is stable. Tuning is needed no more often than monthly, weekly at
most.
Wait 4 hours after pumpdown before tuning or operating your LC/MS. The
analyzer takes about 11 hours to reach thermal equilibrium. Tune files that
are created or data that is acquired before the LC/MS is at thermal
equilibrium can have incorrect mass assignments and other inaccuracies.
Task Instructions Comments
To use Autotune 1 From the MSD Tune view, select
Autotune from the Tune menu or click
the Autotune toolbar button.
2Review the tune report that is printed
automatically when tuning is
completed.
Use autotune for automated
adjustment of the LC/MS
performance.

Basic Operation
Tune the LC/MS
20 Agilent 6100 Series LC/MS System Quick Start Guide
To use Check Tune 1 Select Check Tune from the Tune
menu.
2Review the Check Tune report.
Adjustments are suggested for values
that are outside of acceptable ranges.
Use Check Tune to determine quickly
whether the LC/MS is correctly tuned.
It performs a single profile scan of the
tune masses and compares the peak
widths and mass axes with target
values.
To use Manual Tune 1 Select Manual Tune from the Tune
menu.
2Set the desired mass resolution
(adjusting width gain and width
offset).
3Calibrate the mass axis (adjusting
mass gain and mass offset).
4Optimize the ion transmission through
the source ion optics (fragmentor,
skimmer(s), lens 1, lens 2, and
octopole peak).
5Adjust the signal strength (setting iris
and adjusting the multiplier gain).
Fragmentor and gain are method
parameters. The fragmentor affects ion
transmission and fragmentation. For
more information, see the online Help.
Use Manual Tune when you want to:
•Achieve maximum sensitivity by
sacrificing some resolution
•Tune specifically for the very low
end (<150 amu) of the mass range
•Tune with a compound other than
the standard calibrants
Task Instructions Comments