Agilent Technologies 6490 Manual

Agilent Technologies
Agilent 6400 Series
Triple Quadrupole
LC/MS System
Concepts Guide
The Big Picture

2 Agilent 6400 Series Triple Quad LC/MS Concepts Guide
Notices
© Agilent Technologies, Inc. 2012
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G3335-90135
Edition
Revision A, November 2012
Printed in USA
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Software Revision
This guide applies to the Agilent
MassHunter Workstation Software -- Data
Acquisition for 6400 Series Triple Quadru-
pole program version B.06.00 or higher until
superseded.
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Agilent 6400 Series Triple Quad LC/MS Concepts Guide 3
In This Guide...
The Concepts Guide presents “The Big Picture” behind the
operation of the Agilent 6400 Series Triple Quadrupole LC/MS
System by helping you understand how the hardware and
software work.
1 Overview
Learn how the Agilent 6400 Series Triple Quadrupole helps you
do your job.
2Inner Workings – Triple Quadrupole MS versus Single
Quadrupole MS
Learn the concepts you need to understand how the Agilent
triple quadrupole mass spectrometer works.
3Agilent Triple Quadrupole MS and Sensitivity
Learn how the Agilent triple quadrupole mass spectrometer
achieves high sensitivity.
4Agilent MassHunter Workstation Software - Data Acquisition for
6400 Series Triple Quadrupole
Learn concepts behind the design of the Agilent MassHunter
Workstation Software - Data Acquisition for Triple Quadrupole
program.

4 Agilent 6400 Series Triple Quad LC/MS Concepts Guide

Agilent 6400 Series Triple Quad LC/MS Concepts Guide 5
Contents
1 Overview 7
What kind of system do you have? 8
Help for applications 9
Help for acquisition 10
Help for data analysis 11
2 Inner Workings – Triple Quadrupole MS versus Single Quadrupole
MS 13
Single quadrupole MS operation 14
Design for a single quadrupole mass spectrometer 14
How a single quadrupole mass spectrometer works 15
Triple quadrupole MS operation 21
Design of the Agilent Triple Quadrupole MS 21
Innovative Enhancements in the 6490 Triple Quadrupole 23
Innovative Enhancements in the 6460 Triple Quadrupole 25
Innovative Enhancements in the 6430 Triple Quadrupole 27
Innovative Enhancements in the 6420 Triple Quadrupole 27
How a triple quadrupole mass spectrometer works 27
How Dynamic MRM works 30
How Triggered Dynamic MRM works 33
3 Agilent Triple Quadrupole MS and Sensitivity 39
How the Agilent Triple Quadrupole MS improves sensitivity 40
Noise reduction 40
Example of chemical noise reduction 43
Linearity of the Agilent 6400 Series Triple Quadrupole MS 45
How each component works to improve sensitivity 46

6 Agilent 6400 Series Triple Quad LC/MS Concepts Guide
Agilent iFunnel Technology 46
Agilent Jet Stream Technology 47
LC/MS ion sources 49
Front-end ion optics 55
Collision cell 57
Detector 62
Pumping system 63
4 Agilent MassHunter Workstation Software - Data Acquisition for
6400 Series Triple Quadrupole 65
Tuning 67
Acquisition 69

7
Agilent Technologies
Agilent 6400 Series Triple Quadrupole LC/MS System
Concepts Guide
1
Overview
What kind of system do you have? 8
Help for applications 9
Help for acquisition 10
Help for data analysis 11
This chapter provides an overview of the Agilent 6400 Series
Triple Quadrupole LC/MS components and how they help get
the job done.

8 Agilent 6400 Series Triple Quad LC/MS Concepts Guide
1Overview
What kind of system do you have?
What kind of system do you have?
You can set up an Agilent 6400 Series Triple Quadrupole LC/MS in
several configurations:
ESI – Electrospray Ionization
APCI – Atmospheric Pressure
Chemical Ionization
APPI - Atmospheric Pressure
Photo Ionization
HPLC-Chip/MS – High Performance
Liquid Chromatography on a Chip
MMI - Multimode Ionization
•For normal flow LC/MS with a binary pump, quaternary pump,
well-plate sampler (or autosampler or CTC PAL autosampler).
The supported ion sources are ESI, APCI, APPI, and MMI.
•For microflow LC/MS with a capillary pump, micro well-plate
sampler (or CTC PAL micro-plate autosampler) and ESI, APCI or
MMI ion sources
•For nanoflow LC/MS with a nanoflow pump, capillary pump,
micro well-plate sampler and HPLC-Chip/MS interface (used
in place of a standard nanospray source) to increase
reliability and boost performance with narrow peak
dispersion and lower dead volumes.
Each Agilent combination has advantages for different
applications. Each uses the same Data Acquisition program,
Quantitative Analysis program and Qualitative Analysis
program to enable these advantages.
The Agilent 6460 and 6490 Triple Quadrupole LC/MS systems
are the only Triple Quadrupole that can use the Agilent Jet
Stream Technology. This technology utilizes a super-heated
sheath gas to collimate the nebulizer spray which dramatically
increases the number of ions that enter the mass spectrometer.
The Agilent 6490 Triple Quadrupole LC/MS system also utilizes
the iFunnel Technology which includes the Agilent Jet Stream
Technology, shorter desolvation assembly with Hexabore
Capillary, and the Dual Offset Ion Funnel.

Overview 1
Help for applications
Agilent 6400 Series Triple Quad LC/MS Concepts Guide 9
Help for applications
You can use one or more of the Agilent 6400 Triple Quadrupole
LC/MS combinations to quantitate trace organic compounds in
complex matrices:
•Food safety studies
•Environmental studies
•Drug discovery
•Toxicology
•Forensics
•Bioanalysis
Paired with Agilent’s 1260 and 1290 Infinity Series LCs, the
6400 Series Triple Quadrupole MS delivers sensitive,
reproducible analyses of target compounds in complex
matrices.
•Femtogram-level limits of detection and quantitation for the
6430 and 6460
•Zeptomole-level limits of detection and quantitation for the
6490
The dwell time is the amount of
time allotted for analyzing
each ion during a scan.
•Minimized memory effects even at very short dwell times
•Simplified operation with Agilent’s data analysis software

10 Agilent 6400 Series Triple Quad LC/MS Concepts Guide
1Overview
Help for acquisition
Help for acquisition
To help you use the Agilent Triple Quadrupole LC/MS for these
applications, the software lets you do these tasks in a single
window with the Data Acquisition Program:
Prepare the instrument
To learn how to install the Agilent
Triple Quadrupole LC/MS, see the
Installation Guide.
To learn how to get started with the
Agilent Triple Quadrupole LC/MS,
see the Quick Start Guide.
To learn more about how to use the
Agilent Triple Quadrupole LC/MS
with real samples and data, see the
Familiarization Guide
To learn how to do individual tasks
with the LC/MS, see the online
Help.
To learn more about an Agilent
1260 or 1290 Infinity LC module,
see the Agilent 1260 or 1290
Infinity LC User’s Guide for the
module.
•Start and stop the instruments from the software
•Download settings to the Agilent 1260 or 1290 Infinity LC
and the Agilent 6400 Series Triple Quadrupole mass
spectrometer in real time to control the instrument
•Evaluate if the MS parameters are within the limits to
produce the specified mass accuracy and resolution with
aChecktune report
•Optimize MS parameters automatically (Autotune) or
manually through Agilent tuning programs and print an
Autotune report
•Monitor the actual conditions of the instrument
•View the real-time plot for chromatograms and instrument
parameters (both UV/Vis and MS) and print a real-time plot
report
•View the centroided line spectrum of a peak or the mass
range profile spectrum of a peak in real time
Set up acquisition methods
•Enter and save parameter values for all LC modules and the
MS to an acquisition method
•Select and label the total ion chromatograms or extracted ion
chromatograms that you want to appear in the real-time plot
•Set up time segments for each scan type and analysis where
parameters change with the time segment or with the scans
within the time segment
•Print an acquisition method report