Agilent Technologies 6490 - User Manual

Agilent 6400 Series Triple Quadrupole
LC/MS System
Quick Start Guide
Where to find information 3
Getting Started 5
Step 1. Start the Data Acquisition software 6
Step 2. Prepare the LC modules 12
Step 3. Prepare the Triple Quad instrument 16
Step 4. Set up and run an acquisition method 20
Step 5. Review results with the Qualitative Analysis program 27
Step 6. Analyze data with the Quantitative Analysis program 27
Use this guide for your first steps with the Agilent 6400 Series Triple Quad LC/MS, and as a
road map for your user information.
What is the Agilent 6400 Series Triple Quad LC/MS system?
The Agilent Triple Quadrupole LC/MS is a liquid chromatograph triple quadrupole
mass spectrometer that performs MS/MS using three sets of parallel rods (in this
case, quadrupole, hexapole, quadrupole). The first quadrupole separates ions into
precursor ions that are fragmented in the hexapole into product ions, which are
separated by the second quadrupole. Often, two or more precursor ions and their
product ions are monitored in sequence in MRM (multiple reaction monitoring)
mode. You can monitor up to 4000 MRM transitions by using Dynamic MRM.
The Agilent 6490 and 6495 Triple Quadrupoles contain the iFunnel Technology
which provide more efficient sampling of ions into the mass spectrometer. The
iFunnel Technology includes the Dual Offset Ion Funnel and these other
technologies: the Agilent Jet Stream Technology, and shorter desolvation assembly
with Hexabore Capillary.

Summary

What is the Agilent 6400 Series Triple Quad LC;MS system?

Whats New in Data Acquisition

Where to find information

Help

Access help via F1 key or Help menu for software details and guidance.

Documents

Lists available manuals for installation, upgrade, maintenance, and guides.

Training

Information on training courses and guides for software programs.

Getting Started

Start the Data Acquisition software

Step 1: Initiate the Data Acquisition program and explore its interface.

Prepare the LC modules

Step 2: Prepare LC modules, including switching to waste and purging.

Prepare the Triple Quad instrument

Step 3: Prepare the Triple Quad instrument by performing Checktune and Autotune.

Set up and run an acquisition method

Step 4: Set up and run acquisition methods, including parameters and worklists.

Review results with the Qualitative Analysis program

Step 5: Review acquisition results using the Qualitative Analysis program.

Analyze data with the Quantitative Analysis program

Step 6: Analyze acquired data using the Quantitative Analysis program.

Overview

1. Data Acquisition Program
2. Quantitative Analysis Program
3. Qualitative Analysis Program
4. Usage Features
5. Maintenance Features

The Agilent 6400 Series Triple Quadrupole LC/MS System is a liquid chromatograph triple quadrupole mass spectrometer designed for MS/MS analysis. It utilizes three sets of parallel rods (quadrupole, hexapole, quadrupole) to separate ions. The first quadrupole isolates precursor ions, which are then fragmented in the hexapole into product ions, and finally separated by the second quadrupole. This system is particularly adept at Multiple Reaction Monitoring (MRM) mode, allowing the sequential monitoring of two or more precursor ions and their product ions. With Dynamic MRM, it can monitor up to 4000 MRM transitions.

The Agilent 6490 and 6495 Triple Quadrupoles incorporate iFunnel Technology, which significantly enhances the sampling efficiency of ions into the mass spectrometer. This technology comprises the Dual Offset Ion Funnel, Agilent Jet Stream Technology, and a shorter desolvation assembly with a Hexabore Capillary. The Agilent Jet Stream Technology, a standard feature on the 6495, 6490, and 6460 Triple Quad LC/MS models, employs a super-heated sheath gas to collimate the nebulizer spray, leading to a dramatic increase in the number of ions entering the mass spectrometer.

The system is compatible with Agilent 1100, 1200, 1260, or 1290 Infinity LC modules. It operates with Agilent MassHunter Workstation Software, which includes three primary programs: Data Acquisition, Quantitative Analysis, and Qualitative Analysis.

Data Acquisition Program:

This program provides a single interface for tuning the mass spectrometer, controlling and monitoring instrument parameters, setting up acquisition methods, and managing worklists for multiple samples. It also allows real-time monitoring of run plots. The Data Acquisition program for the 6400 Series Triple Quadrupole offers several new features in revision B.07.00. It supports models 6420A, 6430A, 6460A, 6460C, 6490A, and 6495A, as well as LC models 1100, 1200, 1260, 1290, HTS, and HTC. Autotune functionality is available for the 6495 with Agilent Jet Stream and is faster for both the 6490 and 6495. The 6495 model supports Unit, Wide, and Widest resolutions, though fast scan autotune is not supported for it. The Optimizer feature allows users to set injection volume and the number of transitions for compound optimization, and to open different databases.

The main window of the Data Acquisition program is organized into eight key windows: Instrument Status, Chromatogram Plot, Method Editor, Spectrum Plot, Actuals, Sample Run, Worklist, and Tune.

• Instrument Status window: Displays the status of each configured device (Error, Not ready, Pre-run, Post-run, Running, Injecting, Idle, Offline, or Standby) through text and color-coding. It also allows setting non-method control and configuration parameters for LC devices and the MS instrument.
• Actuals window: Shows the current values of selected instrument parameters in real-time. Users can set up which parameters to monitor and customize their background and text colors, as well as define ranges that, if exceeded, will highlight the parameter in red.
• Chromatogram Plot window: Monitors chromatogram plots in real-time, displaying user-defined signals and/or instrument parameters.
• Spectrum Plot window: Monitors spectral plots in real-time.
• Method Editor window: Used to enter acquisition parameters for the method. Clicking the tune button allows viewing tune values in the Tune Parameters dialog box.
• Sample Run window: Facilitates interactive running of individual samples. Users can set sample information, specify an Override DA Method, and select whether Data Analysis runs as part of the method.
• Worklist window: Used to enter sample information for multiple samples, which are then run automatically in sequence. Users can choose to run Acquisition Only, Both Acquisition and DA, or DA Only.
• Tune window: Used to tune the mass spectrometer, either automatically using provided algorithms or manually. This window is accessible in the Tune Context.

Quantitative Analysis Program:

This program is a primary tool for analyzing and reporting Triple Quad LC/MS results. It enables users to set up batches and methods for automatic quantitation of acquired data files, review results through the Batch-at-a-Glance screen, and identify and use outliers to refine methods and requantitate data for improved calibration curve fits or other settings.

Qualitative Analysis Program:

This program allows users to review results for acquisition method development, select appropriate precursor and product ions for MRM analyses, find and identify compounds, and perform molecular feature extraction.

Usage Features:

• Instrument Configuration: The Installation Guide provides instructions for configuring the instrument initially and whenever the LC configuration changes.
• Starting Data Acquisition: Double-clicking the Data Acquisition icon on the desktop launches the program. The software engines start automatically, but can be restarted by right-clicking the Acq System Launcher icon and selecting Start Engines.
• Window Management: Users can show one to seven windows at a time, hide them via the View menu or by clicking the 'X' icon, resize them by dragging borders, and float/dock them by double-clicking the title bar or right-clicking and selecting Floating.
• Context Switching: The system allows switching between Acquisition and Tune contexts to access different functionalities.
• LC Module Preparation: Before data acquisition, the LC stream should be switched to Waste when not acquiring data. The LC pump needs to be purged according to the User Guide. LC parameters are typed into the Method Editor and downloaded to the LC by clicking Apply. Non-method control parameters for LC modules can be adjusted by right-clicking the module in the Instrument Status window.
• Real-time Monitoring: Users can set up real-time parameter values in the Actuals window and configure chromatogram plot displays to monitor effluent and baseline stability.
• Method Setup: Acquisition methods are set up by typing values into various tabs in the Method Editor. Methods can be saved and downloaded to the instrument. The Scan Type can be selected from a list, and Scan segments can be added and configured.
• Data Analysis Parameters: Methods can include qualitative and/or quantitative analysis parameters. Users can link or copy Qualitative Analysis and Quantitative Analysis methods, generate reports, and publish data in various formats (CSV, TXT, PDF).
• Interactive Sample Runs: Individual samples can be run interactively via the Sample Run window, where sample name, data file name, path, and additional information are entered. Runs can be started by clicking the Run button.
• Worklist Runs: Worklists for multiple samples are set up in the Worklist window. Users can add multiple samples, specify sample positions, and configure worklist run parameters. Worklists can be run in locked or unlocked mode.
• MRM Transitions: For Dynamic MRM or Triggered MRM, transitions can be copied and pasted from the original Scan segments table to the new one.
• Fragmentor Voltage: For Agilent 6490 or 6495 instruments, the fragmentor voltage in Acquisition is automatically set by the tune file and cannot be manually adjusted.

Maintenance Features:

• Checktune: This function evaluates if MS parameters are within limits for mass accuracy and resolution. It takes approximately 3 minutes per polarity. If the tune file was last tuned with Fast Scan Autotune, Checktune only checks MS2; if tuned with Autotune, it checks both MS1 and MS2. Checktune should be performed regularly.
• Autotune: Automatically tunes the MS, taking about 30 minutes per ionization mode for most models (25 minutes for 6490 and 6495). It adjusts tune parameters automatically. If Autotune fails, users can select Start from Factory Defaults and re-run.
• Manual Tune: Allows for manual adjustment of tune parameters if Checktune fails. Users can select Peak Width (Unit, Wide, Widest) and adjust Gain & Offset for MS1 or MS2.
• Tune Reports: Checktune and Autotune reports are automatically generated upon successful completion.
• System Logbook Viewer: Provides a tool to troubleshoot errors and view logged events. Users can enable notifications for new errors and warnings and configure purge settings for logbook entries.

Agilent Technologies 6490 Specifications