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Thermo Scientific ISQ User Manual

Thermo Scientific ISQ
152 pages
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ISQ
User Guide
1R120555-0003 Revision D January 2013

Table of Contents

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Thermo Scientific ISQ Specifications

General IconGeneral
TypeSingle Quadrupole Mass Spectrometer
Ion SourceChemical Ionization (CI)
ResolutionUnit resolution
InterfaceLiquid Chromatography (LC)
DetectorElectron Multiplier
InletDirect Probe
Vacuum SystemTurbomolecular pump

Summary

Preface

About Your System

An overview of the ISQ GC-MS system's capabilities and design.

Related Documentation

Lists manuals and resources for the ISQ system and related software.

System Requirements

Details the hardware and software specifications needed for the ISQ data system.

Safety and Special Notices

Highlights essential safety information, warnings, and special notices in the guide.

Hydrogen Safety Precautions

Provides critical safety guidelines and precautions for using hydrogen gas.

Hazardous Substances Precautions

Outlines safety measures for handling hazardous chemicals and biological materials.

Contacting Us

Lists methods to contact Thermo Fisher Scientific for support and information.

Confirming Your GC/MS System is Working

Checking Power to the System

Verifies that the ISQ system is powered on and the power indicator is lit.

Verifying the Carrier Gas Flow Rate

Confirms that the carrier gas flow rate is set to the expected value.

Checking Your Carrier Gas Tank Pressure

Ensures adequate pressure in the carrier gas tank for sample runs.

Checking the Vacuum and Temperature

Uses indicator lights to confirm proper vacuum and temperature levels.

Changing the Column

Column Selection Criteria

Discusses column material, stationary phase, ID, film thickness, and length.

Replacing the Factory Installed Column

Provides step-by-step instructions for replacing the instrument's column.

Connecting the Column to the Transfer Line

Details the procedure for connecting a new column to the transfer line.

Tuning the ISQ

Accessing ISQ Autotune

Describes how to open the ISQ Autotune window from the ISQ Dashboard.

Tuning the ISQ Mass Spectrometer

Guides on selecting tune types and running the tuning process for optimal performance.

Creating a Method

Creating a Method for the Autosampler

Explains how to configure method parameters for the autosampler.

Creating a Method for the ISQ Mass Spectrometer

Outlines steps to create an acquisition method for the ISQ mass spectrometer.

Creating a Method for the TRACE 1300 or TRACE 1310

Details setting up GC oven parameters and injector settings for TRACE 1300/1310.

Creating a Method for the TRACE GC Ultra

Explains how to configure GC oven parameters and injector settings for TRACE GC Ultra.

Creating a Method for the FOCUS GC

Covers setting up GC oven parameters and injector settings for the FOCUS GC.

Running a Sample

Preparing Your Sample

Discusses the goals and methods for preparing samples for analysis.

Running a Sequence

Provides instructions on setting up and running a sequence of samples in Xcalibur.

Exploring Your Data

Viewing Data in Qual Browser

Introduces the Qual Browser utility for viewing chromatograms and spectra.

Selecting Raw Data Files

Details how to open and select raw data files for analysis in Qual Browser.

Analyzing Chromatograms

Explains how to view and interpret chromatograms, including peak detection.

Setting Mass Ranges and Peaks

Covers adjusting mass ranges and identifying specific peaks for analysis.

Averaging Spectra

Describes how to average spectra to improve signal quality and perform background subtraction.

Optimizing Your Method

Changing the Chromatographic Separation

Suggests adjustments to GC conditions to improve peak shape and resolution.

Finding the Best Way to Make an Injection

Offers methods to optimize sample introduction into the column for better results.

Improving the Way You Prepare Samples

Provides guidance on sample preparation techniques to enhance analytical outcomes.

Changing the Scan Rate

Explains how to adjust the scan rate for optimal chromatographic peak definition.

Narrowing the Mass Range

Discusses refining scan parameters to focus on specific compounds of interest.

Adjusting the Transfer Line Temperature

Details setting the transfer line temperature to prevent column damage or compound loss.

Modifying an Automatic Tune

Guides on customizing tune types to optimize system performance and tune parameters.

Troubleshooting

No Ions Present in Scans

Lists potential causes and solutions when no ions are detected in scans.

Checking the ISQ System Firmware

Explains how to verify the installed firmware version for the ISQ instrument.

How to Know When Your System Needs Maintenance

Identifies common indicators of contamination or issues requiring maintenance.

Investigating Baseline Issues

Provides a table of baseline behaviors, causes, and remedies for data analysis problems.

Investigating Peak Issues

Offers solutions for common peak shape problems like broadening, fronting, and tailing.

Investigating Results Issues

Addresses problems related to low reproducibility, poor sensitivity, and retention time variations.

Reconfiguring Your Instrument

Outlines steps to reconfigure the ISQ instrument if communication is lost or software is reinstalled.

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