Agilent MassHunter Qualitative Data Analysis - Spectrum Functions
Summary
Importance of the topic
Qualitative mass spectrometry plays a crucial role in chemical analysis by enabling the identification and characterization of compounds in complex mixtures. Efficient data review, spectral interpretation, and reporting streamline workflows across fields such as pharmaceutical development, environmental testing, and quality control.
Goals and overview of the webinar
This presentation introduces key features of Agilent MassHunter Qualitative Analysis Software B.07.00. The webinar covers chromatogram functions, spectrum display and extraction methods, accurate mass considerations, annotation tools, report generation, file management, and training resources.
Methodology and Instrumentation
The software toolkit includes:
- Chromatogram integration and peak finding for automatic spectrum extraction
- Spectrum Results and Spectrum Preview modules for on-the-fly and saved spectral display
- Background subtraction functions for manual spectra refinement
- Accurate mass parameters with isotope models and saturation checks
- Annotation tools: text, graphics, molecular structures, anchored vs. floating annotations, delta mass caliper for mass difference measurement
- Report generation: Excel-template (.xltx) and PDF-template (.xslt) workflows, compound and analysis reports
- Data Navigator tools for method editing, file saving options (minimal vs. complete), and result archival
Main results and discussion
The webinar demonstrates:
- How to extract single-scan and averaged spectra via double-click, right-click, and range selection tools
- Implementation of background subtraction using user-defined and current background spectra
- Integration-driven peak spectrum extraction, including automatic batch processing
- Accurate mass recalibration on user-selected spectra to correct mass errors without altering raw data
- Annotation workflows that enhance spectral and chromatographic visualization for data interpretation
- Flexible reporting options that integrate seamlessly into automation scripts and worklists
- Best practices for saving qualitative results within data files, ensuring robust data archiving
Benefits and practical applications
Agilent MassHunter Qualitative Analysis Software offers:
- Improved throughput through intuitive spectral extraction and background correction
- High-confidence compound identification with accurate mass and isotope modeling
- Enhanced data presentation via versatile annotation and reporting modules
- Seamless integration into laboratory automation for standardized workflows
- Comprehensive data archival ensuring reproducibility and regulatory compliance
Future trends and potential applications
Ongoing developments aim to integrate machine-learning algorithms for automated peak annotation and compound identification. Cloud-based collaboration and real-time data sharing will further accelerate decision-making in multi-site laboratories.
- Advanced spectral deconvolution using artificial intelligence
- Expanded support for high-resolution imaging mass spectrometry
- Real-time feedback loops for process analytical technology (PAT)
Conclusion
The MassHunter Qualitative Analysis B.07.00 platform enhances every stage of qualitative mass spectrometry—from data review and spectral processing to reporting and archiving. Its comprehensive toolset supports diverse analytical workflows, driving accuracy, efficiency, and data integrity in modern chemical laboratories.
References
No formal literature references were provided in the source material.
Content was automatically generated from an orignal PDF document using AI and may contain inaccuracies.
Agilent MassHunter
Qualitative Data
Analysis
Presenters: Howard Sanford
Stephen Harnos
MassHunter Qualitative Analysis
Spectrum Functions
MassHunter Webinar Series
1
MassHunter Qualitative Analysis Software B.07.00
Topics
• Review Chromatogram Functions
• Spectrum Functions
- Spectral Display
- Extract a Spectrum and Averaging
- Background Subtraction (MS Spectrum)
• Accurate Mass Considerations
- Isotopic Model
• Spectrum Peak List
• Annotation
- Text and Graphics
- Anchoring and Floating
• Report Generation
- Analysis and Compound Reports
• File Save Options
• Tools
• Training Resources
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MassHunter Webinar Series
Mass Spectral Display Options
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Spectra Display – MS Spectrum Results
When the Spectrum Results tool is
selected, the spectrum is displayed and
sent to the Data Navigator. The
selected spectrum can be saved with
the data file.
Spectrum Results Selected
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MassHunter Webinar Series
Spectrum Display - Preview
When Spectrum Preview
is selected, spectra are
not saved to the Data
Navigator automatically.
Preview
Easily preview spectra
before saving to the
Data Navigator.
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MassHunter Webinar Series
Add Preview Spectrum to Results
•Right-click
•Select Copy to User Spectra
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Extract Single Scan Spectrum
Extract Spectra
•Double-click on data
point.
•Right-click on data
point then, Extract
Spectrum.
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Extract Averaged Spectra
Use Select Range tool
then drag across region
for spectral averaging.
Double-click to view aver-
aged spectrum.
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Background Subtraction for Manual Spectra
Use the Ctrl Key
to average multiple
range selections then
Extract Spectrum.
Change manual spectrum
background to Current
background spectrum
.
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Background Subtraction for Manual Spectra
Description indicates
subtraction occurred.
Extract Spectrum
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Extract Peak Spectrum
Extract an averaged spectrum
from a chromatographic peak
automatically. Must integrate
to define chromatographic peaks.
Integrate the chromatogram
to locate chromatographic
peaks. Four step process.
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Extract Peak Spectrum
Set up Peak Spectra
Extraction
Enable Peak Select tool.
Double-click on peak.
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Extract Peak Spectra Automatically
Select Integrate and Extract
Peak Spectra
from the menu.
Spectra Results from each Integrated Peak
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Considerations for Accurate Mass Data
Using Extract Peak Parameters – Saturation
Change 5%
Change 20%
For very narrow
chromatographic peaks
that are completely
saturated you may
have to turn this
function off or error
occurs: No Data
Found.
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MassHunter Webinar Series
Using Extract Peak Parameters – Isotope Model
Chose Isotope model that
Corresponds to workflow.
Common organic molecules
Peptides
Unbiased
Glycans
For Small Molecule Applications: Set to 2
For High Molecular Weight Apps: Uncheck or Max 10
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Extract Spectra – Peak Filters
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Context Sensitive Help
?
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Walk Chromatogram
Walk Chromatogram
Use left and right
arrows on keyboard
to step through
spectra.
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MS Spectrum Peak List One
•Right-click spectrum.
•MS Spectrum Peak List One.
•Tool is also available.
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MS Spectrum Peak List Two
• CRTL click at 2nd spectrum
•MS Spectrum Peak List Two
•Tool is also available.
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MassHunter Webinar Series
MS Spectrum Peak List
For relative abundance,
right-click table header.
and Add/Remove
Columns
. Select
desired columns.
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MS Spectrum Peak Filter
Only affects MS Peaks
table.
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MS Spectrum Peak Filter Interactive Setup
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• Position the
cursor at the
location for the
threshold.
• Right click and
select Adjust
Peak
Threshold
.
Accurate Mass Considerations
How to Recalibrate a Mass Spectrum
Use on User Spectra only.
Do not background subtract.
Right-click in MS Spectrum Results
window and select Recalibrate.
Calculates and applies new calibration
to highlighted spectra.
Select to apply current
recalibration to highlighted spectra.
Saves new calibration to highlighted
spectra.
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MassHunter Webinar Series
Save new calibration to whole
datafile.
Restores original calibration.
Let’s take a moment
for chat questions
on Working with
Mass Spectra
Up Next:
Demo
Up Next:
Annotation Functions
Annotation of Chromatograms and Spectra
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Place Graphic into Annotation Mode
•Click Annotation Mouse Tool
•Annotation Toolbar and Annotation cursor appear
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Add a Text Annotation
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Text and Pointer Can Be Repositioned
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Image Annotation
• Same steps as adding Text
• JPEG and MOL (molecular structure) files are supported
• Image may be scaled and pivoted
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Anchored vs. Floating Annotation
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Delta Mass Caliper
•New tool to calculate and display mass differences between two ions.
Drag and drop
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Delta Mass Caliper - Mass Caliper Mode
Click Delta Mass Caliper Mouse icon
Caliber Toolbar and Caliper cursor appear
Add or edit Calipers
Calipers can only be placed where there is a signal and “snap” to closest ion
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Delta Mass Caliper – Profile Options
•Only used on profile data
•Profile Peak to Peak will “snap” Caliper to profile peak apex
•Profile Point to Point will allow the user to position the Caliper to any point
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MassHunter Webinar Series
Let’s take another
moment for chat
questions on
Annotations
Up Next:
Demo
Up Next:
Reporting
Print a Report from Qualitative Analysis
Print Qualitative Reports:
•Directly from menu.
•Indirectly from Automation
•File Open Actions
•Worklist Automation
•Covered in the
Familiarization Guides.
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Report Generation Options
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Common Reporting Options
Excel Based Reporting
Uses xltx files
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Common Reporting Options
PDF Based Reporting
Uses xslt files
New to Qualitative Analysis
B.07.00 SP1
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Compound Report Options
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Tools
Open data
files
Close data
file
Save
results to
data files
Qualitative
Analysis
Report
Choose
defined
color
Show all items (relates to
Data Navigator)
Linked
Navigation
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MassHunter Webinar Series
Tools
Data
Navigator
Method
Explorer
Method
Editor
Chromatogram
Results
Spectrum
Preview
Sample
Information
Spectrum
Results
Structure
Viewer
Compound
Identification
Results
Compound
List
MS
Actuals
Integration Peak
List
Difference
Results
MS
Spectrum
Peak List
1 & 2
Spectrum
Identification
Results
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Saving Data Files and Opening Data Files
Open data
files
Save
results to
data files
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File Save Options -The Results File
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Default is
Save
Minimal.
• Save minimal – only the compound level nodes are saved. No
spectra or compound chromatograms are saved. If you open
again, you will need to re-extract the complete result set.
• Save complete – all compound results are saved including
spectra and chromatograms.
• In this example, all the User Chromatograms, User Spectra and
Background Spectra are saved.
The Results File
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• The results file is saved within
the data file as QualResult.bin.
• A copy of the qualitative analysis
method is also saved.
• Only one results file and method
can be saved.
• The results file is easily loaded
with the data file.
• Complete data archival.
Let’s take a few
moments for questions
on Reporting.
Up Next:
Demo on Reporting
Up Next:
Training Resources
Training Resources
2/1/2018
MassHunter Webinar Series
50
Training resources that are available.
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MassHunter Qualitative Analysis
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