Agilent MassHunter

Qualitative Data
Analysis
Presenters: Howard Sanford
Stephen Harnos
MassHunter Qualitative Analysis
Spectrum Functions

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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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Mass Spectral Display Options

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Spectra Display – MS Spectrum Results
Spectrum Results Selected

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.

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Spectrum Display - Preview
Preview

When Spectrum Preview

is selected, spectra are
not saved to the Data
Navigator automatically.

Easily preview spectra

before saving to the
Data Navigator.

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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

Extract Spectrum

Description indicates
subtraction occurred.

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 Extract an averaged spectrum
Extract Peak 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  Enable Peak Select tool.

 Double-click on peak.


Set up Peak Spectra
Extraction

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Extract Peak Spectra Automatically

Spectra Results from each Integrated Peak

Select Integrate and Extract

Peak Spectra from the menu.

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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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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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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
• Position the
cursor at the
location for the
threshold.
• Right click and
select Adjust
Peak
Threshold.

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 Accurate Mass Considerations
How to Recalibrate a Mass Spectrum
Use on User Spectra only. Save new calibration to whole
datafile.
Do not background subtract.
Restores original calibration.
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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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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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
New to Qualitative Analysis PDF Based Reporting
B.07.00 SP1
Uses xslt files

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Compound Report Options

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Tools

Save Choose
Open data results to defined Show all items (relates to
files data files color Data Navigator)

Close data Print Linked

file Qualitative Navigation
Analysis
Report

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Tools
Spectrum
Identification
Results
MS
Spectrum Compound
Difference Peak List List
Data Method Spectrum Structure
Results 1&2
Navigator Editor Preview Viewer

Compound
Method Integration Peak
Chromatogram Identification
List
Explorer Results Results Sample
Information
Spectrum MS
Results Actuals

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Saving Data Files and Opening Data Files

Save
Open data results to
files data files

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File Save Options -The Results File

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.
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The Results File

• 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.

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Let’s take a few
moments for questions
on Reporting.

Up Next:
Demo on Reporting
Up Next:
Training Resources
Training Resources

Training resources that are available.

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MassHunter Qualitative Analysis