agilent 6400 series triple quadrupole users workshop · review, reporting 2/21/2014 mh qqq users...

Agilent 6400 Series Triple Quadrupole Users Workshop

2/21/2014

MH QQQ Users workshop

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Agilent 6400 Series Triple Quadrupole Users Workshop MassHunter Quantitation:

Batch and Method setup

QC’s, Outliers, Data

Review, Reporting

2/21/2014


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Agilent 6400 Series Triple Quadrupole Users Workshop David Presser John Hughes

Anabel Fandino David Weil

Doug McIntyre Shane Tichy

Peter Stone Laura Phillips

André Szczesnieski

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MassHunter Quantitative Software Review and Quant Method Optimization

Topics

• Creating a batch of processed results

• Creating a quantitation method

• Applying a previously saved method

• Updating a method

• Outlier setup and flagging

• Data review and manual integration

• Generating a report, modifying graphic output

• Exporting data

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MassHunter Quantitative Software Batch-at-a-Glance

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Important MassHunter Quant concepts and rules

A Batch is a file which contains all the Quant results from a set

of data files and the Quant method used.

All the data files in a Batch must reside in a single directory, so

put them all together before creating a New Batch.

Select the data directory before creating the Batch

I would not recommend using the Browse to Copy Samples

push. You will have two copies of the same files. Preferred

solution is to create the batch in the directory which contains

the data files.

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Important MassHunter Quant concepts and rules: Quant methods

The most common method problem: Calibration/QC level

names in Batch and Quant method do not match, e.g.

- Method: levels are 1,2,3,4,5

- Batch: levels are L1,L2,L3,L4,L5

Second most common problem: a hidden column in the Method

with a key parameter, e.g. Ion Polarity if method created

manually.

Many Quant parameters can be copied between compounds

with Apply to All button.

When in doubt, Right-Click to look for convenient features and

shortcuts, like Fill Down or Fill Column.

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Creating a batch of processed results Batch-at-a-Glance

1) File | New Batch…

2) Create the batch in the directory in which the data files reside

3) Add Samples

4) Method | Open and Apply from existing file…

Or Method | Open method from existing Batch

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Creating a quantitation method for QQQ

Method | New Method from acquired MRM data…

Select a high concentration standard

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Insure there are

no zero RT’s

You may work from

top downwards

Creating a quantitation method

Assign internal standards and provide an ISTD concentration

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Creating a quantitation method

Create a csv file which contains compound names and

concentrations

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Creating a calibration table for B.05.02 and B.06.00

Note: columns B and C are blank (CAS number and purity)

Creating a quantitation method Concentration Setup – import calibration levels

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Creating a quantitation method Although other steps remain, one may analyze at this point

Insure that the level names match before pressing “Analyze

Batch”

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Creating a quantitation method – Analyze Batch A

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MassHunter Quantitation

Set Peak Filter Area Threshold will set the integration area reject

to 50% of the average response of the lowest calibration level

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Setting a reporting threshold:

Creating a quantitation method Edit and then Save method

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Creating a batch of processed results Use an existing method

1) File | New Batch…

2) Create the batch in the directory in which the data files reside

3) Add Samples

4) Method | Open and Apply from existing file…

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Creating a batch of processed results Use existing method

• Method | Open and Apply from existing file…select saved method

• Analyze batch – note calibration curve recalled from method

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Report Generation B.06

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Report Method Edit B.06 Add a report template. Scroll to the right to modify options,

such as creating a .csv file, opening the result file, and

selecting a printer.

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Report Method Edit B.06 Add a report template. Scroll to the right to modify options,

such as creating a .csv file, opening the result file, and

selecting a printer.

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Report Method Edit B.06 Select the Graphics settings tab. If the report has no

graphics, disable graphics generation to save time.

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Report Method Edit B.06 Change graphics options for desired output, such as

disabling normalization of qualifiers and labeling TIC with

compound names.

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Report Method Edit B.06 – Quantifier/Qualifier Example: uncheck normalize qualifiers.

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Report Method Edit B.06 – Sample chromatogram Example: labeling TIC with compound names.

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Report Method Edit B.06 – Sample chromatogram Example: labeling TIC with compound names.

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Report Method Edit B.06 Example: Fixed range graphics settings.

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Report Generation B.06 Example: Fixed range graphics settings.

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Report Method Edit B.06 Save the report method.

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Report Generation Dialogue B.06

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Changing report graphics prior to B.06.00

Right-click in the compound graphics window and select

“Properties…”

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Changing report graphics prior to B.06.00 Select desired attributes such as no gridlines

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Changing report graphics prior to B.06.00 Select desired attributes for qualifier – turn off normalize

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Changing report graphics prior to B.06.00 On B.05.00 and later one can change the sample

chromatogram labels. View | Sample Info. Then Right-click the

chromatogram window, select Properties…

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Changing report graphics prior to B.06.00 On B.05.00 and later one can change the

sample chromatogram labels

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Creating a quantitation method – TOF or Q-TOF Create a library

• Copy and paste from Excel to Library Editor

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Creating a quantitation method – TOF or Q-TOF Create a library

• Synthesize spectra (adds isotopic cluster information)

• Save library

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Creating a quantitation batch –TOF or Q-TOF Create a batch

• File | New Batch

• Create the batch in the directory in which the data files reside

• Add samples

• Method Edit

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Creating a quantitation method –TOF or Q-TOF From Library

• Method | New Method from File…

• Select the library

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Creating a quantitation method – TOF or Q-TOF From Library

• Select “No RT calibration”

• Click Ok

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Creating a quantitation method – TOF or Q-TOF From Library

• Compounds and retention times are imported

• Continue adding concentrations, etc.

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Creating a quantitation method – TOF or Q-TOF From Library • Optional: in Globals, designate Reference Pattern Library

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Creating a quantitation method – TOF or Q-TOF From Library • “red” Exit, Apply to Batch, Analyze Batch, and save.

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Creating a quantitation method – TOF or Q-TOF From .cef • Find the compounds in Qualitative Data Analysis, such as Find by Formula

• Export .cef file

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Creating a quantitation method – TOF or Q-TOF From .cef • In Quant – Method | New Method from File…

• Select .cef file – compounds are imported

• Continue adding concentrations, etc.

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Creating a quantitation method – TOF or Q-TOF From .cef • “red” Exit, Analyze Batch, and save

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agilent 6400 series triple quadrupole users workshop · review, reporting 2/21/2014 mh qqq users...

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