Automatic Post Data Acquisition Data Analysis by

MassHunter Quantitative Analysis Software and Report

Printing on the 7000 series GC/MS QQQ
This document will explain how to configure the 7000 series GC/MS QQQ software to automatically run MassHunter

Quantitative Analysis Software, and optionally generate an Excel based report, after each samples data is

acquired.

Required software:

MassHunter Data Acquisition software versions B.04.00 or B.5.00

MassHunter Quantitative Analysis Software version B.04.00 or B.04.00 SP1

MassHunter Reporting with Quant templates

Save Quant method in .quantmethod.xml file

Automatic reporting will require that the Quant method be available in a .quantmethod.xml file. It is not possible to

access the method information embedded in Quant batch files but this information, along with the calibration data

from its batch, can be made available by use of the Save As menu item under the method menu. This feature is

only available when in the method editor screen.

Using Calibration Data in an existing batch to quantitate the samples being acquired
Calibration data from an existing batch may be applied to samples as they are acquired and placed into a new

batch. This is especially useful when a previous acquired and reviewed calibration curve is to be applied to multiple

batches collected over many days. Care should be taken to save the method, as shown above, only after the

calibration curve information has been reviewed and corrected as needed.

Setting up the Sequence Table

There are three columns in the Sequence Table that direct the software how to process the data and what report to

print. They are:

DA Method File Contains the file name of a MassHunter Quant (.quantmethod.xml) method that should be

applied to the sample.

DA Method Path Contain the path to the method file. This field is loaded automatically when a Quant method file

is selected.

DA Report Template Contains the full path and file name of the Excel report template that is to be generated

after the sample is analyzed. This field may be left blank if no report is required.
The columns are not displayed by default and may have to be added to the sequence table. This may be done by

selecting the Add/Remove Columns Dialog from the Sequence table menu. To access the menu select any cell then

right click to bring up the menu. Add/Remove is under the Columns menu item.

Select the three fields and add them with a click of the Add button followed by clicking OK.

Select a method file with the Open dialog by clicking the indicated button and then navigating to the desired file.
The method file name will appear. If the method was a quant method the path is also filled in.

The fill down feature may be used to copy the method file name to all samples. This same feature may be used a

second time to copy the method path to all samples.

If a report is required then the report template should be added to each sample where a report is needed. This can

be done with a combination of the Open dialog and fill done features.
Checking the Data Collection Method

Make sure that the method that will be used has Data Analysis checked. If Data Analysis is not checked the data

analysis and reporting steps will not take place even when the sequence contains the proper method and report

template information. Set Data Analysis to on and save the method before running the sequence.
Quant Batches and Creating a Single Batch Containing all Samples (Quant only)

When a Quant method is specified the software creates single sample batch (.batch.bin) file for each sample. The

software will automatically create a QuantResults directory in the same directory as the data files are created.

Within the QuantResults directory it will create the single sample batch files using the sample data file name to

identify the batch. This can be seen below for a three sample batch.
However it is possible to direct the software to also create an additional batch that contains all the samples in the

sequence. To do this turn on the single batch creation feature by entering the SaveCompleteBatch 1 command in

the command line of the MassHunter Data Acquisition software as shown below.

The software will confirm that the Complete Quant Batch mode is enabled

The same three sample batch with complete quant batch mode enabled is shown below. Note that the complete

batch file name is taken from the Quant method name.

This command should be entered once before running the 1st the sequence where post data collection data

processing with a complete batch is desired. Once entered this setting will be retained and applied to future

sequences run on the instrument so it need not be done on each sequence.

The decision to create a complete batch file will affect the steps the software performs and how it deals with the

calibration curve data and the calculated concentrations in samples.

Complete Batch enabled

1. If complete batch does not exist create complete batch

2. Add sample to complete batch

3. Apply the calibration information stored in the .quantmethod.xml file to the complete batch

4. Analyze batch on complete sample batch (if Cal or QC samples present recreate calibration curve with Cal

samples added to the batch so far)

5. Create single sample batch

6. Copy calibration information stored in the complete batch to the single batch

7. Analyze batch on single sample batch

8. If report template is specified for this sample generate report from single sample batch

Complete Batch not enabled

1. Create single sample batch

2. Copy calibration information stored in the .quantmethod.xml to the single batch

3. Analyze batch on single sample batch

4. If report template is specified for this sample generate report from single sample batch

Operational considerations

It is important to understand how automated reporting can be different from using Quant interactively to process a

completely acquired sequence. Quant has access to all the samples in the batch regardless of the order in which

they are acquired. Automated reporting only has access to the samples that have been acquired at any given point

in the sequence. Having different data available can lead to different results between the two modes. Some

features, such as Bracket standards, will not work properly because it cannot access calibration samples that have

not yet been acquired. There are also some variances in automated reporting depending complete batch being

enabled or disabled.

Example of operation

The following table shows the difference when the sequence that created the batch above was processed in Quant

at the end of the batch, run with post data acquisition processing with complete batch enabled and disabled.
Sample(s) Quant with full Automatic Reporting Automatic Reporting
batch Complete batch Complete batch
enabled disabled

Blank-1 Results based on Results based on Results based on

calibration samples calibration calibration
in the sequence information stored in information stored in
the the
.quantmethod.xml .quantmethod.xml
file file

Calib-L1 Results based on Results based on Results based on

Calib-L5 calibration samples single data point in single data point in
in the sequence the calibration curve the calibration curve
based on the current based on the current
sample in the sample in the
sequence sequence

QC-L2 and Results based on Results based on Results based on

QC-L4 calibration samples calibration curve with calibration curve
in the sequence no data points with no data points

Sample-1 Results based on Results based on Results based on

Sample- calibration samples calibration samples in calibration
added in the sequence the sequence information stored in
the
.quantmethod.xml
file

Suggested workflows

Run sequences with no Cal or QC using previously validated calibration data stored in the .quantmethod.xml file

using complete batch.

Run sequences with all Cal levels in the first sequence positions. Avoid printing reports on Cal and QC

samples due to invalid calibration curve but print reports for all other samples.

General notes

Normally the same method file and method path would be used for all samples in the sequence but it is possible

to assign a different method file and method path for each sample.
 If the method file and method path are not supplied the single sample batch will not be created for the sample

and that sample will not be included in the complete batch.

As the reports are being generated from a batch that contains a single sample some reports could give errors or

inappropriate results if it was designed to access data from other samples that would normally be present in a

batch containing all samples. Reports will only have access to data on the single sample in the batch and the

calibration data. This should be considered when deciding which report templates should be selected.

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