Enhanced ChemStation Quantitation

Do you already use the ChemStation or MassHunter to quantify compounds in an unknown sample? Then you might be interested in the enhanced evaluation workflow OpenChrom offers:

Download the latest OpenChrom release:

https://openchrom.net/download

Before you start OpenChrom, please check if your computer offers more than 4 GB RAM. In such a case, you can utilize the NIST-DB to perform additional quality checks. A valid NIST-DB (version 08 and newer) needs to be installed on your computer. If you don’t have access to a NIST-DB, you can run the workflow even without a NIST search. Edit the openchrom.ini file and increase the max available RAM to 2 GB. Please use notepad or notepad++ to edit the text file:

-Xmx2048M

Start OpenChrom and switch to the “Sample Quantitation Workflow” perspective. Have a look at the menu or the toolbar. There’s an option to select a perspective.

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The default perspective to analyze the quantitation data will be displayed.

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Please modify the settings, e.g. if you’d like to use a NIST-DB to identify the quantified scans additionally – Menu -> Window -> Preferences:

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You can also edit the sample quantitation preferences. These preferences can be edited also whilst analyzing a file.

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If a valid NIST-DB is installed on your computer, you can also utilize the database to display the unknown mass spectrum against the target of the library in comparison modus. Please select the nist.db file.

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You can start to analyze your ChemStation / MassHunter reports now. Ensure that you’ve already created the rteres.txt and SumRpt.txt files.

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Then start the process. A wizard guides you through the process.

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Please create a project if none is available yet:

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Enter a report name:

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Select the chromatogram which contains the quantitation data rteres.txt and SumRpt.txt files.

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Both report files are detected automatically. If they are not available, please select them manually. Additionally, a targets.txt file can selected which contains the CAS# for each compound. Name and CAS are separated by a “tab“. Comments are marked with a “#“.

#NAME    CAS
Dodekan    000112-40-3
Bisphenyl    000092-52-4
4-Chlorobiphenyl    002051-62-9
Methylpalmiate    000112-39-0

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The report data is parsed an imported. Please verify that the data is valid. Internal standards (ISTD) are marked with a green icon.

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The “Finish” button gets active, after activation of the checkbox “Sample data is valid.“.

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If the NIST-DB option is used, it could take a while to fetch the identification results from the database. After this process has been finished, the report will be displayed for further analysis in OpenChrom. Please feel free to re-arrange the view and e.g. add the “Molecule View“. Additional views can be selected in the same way as the perspective is chosen – Menu -> Window -> Select View.

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Feel free to set a higher min match quality to e.g. 99. A message box warns you, that manual verifications will be overwritten.

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Compounds with a lower match quality than the given one are then displayed yellow.

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A click on the OK checkbox allows you to verify the compound anyhow.

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The raw data of the chromatogram can be opened too. Please double click on the red *.ocb file in the “Project Explorer“. An overview of the file will be displayed. To open the raw data, please click on the the green button to open the chromatogram.

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The chromatogram will be displayed in a new tab.

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The scans are identified and marked with a circle, based on the information given in the ChemStation / MassHunter report files. The “Mass Spectra Identified” tab lists all identified scans.

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A report can be exported in *.csv and *.pdf format. Please select the *.sqr report file and click on “Save As…“.

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Please have a look at the demo PDF file:

SampleQuantReport_1471940351804

This hopefully helps you to analyze your data in a faster and enhanced way.

 

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