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:


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:


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.



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


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


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


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.


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


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


Please create a project if none is available yet:


Enter a report name:


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


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 “#“.

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


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


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


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.


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


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


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


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.


The chromatogram will be displayed in a new tab.


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.


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


Please have a look at the demo PDF file:


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



Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s