ChemStation library conversion

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MassFinder 4: Manual

This page explains step-by step how to convert an HP ChemStation MS Library into a JCAMP-DX file that can be directly imported by the GC/MS software MassFinder.

Contents

Step 1: Parametric Retrieval

Start Agilent HP ChemStation MS and select "Parametric Retrieval" from the "View" menu.

Image:ChemStation-Step1.png

Step 2: Close "Search Parameter" Dialog

ChemStation will automatically display the "search parameter" dialog, which we do not need at the moment. Click the "Cancel" button.

Image:ChemStation-Step2.png

Step 3: Write JCAMP File

Select the entry "Write JCAMP File" from the "Library" menu.

Image:ChemStation-Step3.png

Step 4: Select Entries to be Exported

This ChemStation search dialog box appears to be identical to the previous one, but it will write the results to an external file rather than displaying the results in ChemStation itself.

  • Enter the library to be exported in the edit box on the top.
  • Select "Entry Number" in the "Search parameters" group (i.e. set the checkmark).
  • Enter appropriate numbers in the "from" and "to" fields.
  • If you want to export the entire library, the "to" value only needs to exceed the actual highest entry number. Thus, just enter any number that is certainly a lot higher than the number of library entries. Please note that void entries (deleted entries) still have an entry number assigned and the number of the last entry can be considerably larger than the current number of entries.
  • Please note, that void entries (which are deleted or excluded from search) can not be exported by this method.
  • Important: The field "Number of Hits to Retrieve" on top should not be changed. Just let the number "10" be displayed there. This number has no effect on which or how many entries will be exported. (It is only active when the "Search Parameter" dialog is used to display rather than export entries.)
  • If you want to export only certain entries of your library, feel free to use the other search parameters. Otherwise just leave them unchecked.
Image:ChemStation-Step4.png

Step 5: Enter File Name

ChemStation will now display an input box prompting for the output file name.

  • Type or paste any file name you like into this box. We recommend specifying a complete path, because the location where ChemStation writes the file to might otherwise be difficult to find.
  • Important: Choose ".jdl" as extension, so MassFinder will recognise the file as library. The normal extension for JCAMP-DX files is ".jdx" (if you like to open the file in other software than MassFinder).
Image:ChemStation-Step5.png

Step 6: Watch the library being exported

ChemStation will display the progress in the lower left corner, so you can estimate the remaining time needed for complete export.

Image:ChemStation-Step6.png

Step 7: Import into MassFinder

Start MassFinder and click "open library". Select the new jdl file and MassFinder will import the library. Generally, MassFinder will import the file a lot faster than ChemStation exported the file.

Step 8: Check the library

MassFinder will now display the library and you can work with it without limitations. Please check whether the names, retention times and maybe retention indices have been imported properly.

If in doubt, whether ChemStation exported the data as you desired, you may open the human readable JDL file in any editor like Windows WordPad or MS Word and check for yourself.

Step 9: Save the new library

Save the library. MassFinder will assign the extension ".mfl" for the library, so that the original exported file will not be modified. The new library file is much smaller and can be opened a lot faster. You do not need the exported .jdl file anymore, but you may want to store it for later perusal.

Step 10: Frequently Asked Questions

Can I export the whole NIST or WILEY libraries to use them in MassFinder?

This tutorial is meant to provide a method to convert YOUR proprietary libraries so that they can be used in MassFinder.

Further, MassFinder is not meant to work with such huge libraries, but only accepts libraries of approximately 10.000 entries. MassFinder's concept is to provide a highly convenient and real-time system and this is currently not compatible with huge libraries.

However, you might select and export parts of those libraries relevant to your area of expertise, e.g. by selecting certain molecular formulas like C15H20, C15H22, C15H24. Further, please note that there might be copyright issues involved when exporting or converting third-party mass spectral libraries. Please check into the copyright regulations of the respective third-party library.

I have stored special information in some ChemStation fields. Can they be recognised by MassFinder?

No, not by default, but yes, we assist in customised import.

We know that many scientists store additional data in some ChemStation fields, e.g. retention indices, company-specific registration numbers or alternative identifiers and names. Because this kind of information is personal and strongly varies in format and location, MassFinder can not recognise it automatically.

We offer our registered customers assistance and develop customised import filters that recognise all required data, split fields with multiple entries (e.g. chemical names with trailing retention time or semicolon-separated alternative names, ...) and convert retention times or indices correctly. If possible, we offer such adaptations free of charge or for a nominal fee. For more complex routines we will give you a free quotation. Please do not hesitate to contact us, we will be glad to discuss your requirements!

In most cases we will find a fast and convenient solution. We will need a representative excerpt of your library in JDL format mailed to us. If possible, please select library entries that are not confidential, but contain all kind of special fields you require. Please contact us prior sending large files or confidential data.

Can I convert a MassFinder library to ChemStation, i.e. the inverse direction?

No, currently this is not possible due to copyright considerations of our "Terpenoids Library". You are not allowed to use the Terpenoids Library outside MassFinder.

But yes, should you need to convert a proprietary MassFinder library to ChemStation *.L format or JCAMP-DX format, you may contact us and we can do this for you. We can also convert libraries of many other GC systems to and from MassFinder. Please inquire.

ChemStation takes quite a long time exporting the entries. Is there any possibility to accelerate this process?

Unfortunately, ChemStation indeed exports quite slowly. Use the fastest computer you have ChemStation running on and, if possible, select a target hard drive other than that where ChemStation or the original library is stored on. Do not use network drives when exporting.

There are commercial programs like Palisade MassTransit that convert to and from a variety of formats and are a lot faster than ChemStation itself.

Usually, you will only need to export your proprietary mass spectral library to MassFinder once. Even if you continue to administrate your library with ChemStation, we recommend adding new compounds to your MassFinder library edition as well by opening the data files and adding the new entry. You will notice how fast and convenient this is with MassFinder and maybe you just switch over to using MassFinder as your primary library administration software?

If your system is not able to export your library in a reasonable time, please do not hesitate to contact us. We will gladly assist you.

I have a hit in the NIST or WILEY library for an unknown substance and would like to add this single entry to my MassFinder library? How can I do it?

If you have a data file containing the new substance and its mass spectrum, just open the data file in MassFinder and add this mass spectrum to the library. You have two advantages: First, there are no copyright issues involved, since you add your own spectrum and only use the knowledge about the correct identification. Second, by using your own spectrum the library entry will match your experimental mass spectrum perfectly, while commercial libraries are always recorded on different systems.

Anyway, should the need arise to add a single spectrum or a small set of ChemStation library spectra to an existing MassFinder library, just follow the steps above with the following exceptions:

  • Step 5: Choose the file extension ".jdx" when entering the output file name (instead of ".jdl").
  • Step 7: Click "open GC/MS" and select the new jdx file. MassFinder will display the single spectrum or the small set of spectra on the left side. Open your MassFinder library. Add the left entries to the library as desired.


Please do not hesitate to contact us in case of any ideas, suggestions or problems!

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