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Problem with "Search Using NIST MS program"

Question asked by tny on Nov 13, 2019
Latest reply on Nov 20, 2019 by tny

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I am using Agilent MassHunter Qualitative Analysis B.07.00 and NIST MS Search 2.2. I try to identify the peaks using NIST library. This is the mass spectrum of a peak of interest:

But when I tried to do NIST search, a completely different spectrum appeared in NIST, but with the right retention time showing as the title of the spectrum:

If I click the next scan of the same peak, I got the same mass spectrum as the previous scan:

But when I did NIST search, another completely different spectrum appeared:

Neither of the NIST search resutls gave me the right identification of that peak.

How can I solved the problem? How can I get the correct spectrum pass to NIST MS Search?

Thank you in advance!

tny Nov 19, 2019 5:56 AM

Correct Answer

Hi howard_sanford,

Problem solved!!!

My colleague changed the “Decimal symbol” and “Digit grouping symbol” in my computer, and my problem was solved. I am in Denmark, so the default “Decimal symbol” is a comma “,”. Now it has been changed to a period “.”. And the default “Digit grouping symbol” was changed from a period “.” to a comma “,”.

Maybe other European users should be aware of this potential problem.

Best,

Tny

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howard_sanford

Nov 15, 2019 10:21 AM

Hello tny,

I have updated the tags on this post to increase visibility.

Is this a new issue you are observing, or has this system had issues with NIST searching in the past? Does it only occur for this data file, or are you observing the issue with any data file?

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tny @ howard_sanford on Nov 15, 2019 11:02 AM

Hi Howard_sanford,

Thank you for increasing the visibility of my post!

I recently got a new computer for a new position, and then installed MassHunter Qualitative Analysis and NIST 14 on my new computer. Only in this new computer I got this problem. This problem occurs for all my GCMS data files.

Strangely, my colleagues, who are using the same CDs to install the MassHunter and NIST, have no such problem. So I tried to compare the settings of MassHunter and NIST on my computer with those on their computers, but I couldn’t find out what is different... I also tried to uninstall these two software, install them again, and then restart my computer. I even tried to install the two software in different order. But none of those solved the problem.

It looks like the “wired” spectrum in NIST was generated by sort of processing of the original spectrum in MassHunter, because the spectrum at the same retention time in different data file were “processed” in the same “wired” way and generate the same “wired” spectrum. How can I tell MassHunter or NIST not to “process” the original spectrum?

I really need this to work. Any help would be highly appreciated!

Best regards,

Tny

获取 Outlook for iOS<https://aka.ms/o0ukef>

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howard_sanford

@ tny on Nov 18, 2019 11:02 AM

Tny,

First verify that your new computer is running Windows 7 Professional with Service Pack 1 (64-bit). That is the only supported operating system for Qual B.07.00.

If you are, then I would suggest trying the following. With both Qual and NIST closed, run the Restore Qual Settings tool, found in Agilent->MassHunter Workstation->Qualitative Analysis B.07.00 Tools under the Windows Start menu.

Answer y at the prompt to clear user settings.

Next, navigate to your TEMP folder, which is by default in C:\Users\xxxxxx\AppData\Local\Temp, where xxxxxx is your Windows login name, and delete the file SPECTRA.MSP.

Then try to extract a spectra and perform a NIST search again.

Let me know what you find.

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tny @ howard_sanford on Nov 19, 2019 5:21 AM

Hi Howard_sanford,

Thank you a lot for your time spending on this issue. Unfortunately, my problem remains the same.

In our company, all my colleagues’ computers are running Windows 10, and they don’t have any problem using MassHunter and NIST. So I guess the operations system should not be the issue.

So I tried to follow your instruction to restore the MassHunter settings. But it didn’t work. However, your suggestion reminded me that I might need to format my computer and set everything back to the very beginning status. So, I (our IT service) formatted my computer completely and reinstall NIST and MassHunter. But my problem still exits—when I perform NIST search, the spectrum of the same peak (retention time) in NIST is different than that in MassHunter.

I tried to install NIST and MassHunter in the same directory as my colleague did. But it didn’t help.

My work is heavily dependent on it. I really hope it could work on my computer. Is there something else I can try?

Best,

Tny

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tny @ howard_sanford on Nov 19, 2019 5:56 AM

Hi howard_sanford,

Problem solved!!!

Maybe other European users should be aware of this potential problem.

Best,

Tny

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howard_sanford

@ tny on Nov 19, 2019 11:35 AM

Tny,

I’m glad you were able to resolve your issue, and thanks for sharing that with the community!

I have confirmed that if a comma is used as the decimal separator then the exported spectral data from Qual cannot be read in correctly by NIST. If the m/z and abundance for an ion are reported as

123,4 5678

NIST interprets this as a peak at m/z 123 with an abundance of 4, instead of a peak at m/z 123.4 with an abundance of 5678.

Thanks again for letting us know what you found.

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tny @ howard_sanford on Nov 20, 2019 12:34 AM

Hi howard_sanford,

Thank you for your explanation. That’s why the mass spectrum in NIST was totally different from that in MassHunter when a comma was used as the decimal separator in my computer.

It’s great to have such a supportive forum!

Best,

Ting

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7 Replies

howard_sanford Nov 15, 2019 10:21 AM
Mark Correct
Correct Answer
Hello tny,

I have updated the tags on this post to increase visibility.

Is this a new issue you are observing, or has this system had issues with NIST searching in the past? Does it only occur for this data file, or are you observing the issue with any data file?
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- tny @ howard_sanford on Nov 15, 2019 11:02 AM
  Mark Correct
  Correct Answer
  Hi Howard_sanford,
  
  Thank you for increasing the visibility of my post!
  
  I recently got a new computer for a new position, and then installed MassHunter Qualitative Analysis and NIST 14 on my new computer. Only in this new computer I got this problem. This problem occurs for all my GCMS data files.
  
  Strangely, my colleagues, who are using the same CDs to install the MassHunter and NIST, have no such problem. So I tried to compare the settings of MassHunter and NIST on my computer with those on their computers, but I couldn’t find out what is different... I also tried to uninstall these two software, install them again, and then restart my computer. I even tried to install the two software in different order. But none of those solved the problem.
  
  It looks like the “wired” spectrum in NIST was generated by sort of processing of the original spectrum in MassHunter, because the spectrum at the same retention time in different data file were “processed” in the same “wired” way and generate the same “wired” spectrum. How can I tell MassHunter or NIST not to “process” the original spectrum?
  
  I really need this to work. Any help would be highly appreciated!
  
  Best regards,
  Tny
  
  获取 Outlook for iOS<https://aka.ms/o0ukef>
  Like • Show 0 Likes0
  Actions
  - howard_sanford @ tny on Nov 18, 2019 11:02 AM
    Mark Correct
    Correct Answer
    Tny,
    
    First verify that your new computer is running Windows 7 Professional with Service Pack 1 (64-bit). That is the only supported operating system for Qual B.07.00.
    If you are, then I would suggest trying the following. With both Qual and NIST closed, run the Restore Qual Settings tool, found in Agilent->MassHunter Workstation->Qualitative Analysis B.07.00 Tools under the Windows Start menu.
    Answer y at the prompt to clear user settings.
    Next, navigate to your TEMP folder, which is by default in C:\Users\xxxxxx\AppData\Local\Temp, where xxxxxx is your Windows login name, and delete the file SPECTRA.MSP.
    Then try to extract a spectra and perform a NIST search again.
    Let me know what you find.
    Like • Show 0 Likes0
    Actions
    - tny @ howard_sanford on Nov 19, 2019 5:21 AM
      Mark Correct
      Correct Answer
      Hi Howard_sanford,
      
      Thank you a lot for your time spending on this issue. Unfortunately, my problem remains the same.
      
      In our company, all my colleagues’ computers are running Windows 10, and they don’t have any problem using MassHunter and NIST. So I guess the operations system should not be the issue.
      
      So I tried to follow your instruction to restore the MassHunter settings. But it didn’t work. However, your suggestion reminded me that I might need to format my computer and set everything back to the very beginning status. So, I (our IT service) formatted my computer completely and reinstall NIST and MassHunter. But my problem still exits—when I perform NIST search, the spectrum of the same peak (retention time) in NIST is different than that in MassHunter.
      
      I tried to install NIST and MassHunter in the same directory as my colleague did. But it didn’t help.
      
      My work is heavily dependent on it. I really hope it could work on my computer. Is there something else I can try?
      
      Best,
      Tny
      Like • Show 0 Likes0
      Actions
    - tny @ howard_sanford on Nov 19, 2019 5:56 AM
      Unmark Correct
      Correct Answer
      Hi howard_sanford,
      
      Problem solved!!!
      
      My colleague changed the “Decimal symbol” and “Digit grouping symbol” in my computer, and my problem was solved. I am in Denmark, so the default “Decimal symbol” is a comma “,”. Now it has been changed to a period “.”. And the default “Digit grouping symbol” was changed from a period “.” to a comma “,”.
      
      Maybe other European users should be aware of this potential problem.
      
      Best,
      Tny
      Like • Show 0 Likes0
      Actions
      - howard_sanford @ tny on Nov 19, 2019 11:35 AM
        Mark Correct
        Correct Answer
        Tny,
        I’m glad you were able to resolve your issue, and thanks for sharing that with the community!
        I have confirmed that if a comma is used as the decimal separator then the exported spectral data from Qual cannot be read in correctly by NIST. If the m/z and abundance for an ion are reported as
        123,4 5678
        NIST interprets this as a peak at m/z 123 with an abundance of 4, instead of a peak at m/z 123.4 with an abundance of 5678.
        Thanks again for letting us know what you found.
        Like • Show 0 Likes0
        Actions
        tny @ howard_sanford on Nov 20, 2019 12:34 AM
        Mark Correct
        Correct Answer
        Hi howard_sanford,
        
        Thank you for your explanation. That’s why the mass spectrum in NIST was totally different from that in MassHunter when a comma was used as the decimal separator in my computer.
        
        It’s great to have such a supportive forum!
        
        Best,
        Ting
        Like • Show 0 Likes0
        Actions

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