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Problem with converting NIST library to MS-DIAL

Hello everyone,
I am having hard time to convert Nist (.MSP) file to the format readable by MS-DIAL.
I have tried LIB2NIST with different settings. None of the exported files were accepted by MS-DIAL.
I also tried to export NIST MSP from the librarian in NIST. That file was also ignored by MS-DIAL.
I suspect that MSP file readable in MS-DIAL are having TAB in between m/z and peak intensity values.
In contrary in NIST MSP they are separated with SPACE.
Any suggestion how to cope with these inconsistencies are highly appreciable.
Cheers,
Sergei

Re: Problem with converting NIST library to MS-DIAL

Reply #1
Hi Sergei,

according to my experience (and many users actually), the msp file converted by lib2nist can be imported in msdial program.
1. could you please send one msp spectral record created by lib2nist?
2. could you please share the detail of how you convert your nist library format file to msp file in lib2nist?

Hiroshi

Re: Problem with converting NIST library to MS-DIAL

Reply #2
Hi Hiroshi, Sergei,

I too face same issues from converting entire NIST/ spectra to MS-DIAL readable MSP. (though both MSPs).

I have uploaded 5 files here (A-E, the forum does not allow uploading of .MSP as reading it as .exe so attached them as .txt file)


For “1. could you please send one .msp spectral record created by lib2nist?” see:[/b]
A-“NIST_Spectra_Export”. gif showing exporting individual spectra from NIST (glutamic acid) and it looks as
B- “Glutamic acid_From_NIST_MSP”

For “2. could you please share the detail of how you convert your nist library format file to msp file in lib2nist?” I did following

C-   Converted an openly available EPA Starter Kit  spectral library using LB2NIST program and the process “LIB2NIST_from_EPA”.gif shows it.
D-   “EPA_Library.MSP” .gif shows the library.
E-   “EPA_Starter_LB2NIST_ConvertedMSP” .text is how the spectra looks like.
Hope it helps address our concerns!

Thanks a lot for the help,
Biswa
Biswapriya B. Misra, PhD
Assistant Professor
Center for Precision Medicine
Department of Internal Medicine
Section on Molecular Medicine
Wake Forest University School of Medicine
Cell: +1-352-215-6040
Office: +1-336-713-4622
Profile: http://profiles.wakehealth.edu/display/Person/bmisra

Re: Problem with converting NIST library to MS-DIAL

Reply #3
Hi Biswa,

thanks. I understood. I also encountered the same issue previously.
Which version of lib2nist do you use right now?

It's because the lib2nist you used is an older version for converting nist msms query to the msp format file.
The file you shared is not the msp format file for MS/MS defined by the nist document.

Please download the latest version of lib2nist.
My version is actually

-------
May 01, 2017.

This beta-release of Lib2NIST version 1.0.6.3 mass spectral data
conversion program consists of the following files:
--------

At least it works well. And the msp format from lib2nist is something like:

Name: Desipramine
Synon: $:04267.19
Synon: $:28HCYAFALTSJYZDH-UHFFFAOYSA-N
Formula: C18H22N2
MW: 266
PrecursorMZ: 267.19
CASNO: 50475
Comment: NIST Mass Spectrometry Data Center
Num peaks: 6
196.19 52
208.11 74
208.87 2
210.29 5
222.20 13
236.19 999

by this version.

Thanks,

Hiroshi



Re: Problem with converting NIST library to MS-DIAL

Reply #4
Hi Hiroshi,

Thanks for the quick reply!!! : )

In deed the 2017 (latest) lib2nist version is available for download: https://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:nist17 and the file type in .msp looks fine and compatible (attached screenshot) with MS-DIAL!

Thanks a lot,
Biswa
Biswapriya B. Misra, PhD
Assistant Professor
Center for Precision Medicine
Department of Internal Medicine
Section on Molecular Medicine
Wake Forest University School of Medicine
Cell: +1-352-215-6040
Office: +1-336-713-4622
Profile: http://profiles.wakehealth.edu/display/Person/bmisra

Re: Problem with converting NIST library to MS-DIAL

Reply #5
Hello Hiroshi and Biswapriya,

Thank you for your comments and contributions in the field. I tried your suggestions and it worked well for converting my NIST 08 MS/MS library into MSP using LIB2NIST. But I am really interested in converting the main library which  contains the EI GC-MS data. Unfortunately, I did not find any file for the mainlib to be converted. Also, I tried to export a selected spectrum from the ms search as Biswapriya suggested but it did not contain the retention index data and I think this approach can not be implemented for the whole library (batch export). Any ideas or tips to integrate the NIST GC-MS library (compiled EI-spectra with their retention indices)  with MS-DIAL.
Thanks a lot for your help.

Ahmed Serag, PhD
Assistant Professor
Department of Analytical Chemistry
Al-Azhar University School of Pharmacy


Re: Problem with converting NIST library to MS-DIAL

Reply #6
Hi all,
Thanks for all suggestions.
Unfortunately none of them worked for me.
However, I made the library from NIST work in MS DIAL.
I simply change extension of the file from .MSP [all caps] to .msp [all lowercase].
Thanks again,
Stay safe,
Sergei

Re: Problem with converting NIST library to MS-DIAL

Reply #7
Hi all,
Thanks for all suggestions.
Unfortunately none of them worked for me.
However, I made the library from NIST work in MS DIAL.
I simply change extension of the file from .MSP [all caps] to .msp [all lowercase].
Thanks again,
Stay safe,
Sergei


Is it the main library (EI-GC-MS) sergi or the MS/MS ?

Re: Problem with converting NIST library to MS-DIAL

Reply #8
Hi

>>I am really interested in converting the main library which  contains the EI GC-MS data.
For this, unfortunately, there is no way to convert mainlib to msp. NIST protects this actually.
When I was a master course student (8 years ago), Wiley 10, another very big EI-MS library provider could be converted to msp by lib2nist.

Hiroshi

Re: Problem with converting NIST library to MS-DIAL

Reply #9
Hi

>>I am really interested in converting the main library which  contains the EI GC-MS data.
For this, unfortunately, there is no way to convert mainlib to msp. NIST protects this actually.
When I was a master course student (8 years ago), Wiley 10, another very big EI-MS library provider could be converted to msp by lib2nist.

Hiroshi

Thanks Hiroshi for your reply. I have some updates. I manged to export 20000 compound from NIST into .msp format and then I used R package called  "webchem" to retrieve their retention indices and till now it is working.
Kind Regards
Ahmed

Re: Problem with converting NIST library to MS-DIAL

Reply #10
Great!!

Hiroshi