GC-MS private library usage (NIST, FIEHN in .msp format)

[Stavros Oikonomou]

Dear GNPS community

I've been working with GC-MS data in GNPS. I want to use our fiehn and NIST libraries for library search. The libraries are in .msp format and when i try to run a search spectral library only using our libraries i get  this message: 

There was an error retrieving the result data for block "main" of workflow type "MOLECULAR-LIBRARYSEARCH-GC".

This message appears when job is done and i check the all library hits.

I also try to use a msp to mgf convertor and rerun the job but the job is failing or getting the same error.

So, my questions are:

1) Can i use the .msp files for library search and why i getting this error?

2) Is there any tool/program for msp convertion to mgf where the output is gonna cooperate with GNPS? 

3) Is there any other way to use our private libraries in GNPS without public upload or the only solution is this https://ccms-ucsd.github.io/GNPSDocumentation/batchupload/ ?

Thanks

Stavros

[zipora Tietel]

Dear Stavros,

I've just started to find out how can I  to use NIST for annotation, so I'm a few steps behind.

I'd be thankful if you could share some of your experience in regard to:

1. How you were able to get NIST in .msp, currently I just have it as a .L file.

2. What converter you used for .msp to .mgf conversion.

I also join the questions you raised, in order to be able to incorporate NIST into the GNPS GC-MS analysis.

Thanks,

Zipora

[Aksenov Alexander]

Hi Stavros, Zipora

The msp converter that you could use could be this one:

https://sourceforge.net/projects/msp2mgf/

You cannot use msp for the GNPS search, you need to convert to mgf first.

Regarding the search using private libraries - due to the copyright, it is best if you do the search offline using your private library by downloading the mgf from the deconvolution link (or using your own deconvolution results) and using it for the search software (whatever you use). You can then export the results and import them into your network in Cytoscape, just make sure that feature numbers (Scan#) column is named "shared name" (without ""). You can then select these annotations to be labelled on your network.

Hope this helps.

Best regards

Alexander

[zipora Tietel]

Dear Alexander,

Many thanks for your detailed and helpful reply.

Yet another few questions then: 

Can I use MS SEARCH as a search software? what other options are there?

Is there a documentation on how to do the search as you described?

Also, I was unsuccessful using LIB2NIST to convert NIST to MSP- is that how this should to be done?

My best,

Zipora

[Aksenov Alexander]

Zipora -

NIST only allows to convert 1000 files at a time by selecting them in MSSearch and clicking "Export" button. Other than MSSearch software , most of the vendors offer their own software solutions that integrate with NIST and can do the search, often directly from the acquisition software. NIST provides instructions on how to use MSSearch (https://www.nist.gov/document/nistmspdf).

One thing I am not sure about, is whether it is possible to batch export search results from MSSearch in a format other than pdf (especially as a spreadsheet), and not looking at search results one feature at a time. If you know the solution, would appreciate if you could post it on the forum, it would be useful to many users.

Best

Alexander

[zipora Tietel]

Hi Alexander,

Thank you so much for the info and the explanation!

I will definitely try batch export of search results from MSSearch and see what I get, will update here.

Thanks again,

Zipora

[Stavros Oikonomou]

Hi Zipora and Alexander

Zipora-

For NIST they gave me only the fames. I don't remember if its masshunter or mzmine but we use one of this two softwares that give us the option to export in .msp

The convertor i use is the one that Alexander mentions.

Alexander-

First of all, thank you for your quick response and the info.

So if i understand correctly i can't use my private libraries on GNPS.

Because i'm new in the field do you have any software suggestion in which i can use the mgf file from GNPS's deconvolution and the mgf from FIEHN and NIST and perform the library search? What's the go to option?

Thanks again,

Stavros

[Kourosh Hooshmand]

Hi Stavros,

Try using MS-DIAL user-friendly software. You can simply include your MSP library file to process your raw data to annotate your feature based on MS/MS similarity.

If you have added FAME to your individual samples during the derivatization process, you  also need to include a separate file where the FAMEs information as well as their respective retention time are defined in a text file. 

All the instructions are clearly explained in the MS-DIAL tutorial page: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial.html

Best
Kourosh

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[Andrea Romano]

Dear Community,

like other users in this thread, I have also tried to load my private library (NIST 14) and use it in in MS Hub, after conversion into mgf format.

I converted it into .mgf using  https://sourceforge.net/projects/msp2mgf/,, loaded the mgf into gnps, then ran the library search.

When I try to access the library hits, this results into the following error message:

There was an error retrieving the result data for block "main" of workflow type "MOLECULAR-LIBRARYSEARCH-GC"

Any idea on how to fix this?

Many thanks

Andrea