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Messages - Sisu

1
GNPS / Re: FBMN analysis failure and metadata file not exporting from MS-DIAL
I have run the LC-MS/MS for serum samples, I used MS-Dial and MS Finder to identify the metabolites and tried for FBMN analysis which is always resulting with the below failed message

FAILED
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[Restart][Delete]
Traceback (most recent call last): File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_28.2/scripts/filter_spectra.py", line 29, in <module> max_scan = max(included_scans) ValueError: max() arg is an empty sequence Tool execution terminates abnormally with exit code [1]

What should be modified and how to get the metadata file and successfully run the FBMN and my MS Finder also didnt map the metabolites, could someone help me regarding this

Thank you.
I also want to add another information, my mgf file size is resulting as just 0 KB.
2
GNPS / Re: Feature Networking GNPS with MS-DIAL analysis
HI, I didn't understand the language but this seems to be the same issue I'm facing, I'm not able to export the alignment results with metadata and I also don't have the option to select the spectra type. A solution to this is appreciative.

3
GNPS / FBMN analysis failure and metadata file not exporting from MS-DIAL
I have run the LC-MS/MS for serum samples, I used MS-Dial and MS Finder to identify the metabolites and tried for FBMN analysis which is always resulting with the below failed message

FAILED
[Clone] [Clone to Latest Version]
[Restart][Delete]
Traceback (most recent call last): File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_28.2/scripts/filter_spectra.py", line 29, in <module> max_scan = max(included_scans) ValueError: max() arg is an empty sequence Tool execution terminates abnormally with exit code [1]

What should be modified and how to get the metadata file and successfully run the FBMN and my MS Finder also didnt map the metabolites, could someone help me regarding this

Thank you.
4
MS-DIAL / Re: How to convert NIST library (GCMS) into .msp format to use in MS-DIAL?
I would like to know what all are the libraries should I consider for GCMS analysis. I cannot procure commercial library so I would like to know what all list of libraries I can use for compiling into one .msp file. Below here there is a some information regarding the list and method of compiling the library. But I would like to know if we need more than this.

Biswapriya Misra 2019. Steps for Building an Open Source EI-MS Mass Spectral Library for GC-MS -based Metabolomics. protocols.io
https://dx.doi.org/10.17504/protocols.io.8txhwpn
5
MS-DIAL / Re: Problem with converting NIST library to MS-DIAL
I would like to know what all are the libraries should I consider for GCMS analysis. I cannot procure commercial library so I would like to know what all list of libraries I can use for compiling into one .msp file. Below here there is a some information regarding the list and method of compiling the library. But I would like to know if we need more than this.

Biswapriya Misra 2019. Steps for Building an Open Source EI-MS Mass Spectral Library for GC-MS -based Metabolomics. protocols.io
https://dx.doi.org/10.17504/protocols.io.8txhwpn
6
Other / Re: Access NIST library from R or similar
I would like to know what all are the libraries should I consider for GCMS analysis. I cannot procure commercial library so I would like to know what all list of libraries I can use for compiling into one .msp file. Below here there is a some information regarding the list and method of compiling the library. But I would like to know if we need more than this.

Biswapriya Misra 2019. Steps for Building an Open Source EI-MS Mass Spectral Library for GC-MS -based Metabolomics. protocols.io
https://dx.doi.org/10.17504/protocols.io.8txhwpn



Hello Jan,
There is a way to get data out, but it isn't trivial.  NIST provides .dll packages which can be used for third party software integration.  They are available by request from NIST, and are the tools that companies like Waters and Agilent and Thermo incorporate spectral searching of the NIST library into their software.  We used it when we build RAMSearch.  Unfortunately, I did not write that code and I do not know the details of how difficult it is to incorporate.  I do know that the people that did write the code complained about it...  Big caveat - NIST DOES NOT SUPPORT THIS CODE!  They know it works, but they are not going to provide much in the way of advice as to how to use them.  I think that they are also not freely distributable, but I cannot be certain that is the case. 

Corey
Thanks Corey.

I will try to contact NIST and see what they can provide.


Cheers,
Jan.