Hi!
I wonder if GMD (Golm) mass spectrum reference library are included in demo compound library for GC-MS in MS-DIAL?
If not, is it possible to use them or (better) merge with demo library?
Dmitry
Hi Dmitry,
I feel that the GOLM MSRI library is not included in the Demo cpd library in MS-DIAL.
But, learning from Hiroshi, I have now created a document where you can add any library you wish to the demo and other libraries in .msp. The steps/ workflow is listed now at protocols.io : https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-8txhwpn (see Step 5).
Hope it helps.
Thanks,
Biswa
Hi Dmitry,
please follow the direction of Biswa.
Also, the file of "GMD_20111121_VAR5_ALK_MSL.txt" in GOLM database website should be good to start to merge the library with the existing spectral records on my website.
Hiroshi
Hi,
That file format works OK for AMDIS and MSDIAL.
This is another way how to save text files in msp format: http://golmmetabolomeblog.blogspot.com/2012/03/how-to-integrate-gmd-spectral.html
A bit of Search&Replace is needed to correct name, formula and other lines.
Dmitry
Even though there were some manuals how to make the GMD run, I still experience trouble with respect to the recognition of entrys (like RI, etc). The GMD contains this information but following the instruction of Biswa does not allow to use those features in MS DIAL. Furthermore, if I follow the instruction of Jan Hummel published on the Max-Planck-Institute Website (Golm) AMDIS does not recognize features that have spaces in their name. A short example:
Name: M000000_A097001-101-xxx_NA_959,45_PRED_VAR5_ALK_Unknown#bth-pae-001 is displayed correctly (first entry)
Name: M000880_A098001-101-xxx_NA_986,97_TRUE_VAR5_ALK_Glycine, N,N-dimethyl- (1TMS) is skipped (second entry)
I would like to ask Dmitry to provide a short instruction on the replacements he did. Does anyone has a corrected Version of the GMD_20111121_VAR5_ALK_MSP in MSP format he or she could provide?
Cheers
Stefan
Hi Stefan,
You are right, GOLM library has all needed information inside, but uses slightly different format of MSP file.
It it relatively easy to fix in a text editor (e.g., Notepad++). It is better to open the library provided at the MS-DIAL webpage for reference and the "GMD_20111121_VAR5_ALK_MSL.txt" library file for editing.
Compound name in MSDIAL library file is coded as "NAME: hexanal -b", which corresponds best to "MST N: Glycine, N,N-dimethyl- (1TMS)" in the Golm library file. Golm library uses long identifiers in "Name" field, like: "Name: M000880_A098001-101-xxx_NA_186302,31_TRUE_VAR5_FAME_Glycine, N,N-dimethyl- (1TMS)".
So what is needed for correct compound name visualization is to replace in the whole Golm library file:
1. original "Name" tag with something else, for example, "oldname"
2. "MST N" with "Name"
In the same manner one can "fix" ontology, INCHIKEY, CAS, etc. fields. ;)
Best regards,
Dmitry