Show Posts - kech

This section allows you to view all Show Posts made by this member. Note that you can only see Show Posts made in areas you currently have access to.

Messages - kech

MS-DIAL / Re: GOLM mass spectrum library with MS-DIAL

January 12, 2021, 01:14:46 AM

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

MS-DIAL / Re: GOLM mass spectrum library with MS-DIAL

January 05, 2021, 08:46:55 AM

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

MS-DIAL / GOLM mass spectrum library with MS-DIAL

January 27, 2020, 08:44:58 AM

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