I did GCMS/MS, LCMS of my sample of interest. I got Mass fragments in ionization process. Now facing issues to get the parent molecules name/formula. Due to complexity of sample (its a mixture of compounds) and fragments MS, I could not identify the parent molecules by predicting with basic knowledge of Mass fragments. Is there any free application or database that I can get to know the parent molecule name by inputting the MS fragments values?
And I would like to get experts comments on " What is the best way to predict/analyze/ identify the compounds in a sample by LCMS/MS, GCMS/MS, without using any automatic database paired with instrument."
Hi,
Although I am no expert in small molecule identification by mass spec, I don't think it is possible to get the 'name' of a parent using its MS and MS/MS data.
I assume you mean you obtained mass fragments in a fragmentation (MS/MS) experiment?
If you don't have a database to search your mass spec data against, there are a few options to get an idea of the compound you're dealing with:
- How accurate are your mass measurements? Accurate masses will help in obtaining potential chemical compositions of your parent;
- Can you make sense of the masses and mass differences between the fragments observed and the parent mass? This will help in identifying groups present in your molecule.
I don't think it is possible to identify a compound based on mass data without a database (even if you would have some kind of database, a successful identification is not guaranteed..), but you can at least get some idea of your parent, probably also using its behavior in LC/GC and/or any UV absorbance information.
Hope this helps.
Dr. Eef Dirksen,
First of all, Thank you for your valuable comments. The statements, queries, and suggestions are valuable to me.
Now coming to my subject, Yes, it may be a valuable statement that it is impossible to get parent molecule names for a mixture of samples without databases as you said.
Specific answers to your queries,
1. How accurate are your mass measurements? Accurate masses will help in obtaining potential chemical compositions of your parent
Answer: This is I'm also not confirm, I got the peak with the developed methodology for my sample. Now I am stacked here only. Considering it as accurate, what will be my best move?
2. Can you make sense of the masses and mass differences between the fragments observed and the parent mass? This will help in identifying groups present in your molecule.
Answer: You may be told to separate the mass of various fragments and compare the fragments and their differences. If so please tell. I will do the same. Please let me know, what will be the next step.
Thank You
Pankaj
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