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Topic: Software for analysis of untargeted Metabolomics (Read 126 times) previous topic - next topic

Software for analysis of untargeted Metabolomics

Hey everyone!

I am currently working on Metabolomics for my bachelor thesis, so i am quite new to this topic.
My latest problem is to find the right software for untargeted Metabolomics. I already tried several of the most common ones but nothing really seems to work for me. I am hoping that some of you could suggest Software that you are using.
The tasks that have to be done are matching precursors to according MS2 spectra (which is called deconvolution i guess?), identification and quantification. I would also use multiple softwares to do this, but the import and export should be compatible.
If there is no other way R could also be an option, but I do not have a lot of experience with R so I would be glad to not use R . :D

Leon


Re: Software for analysis of untargeted Metabolomics

Reply #1
Dear Leon,

sorry, I cannot understand your purpose actually.
>>The tasks that have to be done are matching precursors to according MS2 spectra (which is called deconvolution i guess?), identification and quantification.
Maybe, many programs can do these procedures. What is your issue?

Hiroshi


 

Re: Software for analysis of untargeted Metabolomics

Reply #2
Hello Hiroshi,

My intention was just to get feedback about which software is mostly used from other people.
With all programs I have tried minor issues occured so that is why I tried to get a glimpse of commonly used software.
Just to give you some examples:
XCMS - Identification works but the output contains multiple results with no clue how these are sorted or why there are empty names and there is no option to do quantification with the data. Also there is no way to export the identificated compounds to e. g. Skyline for quantification.
MzMine - Matching of precursor to according MS2 spectra did not work so I could only do identification with precursor information. Results also did not conclude anything, just an empty .tsv.

I also tried several other programs but none really worked in a way that I can trust the identification results and either quantificate within that program or export e. g. an .msp file to skyline.
As discussed in my other post I will try to use the HMDB from mona for identification in MS-Dial but I do not know whether I can quantificate the data within MS-Dial or if there is any other way for quantification.

Nevertheless I am still curious to hear what software is commonly used in the untargeted metabolomics community  :)

Best regards,

Leon