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Topic: MZMINE tutorials for undertaking LC-MSMS database search.  (Read 485 times) previous topic - next topic

MZMINE tutorials for undertaking LC-MSMS database search.

Hi I am undertaking a project to determine toxic compounds in edible plant matter using LC-MSMS. This will require searching databases (custom or online) I am new to utilizing the online search function and was wondering if anyone could provide links to any useful tutorials or lecture slides.

I have undertaken a variety of searches and not found useful material.


Re: MZMINE tutorials for undertaking LC-MSMS database search.

Reply #1
MZmine does have database searching modules but the documentation is sparse. I'm afraid I don't know of any tutorials but I'm hoping my explanation can help you with your searches.

>> Custom or Downloaded Database Searching
The easiest way to conduct spectral searching in MZmine is to use the Identification > 'Local Spectra Database Search' module. This tool will allow you to search a local spectral database to infer compound identification. As long as the database is in the proper format (please see the Help file for a complete list) you can search a custom file or a database downloaded from online. If the database you intend to search can be downloaded, I would recommend this option. The remaining parameters in the module can be used to restrict your search to your liking and you can even utilize retention time restrictions, should you happen to have them.
 
To utilize this module, you will follow the normal MZmine processing workflow but you will need to include one additional step to the processing. You will need to conduct an additional 'mass detection' step on the MS2 ions in your raw data file. This step is near identical to the canonical mass detection step that you may have conducted for your MS1 precursor ions but you will restrict the MS level to 2 and adjust the noise parameter to an acceptable MS2 value. You will choose the MS2 masslist when you conduct the local spectra database search on your final peak list.

>> Online Database Searching
It's difficult for me to provide you guidance on conducting an online search without knowing which database you plan on querying. However, most online database searching in MZmine involve exporting the spectral data and using this export as the input to the online search. There are multiple Export modules that can export your MS2 data to a format you will need.
 
I hope this info was useful.

 

Re: MZMINE tutorials for undertaking LC-MSMS database search.

Reply #2
maybe give feature-based molecular networking a try?
This interfaces MZmine with GNPS which provides a molecular network (all features are connected based on MS/MS similarity) and spectrum library matching of the GNPS and other public libraries such as Massbank.

https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-mzmine2/