Skip to main content
Topic: Feature-based molecular networking in the GNPS using MSDIAL processed file  (Read 808 times) previous topic - next topic

Feature-based molecular networking in the GNPS using MSDIAL processed file

Dear all,

After the LC-MS/MS data is processed in the MS-DIAL program, we can look at the molecular spectrum networking using Feature-based molecular networking (FBMN) using MS/MS spectral summary (MGF file) containing the list of representative MS/MS spectra. However, the data we look at is not clean. The contaminant ions, duplicate peaks, Istopoes, and adducts are still present. So, basically, when we visualize our data in FBMN, there are many redundant spectra shown which makes the network looks more complicated.

Does anyone know if there is a way that we can visualize the cleaned dataset (.csv format) on the FBMN GNPS website?

To make it more clear my question is reflected in point number 5 in the below scheme:

1-Load the raw data to MS-DIAL
2-Processed the data in MS-DIAL
3-Export the alignment result (containing the list of representative MS/MS spectra) as a text file
4-Manually clean the .csv dataset (blank subtraction, identify ion adducts, duplicate peak reports, and isotopic features, and remove erroneous peaks)
5- Use the cleaned processed file (.csv file) which contains the feature list together with their MS1 and MS2 information associated with them on FBMN GNPS and look at the network?

Does anyone know how can I perform step number 5? Is there a way to convert the cleaned .csv file to .MGF format that can be loaded to FBMN program?

Best
Kourosh