GNPS analysis

ES Elena Seibel
SU Soohyun Um
MD Marie Dayras
KB Kasun H. Bodawatta
MK Martinus de Kruijff
KJ Knud A. Jønsson
MP Michael Poulsen
KK Ki Hyun Kim
CB Christine Beemelmanns
request Request a Protocol
ask Ask a question
Favorite

Tandem mass spectrometry molecular networks were created using the GNPS platform (http://gnps.ucsd.edu). Data were first converted to the. mzML format with MS-Convert54. The converted files were used to generate an MS/MS molecular network using the GNPS Data Analysis workflow version release 30. The precursor and fragment ion mass tolerance were set to 0.02 Da and to a product ion tolerance of 0.02 Da. Networks were generated using four minimum matched ion fragments, a minimum cluster size of 2 and a cosine score of 0.75–0.8, depending on the experiment. The remaining parameters were kept at default. The library spectra were filtered in the same manner as the input data. All matches kept between network spectra and library spectra were required to have a score above 0.7 and at least six matched peaks. After analysis, data were opened and visualized using Cytoscape 3.8.0 software42.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A