For training purposes, the reader is led through the protocol from recalling a public data set and its sample information to creating and interpreting a molecular network. This protocol provides step-by-step instructions for creating reproducible high-quality molecular networks. Molecular networking creates a structured data table that reflects the chemical space from tandem mass spectrometry experiments via computing the relationships of the tandem mass spectra through spectral similarity. One or the main analysis tools used by the GNPS community is molecular networking. GNPS not only serves as a public data repository for untargeted tandem mass spectrometry data with the sample information (metadata), it also captures community knowledge that is disseminated via living data across all public data. This can be performed within one experiment or at the repository scale. The goal of GNPS is to provide as much chemical insight for an untargeted tandem mass spectrometry data set as possible and to connect this chemical insight to the underlying biological questions a user wishers to address. Herein, we present a protocol for the use of Global Natural Products Social (GNPS) Molecular Networking, an interactive online chemistry-focused mass spectrometry data curation and analysis infrastructure.
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