diff --git a/_episodes/09-metabolomics.md b/_episodes/09-metabolomics.md index 0a61839..233d16e 100644 --- a/_episodes/09-metabolomics.md +++ b/_episodes/09-metabolomics.md @@ -373,15 +373,13 @@ After this, write your email, so you know when your network is finished. Then cl For more information about the rest of the parameters used for molecular networking: -- (visit the GNPS documentation)[https://ccms-ucsd.github.io/GNPSDocumentation/networking/] -- Also visit (Aron, A.T., Gentry, E.C., McPhail, K.L. et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 15, 1954–1991 (2020))[https://doi.org/10.1038/s41596-020-0317-5] +- [visit the GNPS documentation](https://ccms-ucsd.github.io/GNPSDocumentation/networking/) +- Also visit [Aron, A.T., Gentry, E.C., McPhail, K.L. et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 15, 1954–1991 (2020)](https://doi.org/10.1038/s41596-020-0317-5) ## Statistics analysis using FBMN STATS guide web server Now we want to observe how different are the metabolic profiles of our samples. For that, we are going to calculate a Principal Coordinate Analysis (PCoA) -https://fbmn-statsguide.gnps2.org/ - Go into [FBMN STATS guide](https://fbmn-statsguide.gnps2.org/) @@ -392,32 +390,32 @@ Select "Data Preparation" In file origin select "Quantification table and metadata files". --In the Quantification Table section, select the MZMine output file "GM_workshop_Featurelist_complete_quant.csv" This table contains the information of the two strains and the media. We want to observe how different our samples' metabolomic profiles are, in comparison with the culture media. -- in the Meta Data Table section, include our metadata file "metadata_table.tsv" +- In the Quantification Table section, select the MZMine output file "GM_workshop_Featurelist_complete_quant.csv". This table contains the information of the two strains and the media. We want to observe how different our samples' metabolomic profiles are, in comparison with the culture media. +- in the Meta Data Table section, include our metadata file "metadata_table.tsv". FBMN -After loading your files, click "Submit Data for Statistics!" +After loading your files, click "Submit Data for Statistics!". FBMN -Check that your data have been properly submitted by checking that you have the "Data preparation was successful!" +Check that your data have been properly submitted by checking that you have the "Data preparation was successful!". FBMN -Now we should go to the "PERMANOVA & PCoA" section +Now we should go to the "PERMANOVA & PCoA" section. FBMN -Select Principal Coordinate Analysis +Select Principal Coordinate Analysis. FBMN @@ -447,7 +445,7 @@ Also, it is possible to observe that *Streptomyces* sp. H-KF8 metabolomic profil FBMN -There are several statistics that you can do using FBMN STATS guide, you can check the preprint (here)[https://doi.org/10.26434/CHEMRXIV-2023-WWBT0]. +There are several statistics that you can do using FBMN STATS guide, you can check the preprint [here](https://doi.org/10.26434/CHEMRXIV-2023-WWBT0). ## Visualize the network using Cytoscape @@ -467,7 +465,7 @@ Afterward, click on "Direct Cytoscape Preview/Download" If your network is not Done, then we could use a previously computed network, that holds the same data that we used in this workshop -(Cytoscape)[https://cytoscape.gnps2.org/process?task=568cc93ed2e84f20b2b94bd186b48ee8#{}] +[Cytoscape](https://cytoscape.gnps2.org/process?task=568cc93ed2e84f20b2b94bd186b48ee8#{}) Click on "Download Cytoscape File", and save it in your computer @@ -514,7 +512,7 @@ Select the pie chart again in "Image/Chart", and now select ISP2 and ISP2-ASW. T We can observe that some nodes are detected mostly in ISP2. However, several angucycline-related compounds are detected almost exclusively in ISP2-ASW - FBMN + FBMN