TITLE: GNPS Untargeted Metabolomics Workflow 
AUTHORS: Sierra Simpson, Olivier George

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">GNPS is an open-sourced, web-based mass spectrometry ecosystem that is used for community-wide organization / sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). </div><div class = "text-block"><span>GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication. </span><a href="https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">GNPS Website</span></a></div><div class = "text-block"><span>This is a quickstart guide pulled directly from </span><a href="https://ccms-ucsd.github.io/GNPSDocumentation/quickstart" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">GNPS Website</span></a><span>. </span></div><div class = "text-block">This version was intended as an easy to read step by step guide to: </div><div class = "text-block">1) Prepare data</div><div class = "text-block">2) Create a GNPS account </div><div class = "text-block">3) Upload to GNPS</div><div class = "text-block">4) Create a molecular network on GNPS</div><div class = "text-block">This can be found at GNPS.ucsd.edu with more in-depth information. This has been reproduced for use as a workflow within the George Lab for those unfamiliar with GNPS.  More information and other useful tutorials can be found directly on the GNPS website and from Dorrestein publications listed below. </div></div>

[STEPS]
?. [Registration ]
Create a GNPS account at GNPS Signup
?. [Upload Data ]
First convert specific vendor formats to open format using MSConvert locally. MSConvert DownloadmsConvert is a command-line utility for converting between various mass  spectrometry data formats, including from raw data from several  commercial companies (with vendor libraries, Windows-only). For Windows  users, there is also a GUI, msConvertGUI.For any difficulties converting the files - here is a FAQ posted by the Dorrestein lab: https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/
?. [Upload Data ]
Upload converted files using an FTP client such as cyberduck or WinSCP (preffered). They do not like Filezilla as it has malware. Host name: ccms-ftp01.ucsd.edu  username: (yourGNPS login) password:(yourGNPS password) Once files are uploaded they will be available for use within GNPS.
?. [Molecular Networking Input ]
Navigate to the link below - it is the analysis webpage which contains the information for the study. Analysis
?. [Molecular Networking Input ]
Select from the presets either  small dataset ( 5 LC/MS files )medium dataset ( 5-400 LC/MS files)large dataset ( 400+ LC/MS files).
?. [Molecular Networking Input ]
Name your analysis under the "title section"
?. [Molecular Networking Input ]
Select data input files ( that you uploaded in step 3) Within the Basic Options header; to input your spectrum files, select  the input files tab next to the Spectrum files (required) field. A  pop-up window with three tabs will appear; Select Input Files, Upload  Files, Share Files. Proceed by selecting the files you want to analyze  by clicking on the mass spectrometry file or an entire folder. Next  click on the Spectrum Files G1 button to mark these files for analysis.  You may select more files for analysis and put them in the separate  groups (G1, G2, G3, G4, G5, G6) to reflect your experimental design. If  you are performing an analysis with more than six groups, a metadata  file may be used
?. [Molecular Networking Input ]
For metadata creation see this link: Metadata FAQ
?. [Molecular Networking Input ]
Once you are done selecting files to be analyzed, close the pop-up and hit submit.
?. [View Analysis Results ]
To quickly glance at all the molecules in your data matching to the GNPS  community knowledge of reference MS/MS spectra, click on "View All  Library Hits".
?. [View Analysis Results ]
To visualize the molecular networks in the browser, click the "View Spectral Families (In Browser Network Visualization)". This brings you to a list of all the individual networks (connected  components) that are in your data. Click on the "Visualize Network" link  to explore each network individually. Your selection can be guided by  the identifications within each network if there is a specific molecule  of interest.
?. [View Analysis Results ]
For advanced visualization see this link: https://ccms-ucsd.github.io/GNPSDocumentation/networking/