WebMetabase

You can type the m/z, the molecular formula, or the formula change (+O, -2H, etc). You can also use the following abbreviations:  

“+GS” -> “+C10H15N3O6S” 

“+GLUCYS” -> “+C8H12N2O5S” 

“+CYSGLY” -> “+C5H8N2O3S” 

“+CYS” -> “+C3H5NO2S” 

“+NAC” -> “+C5H7NO3S” 

“+GS+H” -> “+C10H16N3O6S” 

“+GLUCYS+H” -> “+C8H13N2O5S” 

“+CYSGLY+H” -> “+C5H9N2O3S” 

“+CYS+H” -> “+C3H6NO2S” 

“+NAC+H” -> “+C5H8NO3S” 

“+GLY” -> “+C2H3NO” 

“+TAUR” -> “+C2H5NO2S” 

“+GLN” -> “+C5H8N2O2” 

“+ACET” -> “+C2H2O” 

“+GLUC” -> “+C6H8O6” 

“+CO2+GLUC” -> “+C7H8O8” 

“+GLC” -> “+C6H10O5” 

The platform needed to host Oniro has these minimum requirements: 

• Windows or Linux platform (64 bits) 

• 8 (or more) CPU core 

• 16 (or more) Gb of RAM 

• 500 Gb of disk space (1.5 Tb or more if the database server has to run on the same machine) 

Oniro application needs the following software to be installed prior to its deployment: 

Java JDK/OpenJDK (could run on JRE too), version 8 minimum; 64 bit platform is needed, 

Application Server, Apache Tomcat (version 8 or 9) 

Database system: The database can be installed in the same computer as the Application Server or at an external machine or cluster (having a good connection to the Application Server).
WebMetabase can be used in the following database systems: 

• MySQL 

• Oracle 

Yes. Settings should be imported as .set or .cset files.  

Instructions 

1. Export the settings from MassMetaSite. 
2. Within Oniro, navigate to WebMetabase –> Settings –>MassMetaSite Settings.  
3. In the list of Saved Settings on the left, right click and select “Import Settings” 

      4. Provide a name for the process settings and browse to find the file. Then click OK.  

The settings have now been imported and can be used within WebMetabase.  

Yes, you can change both the content and the order of columns in the Chromatable.

Instructions

1. In the header for any column of the table, click the arrow to the right.

2. In the new menu, navigate to Columns. Here, you will see the list of available columns. Use the check boxes to select or deselect columns.

3. To re-order the columns, click the header of a column and drag it to the desired location in the table.

4. If you would like to save this layout for the experiment, right click on any column header and click Save grid layout.

Yes, the colors used for the spectra can be changed. Keep in mind that these changes will go in effect for all users on the WebMetabase server.

Instructions

1. Within WebMetabase, go to Settings à Experimental data.
2. On the bottom right is a section called Custom spectra colors.

3. Click on each row to customize the color for each type of signal.

4. Click Save before exiting.

The information in the Chromatable can be exported to an Excel report from both pending and approved experiments.

Instructions

1. Right click on any row in the Chromatable. Then click Add to report.

2. In the new window, provide a Report Name.

3. Select the columns that you would like included in the report. The Column titles listed in the right-hand panel are those which will be included in the report. The Columns listed in the left-hand panel are the remaining options for columns, which will not be included in the report. Use the arrows in the center to move the columns as desired.

4. Click OK.

5. You will automatically be taken to the Analysis tools tab of the experiment, where you can see the Excel report in the list of analysis tools executions.

6. Double click the line to open the report. Click Export on the bottom right if you would like to export the report as an Excel file.

Instructions

1. In a Pending experiment in WebMetabase and go to the Chroma-browser tab.
2. In the Signals panel on the left, right-click on one of the signals and click Extract chromatogram.
3. In the new window, select the m/z you want to extract. There are a number of ways to do this. Click OK.
4. Check the box for the signal you want to visualize in the center of the screen.

5. Click and drag across the EIC to zoom. Click on the signal in the chromatogram so that it appears bold.

6. Click and drag across a peak to integrate it. The peak will appear shaded.

7. Click the Generate button at the top.

8.Click the Run MassMetaSite radio button at top. Then examine the chromatograms and re-integrate any signal as needed. Then click Execute. MassMetaSite will now process the new peak. A window will pop-up to say when the processing is complete and the compound has been added to the experiment.

The new metabolite will appear in the list of metabolites, and the fragmentation analysis will be provided as it is for any previously detected metabolite.

Instructions

1. In a Pending experiment in WebMetabase, go to the Compounds tab, and select a metabolite to edit.
2. Click the Edit button near the top.
3. Use the structure editor to manually edit the metabolite structure. The information in the table on the bottom will automatically be updated as you edit the structure.
4. Click the Fragmentation button at the bottom. A window will first pop up with settings for the fragmentation analysis. Edit the settings as desired and click OK. Now you can visualize the fragmentation analysis for the newly drawn structures.
5. Click Save on the fragmentation window and Save in the structure editor window.

The structure of the compound will now appear updated, and the new fragmentation analysis will be provided as it is for any other metabolite.

First, your user must have permissions in order to use the reporting system, so you will need to log into Oniro as an admin user and give the right permissions to the user.

The permissions you must activate for your user are “Report templates” and “Report writer”. “Report templates” will allow you to import the report templates into the system, and “Report writer” allows you to use them in experiments.

Instructions

1. Once your user has the permissions, go to the WebMetabase (small molecule) module, click on the Settings button, and then navigate to the “Report templates” tab. Here, you will manage all the templates to be used for creating reports.

2. In order to upload a report template, provide a name for the new template in the text box “Name”, and select the type of report. In the present version of WebMetabase, there are two report types: Experiment report—to be applied to a single experiment—and Multi experiment report—to be applied to a group of experiments. The “Experiment report” is the option you will use most of the time.

3. Click the Browse button to select a zip file, which we will provide you, to upload the template.

4. Click the Save button. This will upload the files into the server so that the report template is available to everyone.

• New: to start a new report template upload
• Delete: to delete the template from the database
• Download: downloads all the files of the template to the user’s computer
• Close: to exit of the report templates manager.

When you have some template files in WebMetabase, you are ready to create your reports. There are two different ways to create reports: by opening the approved experiments or by right clicking on the list of experiments you have in pending or approved.

Instructions

1. When you open an approved experiment, go to the ‘Analysis tools’ tab. Click on the Report button, and a dialog window will appear.

2. From this dialog window, select the options to generate the report. Some options are set by default, and we will explain in detail what each one means:

• Report template: The user can select from the templates uploaded to the system.
• Output type: The user can select to output the report in different formats: PDF, XML, Excel, Word or PowerPoint.
• Report name: The user can type the name of the report file.
• Mets group: The user can select the metabolite groups, if any, to be reported.
• Use complete chromatogram range if available: Check this check box in order to draw the chromatograms in the report with the full time range. This option is only available after the MassMetaSite 3.2 version uploaded files.
• Scale MS chromatography: Check this check box if the user wants to have a single scale for the chromatography.

UV chromatogram options

• Background subtraction: When UV data are available, check this box to draw the chromatogram by subtracting the chromatogram of the parent sample.
• Baseline correction: When UV data are available, check this box to draw the chromatogram by doing a correction in the baseline.

Substrate UV spectrum options

• Baseline correction: When UV data are available, check this box to draw a baseline-corrected UV spectra.
• Experiment conditions: This option is only shown if there is more than one sample within an experiment. There is a check box next to each condition, and the user can select which conditions should be included in the report.
• Generate: Click this button to generate the report. After the selection is done, a file with the specified name and options will be downloaded from the server to the client computer. Typically, it will be saved under the Downloads folder.
• Cancel: Go back to the previous window without generating the report.