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Recently Asked Questions

In this section you will fine the most typical questions and answers that we have collected over the years.

WEBMETABASE - How to process experiments with 'big' small molecules (MW>500mDa) in WMB4?

In MassMetaSite molecules can be imported in different modes: small molecule modes (different file types) and SD file (Macromolecules). Experiments can processed in MassMetaSite in two different modes: Standard and Peptide mode.

Depending on how molecules were imported and experiments were processed we can describe four main workflows:

  1. Imported in SM mode and processed in Standard mode – usual SM workflow. Ms3 files generated with this workflow should be uploaded into SM module in WMB4.
  2. Imported in MM mode, processed in Peptide mode -> usual MM workflow. Ms3 files generated with this workflow should be uploaded into MM module in WMB4.
  3. Imported in MM mode and processed in Standard mode-> this workflow can be used to process ‘big’ small molecule (MW>500mDa). It helps to speed up processing because 3d conformers generation and SOM prediction are skipped.

Uploading procedure into WMB4 will change depending on WMB4.0.X version.

WMB 4.0.4

Ms3 files generated with this workflow should be uploaded into SM module in WMB4. If they are uploaded in MM module, parsing will be blocked. Status “Parsing” will be marked in red bold font.

WMB 4.0.3

Ms3 files generated with this workflow could not be uploaded into SM module in WMB4. If they are uploaded in MM module, parsing will be blocked. Status “Parsing” will be marked in red bold font.

It is highly recommended to update WMB version to 4.0.4.

In all build WMB4 before 4.0.3 – Ms3 files generated with this workflow could not be uploaded into SM module in WMB4. If they are uploaded in MM module, they are parsed.

For each molecule in these experiments monomer generation and HELM notation generation will be executed. It can cause problems with the WMB performance. Also these experiments are not considered by Analysis tools for SM. It is highly recommended to update WMB version to 4.0.4.

In case if WMB can’t be updated, experiments should be re-processed in MassMetasite with workflow 1 and uploaded in SM module.

WEBMETABASE- During migration from WMB3 to WMB4 what happens to the uploaded experiments if User has experiments with small molecules processed imported MassMetasite in Macromolecules mode?

In MassMetaSite molecules can be imported in different modes: small molecule modes (different file types) and SD file (Macromolecules). Experiments can processed in MassMetasite in two different modes: Standard and Peptide mode.

Depending on how molecules were imported and experiments were processed we can describe four main workflows:

  1. Imported in SM mode and processed in Standard mode – usual SM workflow;
  2. Imported in MM mode, processed in Peptide mode -> usual MM workflow;
  3. Imported in MM mode and processed in Standard mode-> this workflow can be used to process ‘big’ small molecule (MW>500mDa). It helps to speed up processing because 3d conformers generation and SOM prediction are skipped;
  4. Imported in SM mode, processed in Peptide mode -> this workflow can be used to process ‘big’ small molecule. It helps to speed up processing because less bonds have to be fragmented.

In WMB4 Macro molecule (MM) experiments and Small Molecule experiments are separated in two modules. MM experiments are parsed in WMB in a different way comparing to SM.

 

During migration from WMB3 to WMB4 all experiments in database are automatically separated in SM module and MM module, depending on the way how they were processed in MassMetasite.

  • Experiments processed with workflow 1 and 4 are automatically assigned into SM module.
  • Experiments processed with workflow 2 are automatically assigned into MM module and will be parsed in a new way (here we need to add hyperlink to previous question).
  • User has to notify Lead Molecular before migration if there are experiments processed with workflow 3. In this case SQL script is provided and after script execution these eperiments are automatically assigned into SM module.

 

If SQL script is not executed during migration, experiments processed with workflow 3 will be automatically assigned into MM module and will be processed in different ways depending on WMB4 version.

WebMetabase 4.0.1, 4.0.2 and 4.0.3

For each molecule in these experiments monomer generation and HELM notation generation will be executed. It can cause problems with the WMB performance.

Also these experiments are not considered by Analysis tools for SM.

Unfortunately, to avoid this, experiments should be deleted manually from MM module.

WebMetabase should be updated to 4.0.4 and these ms3 files should be manually re-uploaded in SM module in newly manually created protocols.

In case if WMB can’t be updated, ms3 files processed with workflow 3 can’t be directly uploaded in SM module in WMB.

Experiments should be re-processed in MassMetasite in workflow 1 and after uploaded in SM module. Thus it is highly recommended to update WMB version to 4.0.4.

WebMetabase 4.0.4

No additional processing will be done for these experiments.

But it is still highly recommended to re-upload them into SM module in other way these experiments are not considered by Analysis tools for SM.

WEBMETABASE - What is different in Macro molecule processing in WMB4 comparing to WMB3?

In WMB4 Macro molecule (MM) experiments and Small Molecule experiments are separated in two modules.

MM experiments are processed in a different way comparing to SM. A new visualization with HELM notation was added for the MM.

Now MM can be seen not only as a 2D chemical structure but also in HELM notation (sequence of monomers).

Therefore Macro molecules are processed in a different way comparing to small ones.

During experiment parsing in WMB4 every MM is virtually broken by amide bonds into structural blocks between bonds (monomers).

These monomers and their connectivity map are used to generate HELM notation.

It is important to know that it can potentially increase experiment parsing time in case if experiment contains a lot of potential metabolites structures.

WEBMETABASE - Where do I find a report template?

WEBMETABASE - What are the server requirements to run WebMetabase?

The platform needed to host WebMetabase has this minimum requirements:

  • Windows or Linux platform (64 bits)
  • 4 (or more) CPU core
  • 8 (or more) Gb of RAM.
  • 250G of disk space (500G or more if the database server has to run on the same machine).
    WebMetabase application needs the following software to be installed prior it’s deployment:

Java JDK (could run on JRE too), version 7 minimum; 64 bit platform is needed,

Application Server, WebMetabase system has been tested on the following application servers:

  • Apache Tomcat (version 7 or 8)
  • Jetty
  • Oracle GlassFish (version 4.0)

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

  • Cloudscape
  • Cubrid
  • DB2
  • Derby
  • Firebird
  • H2
  • Hsqldb
  • Informix
  • MySQL *
  • Oracle *
  • Pointbase
  • Postgres
  • SAPdb
  • Solid
  • SQLserver
  • Sybase

WEBMETABASE - Where do I find information about WebMetabase installation?

The user can find information about the WebMetabase installation at Moldiscovery webmetabase web page

MASSMETASITE - Why am I unable to process Thermo RAW files?

Problem

Error messages might be:

  • RUN ERROR(Unable to process negative control file)
  • mzqt exception: THERMO INTERFACE ERROR(Unable to init interface)
  • Unrecognized option: P
Solution
  1. Install Thermo MSFile Reader 3.1 SP3 followed by MSFile Reader 3.1 SP4. You need to have or to create a Thermo account to access the file. INSTALL THERMO MSFILE READER IN ADMINISTRATOR MODE
  2. Install The last version of the msfile-converter (2.3.12-msvc64).
  3. Install  Visual C++ Redistributable 2012
  4. Install  Visual C++ Redistributable 2013
  5. Install  Visual C++ Redistributable 2015
  6. Restart MassMetaSite
  7. Update The msfile-converter path in MassMetaSite settings

MASSMETASITE - Unable to init WiffReader2: IDISPATCH ERROR

Typically you will get that message during file conversion if you have never processed any wiff files before. Or if you had been working with a 32 bit version of MassMetaSite having version 1 of the wiff access patch

You need to install the new wiff reader available at: http://download.moldiscovery.com/MMS%20Wiff%20Access%20Patch%202-win64.exe

Install it in administrator mode and with .Net 4 installed.

To know if .Net 4 is properly installed please check that the folder ‘C:\Windows\Microsoft.NET\Framework64\v4.0.30319’ exists

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