Thursday, 19 June 2014

code signing with 'Deutsche Telekom Root CA 2' root certificate

I used to sign my applications (several GMD tools, GoBioSpace Search Application) with a certificate which was trusted up the chain by the MPG,  the DFN and the Deutsche Telekom.

This certificate was issued 24.04.2012 and was working fine until recently. Out of blue several users reported that they could not install any more application I signed. It turned out that something changed in the certificate store of windows and you need to except the root certificate for code signing.
This post will guide you through.

Normally, after clicking to install the application from the internet explorer you will see on the bottom of the page a dialog like this, asking for permission to run the installer.

 Now you will experience something similar to this error message 'The signature of setup.exe is corrupt or invalid.'
 or, if you click to see the details
To solve this, press the Windows Key + R and type "mmc" and click OK.
you will see the Microsoft Management Console
click File and "Add/Remove snap-In" to add the certificate Plug-In
activate "my user accout" and click finish
you will see the certificate plug-in on the right. now click OK.
 In the left panel activate Trusted Root Certification Authorities and then Certificates. Search for the 'Deutsche Telekom Root CA 2' certificate in the right hand panel. Right click this certificate and select properties. Activate the the purpose 'code signing' as shown below and press OK.
Problem solved. If you retry to install some application my certificate will be accepted for code signing and, hence, the software will get installed.

Wednesday, 11 June 2014

GMD service unavailable

Our service is unavailable this morning due to network maintenance. We apologize for any inconvenience and we are working to bring the site back online as soon as possible.

Monday, 26 August 2013

Most Abundant Compounds in their Elution Order for Arabidopsis Sample

Last week I got this question asked:

"... I might as well ask if you know of a source of peak identification for typical Arabidopsis rosette polar compounds derivatized to typical MeOX/TMS forms (sugars, organic acids, amino acids, etc. obtained from a typical MeOH/H20 extraction)? I am trying to identify the most abundant polar compounds (top 100 or so) in Arabidopsis leaf tissue but I have limited access to standards and I am sure this has already been done. Here is what I would ideally need: a list of the most abundant compounds in their elution order on a ms5 column or similar with spectra. Any idea if such a list can be found on the GMD site or elsewhere?"

Friday, 28 June 2013

Metabolomics Society 2013 Conference

If you are going to the Metabolomics Society 2013 Conference in Glasgow next week then I hope to see you there. Stop by the poster P9-12 during poster session II and say hi! There is a lot going on in Metabolomics and we will be reporting on some of our latest developments towards Big Data science. I also post the link to our last year's poster from the Metabolomics Society 2012 Conference in Washington, DC.
During this year's Metabolomics Society Award Ceremony our work on Decision tree supported substructure prediction of metabolites from GC-MS profiles will be award 2013 Best Paper Runner up for the second highest total number of citations during the previous three years. Wow! What a pleasant surprise.

Wednesday, 12 June 2013

Cross Experiment Comparison of One Metabolite

The cross experiment control on the metabolite detail page has been updated to convey more information at glance. Instead of a big box plot comparing all experiments to one another, a list with experiments has been added. Each row consists of a heat map and a tiny box plot, as well as the experiment name, organism, the variance, the anova F score and the main experimental conditions. When hovering above a row, a bigger version of the box plot with more detailed experimental conditions appears.


Friday, 11 May 2012

How to import the GMD refenrence library into NIST MS Search

I got this question asked today and thought this is worth be documented. I only have version 2.0 of the NIST ms search software at hand, but I assume that the way to import the reference library is pretty similar in later versions.
  1. Start the program.
  2. Click Librarian on the tab control at the bottom.
  3. Create a library by clicking the most right button in the toolbar.
  4. Type an appropriate library name - "GMD".
  5. Close the dialog by clicking OK. The click on the Import button, left in the toolbar.
  6. Select the msp-file downloaded from the GMD. Make sure to first select "All files" in the file type menu.
  7. In the option check "include Synonyms" Click "Import All".
  8. The import is starting.
  9. You can cancel the library matching process.
  10.  The GMD reference library is imported and ready for use.

Thursday, 22 March 2012

3 question about the GMD mass spectral reference library

I got this three questions and think I should answer those here because the topic might be interesting to other people as well...
1.- Could I consider the following examples (VAR5-Alk-NA 170001  (Classified unknown); VAR5-Alk-NA and VAR5-Alk-unknown)  as unknown or do they mean something different?
These terms do all refer to a unknown compound. This just points to a lack in annotation. As we also ask other laboratories for their spectral libraries it may happen that users use different terms. However, in your example with NA170001 (classified unknown) Joachim Kopka tried to highlight, that there is a chance of identification either as "[C5H12O5 (5TMS)|C20H52O5Si5]" or "[Pentitol (5TMS)|C20H52O5Si5]".
2.- Sometimes the compounds are label as True-VAR5-Alk, False-VAR5-Alk and Pred-VAR5-Alk. can I understand that the database was not curate?  therefore there are some False. However the ones that are PRED  (=predicted?) Can i trust in this prediction? or do i need only to pay attention to the compounds that says true?
This "True", "False" and "pred" just refers to the Retention index. The retention index is specific to the chromatographic setup. As the GMD is a collection of reference spectra from different labs utilising different chromatographic setups we differentiate the quality of the retention index values.
  • "true" is the best and refers to the fact, that this RI was actually experimentally observed on this chromatographic setup.
  • "pred" means predicted and is the next lower quality level. Importing a library from a other laboratory we can correlate the retention indexes values for all compounds which were measured in both labs. Next we use this correlation (a polynomial fitting or whatever) for a regression of the RIs from new Compounds in the other laboratory's library into our own chromatographic system.
    The quality of the retention index values from such regression depends on the similarity of the chromatographic variant in terms of column polarity, temperature programming and so on. This retention index prediction looks perfect, however as can be seen from the plot, the estimated error in such an predicted retention index is already too large for an automated spectral identification processing. Nevertheless, it is a valuable information in the identification process of unknown spectra.
    A retention index prediction with a quality near to experimental observed retention indexes is shown in plot below.
    If we don't have any experimentally measured retention index available, but can predict one from different chromatographic setups, we chose the one which makes the best sense from a chromatographic similarity point of view.
    As far as I understand this field, a final identification can only be proofed by using authentic reference substances.
  • "False" refers to the fact, that we don't have a retention index available for the selected chromatographic setup.
retention index regression between very similar chromatographic variants but different retention index markers.
3.-PRED-Var5-Alk-Similar Does mean there is a high probability that  this compound  will be true?
Again, predicted refers only to the retention index. And "similar" comes from a user input. In this case it is a unknown compound measured in a other lab with different chromatographic setup. That’s why we just have a predicted RI available.