Proteomics:Programmers Meeting on 2011-01-21

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Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht.
  • Time: 9:00-10:30



  1. Action points and status updates
  2. Next meeting

Action points and status updates


  • Don is working on iPAS, a web client written in PHP for MS PRUNA which is used internally at Erasmus MC.
  • He is also helping Elizabeth getting MS PRUNA working in Galaxy.
  • Their plans for 2011 are: 1. get MS PRUNA working in iPAS, 2. get MS PRUNA working in Galaxy and 3. look at possibilities for combining MOLGENIS and MS PRUNA.

Elizabeth (update by Don):

  • Elizabeth is currently working on increasing the identification rates for MS PRUNA.


  • The computational management works and will be improved by added better error handling.
  • Changes in MOLGENIS' data model are possible, but can be difficult. Existing data can be migrated by exporting to Excel, changing the data model and importing from Excel again.
  • George has the following plans for 2011: 1. improve error handling, 2. connect to Galaxy and maybe Taverna (work flows), and 3. logging system.

Ishtiaq (update by Peter via Skype):

  • Ishtiaq and Carsten (AMC) are on a Pattern Recognition course (TU Delft) this week.
  • Ishtiaq's plans for 2011 are: 1. add msCompare to DAF, 2. combine MOLGENIS with DAF, 3. finish the work on the dynamic light paths and write a paper and 4. add a graphical workflow editor to DAF (if funding is available).

Berend (update by Peter via Skype):

  • His plans for 2011 are: 1. provide 2D-LC additions for msCompare, 2. coordinate changes with AMC, since high resolution data requires some changes and 3. incorporate OMSSA.


  • Wim is working on a very light LIMS system to store meta data related to their raw files (which are put on their new storage cluster).
  • He is writing a desktop client for information retrieval and a client for meta data entry which will be used with the MS machines. The first version is out for feedback from the users.
  • He is also working on software to analyze overlapping isotopes in non-labeled, high resolution data. This work could lead to a publication. It might be interested to add this tool to Galaxy, although probably not so many groups will face this problem.
  • Peter tells that his team has plans for a lights LIMS system.
  • Pieter explains that after evaluating several LIMS systems, the team in Utrecht decided to develop a small system of their own to improve the current situation (a network drive with large files and a limited amount of meta data in file and directory names). This situation is recognized by other research groups.


  • After the discussion on OMSSA during the NPC Progress Meeting, he has integrated OMSSA in his local Galaxy server and is now working on doing the same for the NBIC Galaxy server. A subset of the command line options is now supported, which we can expend as needed.
  • His plans for 2011 are: 1. work on quantitation with PVIEW 2, 2. finish the proteogenomics work on Trichoplax and 3. work on post-translational modifications (store PTMs and compare them to online databases).

Henk (update by Pieter):

  • He is working on the Trichoplax project as well to search for peptide sequences indicating currently unknown genes. The PEPslice program is now working, which was quite a chanllenge considering the lack of documentation.
  • His plans for 2011 are: StatQuant version 2.


  • NBIC will organize another hackathon on April 13th and 14th. Anyone interested in participating and/or with small projects that can be done please get in touch.
  • There was a meeting with some members of the metabolomics task force and the proteomics task force. Peter is looking at the Study Capture Framework that is being developed by the metabolomics team. Theo Reijmers (Leiden University) will participate in a grant application by Peter. Theo will send some of his data for proteomics analysis to Peter.
  • I am collecting our posters from the NPC Progress Meeting and will put those on the wiki.
  • For the NBIC year report, I am collecting information on collaboration partners, new projects/funds, patents/licenses and the number of meetings we had.

Next meeting

Friday February 18th 9:00-10:30 will be our next programmer's meeting.