Proteomics:Programmers Meeting on 2012-08-17

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Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Date: Friday August 17th
  • Time: 9:00-10:30



  1. Action points and status updates
  2. Pipeline article todo list
  3. Announce changes in Galaxy
  4. Next meeting

Action points and status updates


  • Bas is getting the combined differential expression tool (created by Perry Moerland and Elizabeth McClellan from AMC and EMC) to work in Galaxy.
  • He is also rewriting the Galaxy integration of NetWeaver (MS PRUNA) from multiple pages of input parameters to a single page to enable putting it in a workflow.


  • Pieter is refactoring the "X! Tandem to mzIdentML" transformer from Andy Jones (University of Liverpool).
  • He is also helping Andy with an article on a mzIdentML tool (Pieter will be co author).
  • Finally, he also reported some bugs in X! Tandem which will be fixed by the development team.


  • George is busy merging several branches of the Molgenis Compute code into one (command-line interface and web interface; support databases, clusters and grids).
  • He is also working on several articles and a grant proposal.
  • George and Peter Horvatovich (RUG) are looking at 8 pipelines from the organization.


  • Freek is participating in the team that is finding the best candidate for the TraIT position (which will be 50% proteomics). We have spoken to a lot of candidates and hope to make our decision soon.
  • He is also working with the group of people (from many organizations) that is starting up the DISC (Data Integration and Stewardship Centre, see for more information).

Pipeline article todo list

1. Add additional tools for identification: SpectraST from the Trans Proteomics Pipeline (TPP). Peptide/ProteinProphet is part of SpectraST so these tools will become available as well.

  • Progress: Ishtiaq has further investigated adding SpectraST.
  • Action point: Ishtiaq will add SpectraST?

2. Link between SedMat's APML and ExpressionSet (m/z and retention time) to annotate the aligned peaks in the consensus matrix. Consensus protein for each peak.

  • Progress: Pieter and Perry discussed the solutions.
  • Action point: Pieter will implement it and Perry will update the APML parser to incorporate the identifications in the ExpressionSet.

3. Converter between output of differential expression module and input for MS PRUNA. Also transfer peptide and protein ID annotations.

  • Progress: Elizabeth and Perry decided to rewrite the peptide/protein summarizer in two ways:
    • summarization on ExpressionSet followed by differential expression analysis and MS PRUNA;
    • differential expression analysis followed by summarization of p-values (Fisher's omnibus) followed by MS PRUNA).
  • Action point: Elizabeth will combine the tools and support two different orders in which processing can be done.
  • Action point: Bas will integrate the combined tool in Galaxy.

4. Documentation: extend and make more uniform. See ‘Differential Expression Analysis’ for a template.

  • Progress: this task was not worked on.
  • Action point: Bas has started evaluating the documentation some time ago. He will pick this up and propose an update.

5. Rearrange Galaxy tools with NPC tag in a more logical way.

  • Progress: Bas has looked at this before; Perry, Peter and Ishtiaq have made a proposal for a new menu structure; Thang looked at it during the dev day. All ideas where discussed.
  • Action point: Freek will make a unified proposal.

6. Use the experiment design for one of the tools in the pipeline.

  • Progress: Henk is working on this for pview.
  • Action point: He will check in his (not yet finished) code.
  • Questions: is this a separate project? Which repository will we use? Can you give an estimate for the finish date?

Announce changes in Galaxy

Pieter urged everyone to announce additions or major modifications of tools in Galaxy, so we are aware of the progress of things we can use and/or have to interface to.

Next meeting

Friday September 14th 9:00-10:30 will be our next programmer's meeting.