Proteomics:Gaining Momentum Meeting on 2011-11-14

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Location and time

  • Location: Kruytbuilding (6th floor, east wing), Padualaan 8, 3584 CH Utrecht
  • Date: Monday November 14th, 2011
  • Time: 13:00-17:00



  1. Status updates
  2. Action points
  3. Next meeting

Status updates

  • Pieter presented the new plans from Wageningen for the task force pipeline.
  • Bas explained more about pview and what makes it an interesting tool.
  • Péter showed mcCompare. We discussed the possibility to include pview in msCompare (this would require the functionality to be divided for the two phases).
  • Ishtiaq gave an update on the statistical tools from AMC.
  • We talked about proteomics search tools that we can use in Galaxy: X! Tandem, OMSSA and Mascot. Pieter will investigate Mascot and X! Tandem.
  • Bas advised Thang to consider using massQC (approx. 5,000 euro) as a short term solution for quality control and switching to PRIME-XS tools in the long term.

Action points

  • November 2011 - Ishtiaq: help EMC with VM updates and report generation.
  • November 2011 - Andrew: supply data to Pieter and Twan.
  • November 2011 - Péter: supply data to Pieter and Twan.
  • November 2011 - Andrew, Bas and Henk: exchange information on pview CLI, functional requirements.
  • November 2011 - Pieter: get data & Galaxy workflow from Péter and get it running.
  • November 2011 - Freek: create overview page of available test data on the wiki, plan next meeting and create minutes.
  • December 2011 - Berend: documentation and test data for msCompare.
  • December 2011 - Pieter: integrate SetMat in the pipeline, database search and feature alignment.
  • December 2011 - Thang: put VUmc statistical tool on NBIC Galaxy server (with help from Ishtiaq and Freek).
  • December 2011 - Henk: look at possibilities for splitting pview in two phases to fit msCompare model.
  • December 2011 - Bas: get quality control (QC) list from PRIME-XS plans (file formats, reference implementation).
  • January 2012 - Henk, Ishtiaq, Ivo Palli (EMC) and Freek: command-line interface for pview, integration in Galaxy.

Next meeting

The NPC Progress Meeting 2012 is coming up on 7 February 2012 in Media Plaza (Jaarbeurs), Utrecht. We will have our Gaining Momentum Meeting from 9:30 until 12:30 (as one of the theme sessions for NPC project groups). The whole day runs from 9:00 until 18:00.

For more information: