# Presentation: 844511

## Gap analysis of proteomics tools and & data in caBIG 

- Proteomics SIG meeting June 12, 2006

## Agenda

-  Introduction of Simon Lin as the new Proteomics SIG lead
-  Follow-up of the ICR face-to-face proteomics gap analysis session
-  Current status of proteomics
-  Proteomics moving forward

## Simon Lin

- Assistant Professor, Associate Director Bioinformatics Facility, Northwestern University
- Research interests
- Noncoding regions (1999-2001)
- Microarrays (2000-2005)
- Mass Spectrometry (2003-now)
- Contact details
- _[s-lin2@northwestern.edu](mailto:s-lin2@northwestern.edu)_
- 312-695-1331

## Follow-up of the ICR F2F

- Gap analysis led by David Fenstermacher; currently under-represented technologies in the SIG.
- Some topics will be covered today (not nearly an exhaustive discussion of the ICR F2F breakout session—see webpage for a complete list). A few topics offer a way to focus.
- Protein Arrays
- Same as DNA microarrays? Imaging processing, normalization/calibration, annotation, etc.
- How to integrate the results with gene-based microarrays?
- Data repository? Workflow?

## Proteomics: Current Status

- Proteomics (compared with microarrays)
- Established or evolving?
- Engineering optimization or scientific investigation?
- Adopting standards or help the establishment of standards?
- Liquid Chromatography(LC) - MS
- Example: Nanospray ESI
- The LC dimension
- Modeling of the LC part: variations

## Integration of Proteomics Tools with caBIGTM Components

- Interactions with other ICR groups
- Integrating proteins, genes, and pathways
- Integrating with caWorkbench (Duke)
- Integrating with Bioconductor (Northwestern)
- Interactions with the Architecture WS
- Moving data to tools or moving tools to data? (FHCC)
- Workflow (Duke)
- Large binary data: mzXML (Duke), mzHDF (Northwestern)
- Interactions with tissue banks
- ProLIMS (Fox Chase)

## Proteomics: what can we do about it

- Other topics discussed at the ICR F2F gap analysis breakout:
- Issues:
- plug in at multiple entry points
- proteomics is a “moving target.” Might need to have multiple sites since we don’t know what will survive in the future.
- standardization around data for analysis.
- where is the data going to live? We don’t have a database repository for caBIG. It would be great if database schema is standardized.
- we don’t have the bandwidth for proteomics.
- use this group as a way to drive standardization.

## Proteomics: what can we do about it

- Role of task forces (for each identified topic):
- Use of Gforge wiki to facilitate information transfer
- Assess the status
- Suggest solutions
- Write white papers

## Future SIG Meetings

- Yr 1 caBIG Project Presentations
- Feedback from end-users
- Invited Speakers
- E.g. in the past CPAS, HUPO
- Task force Presentations
- Protein arrays, object model for protein identification results, etc.
- Wiki: use this as a basis for discussion in this meeting
- White papers: Strategic planning for proteomics in caBIG

## Contact details

- Simon Lin  M.D. (Robert H Lurie Cancer Center)
- 312 695 1331
- _[S-Lin2@northwestern.edu](mailto:S-Lin2@northwestern.edu)_
- Vivien Bonazzi  Ph.D. (Booz Allen)
- 301 998 6851
- Bonazzi_vivien@bah.com