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Date/Location

March 17-19, 2004
Fred Hutchinson Cancer Research Center, Seattle, WA

Hosted by:

The University of Alabama at Birmingham
Principal Investigator: William E. Grizzle, M.D., Ph.D.
(Validation Laboratory of the EDRN) &
The Fred Hutchinson Cancer Research Center
Principal Investigator: Ziding Feng, Ph.D.
(Data Management and Coordinating Center of the EDRN)

Goals

Goal 1: To familiarize bioinformatic/statistical personnel with the analysis of SELDI data currently performed by the DMCC. This will include hands-on use of macros used in SELDI analysis. Methods used by other bioinformatics groups in the analysis of SELDI-TOF-MS and MALDI-TOF-MS data will be introduced.

Goal 2: To identify new approaches to SELDI MALDI analysis and how software and biomathematical approaches developed for analysis of gene arrays may be adapted to proteomic techniques.

Goal 3: To educate statisticians/bioinformaticians in the limitations of SELDI/MALDI technology and the potential effects of these limitations of analytical approaches.

Goal 4: To ensure attendees become familiar with the features of Ciphergen/DMCC software/macros.

Goal 5: To establish working groups and collaborations among statisticians/bioinformaticians toward new approaches and software development for SELDI/MALDI analysis and collaborations among attendees in these areas.

Presentations

The following presentations are available from the conference/workshop. All presentations are in Adobe PDF format. Some files are large and may require a long download time. Please note the file sizes listed after the presentation title.

• Classifier construction via Boosting (pdf, 488kb)
• What Approaches are Needed to Advance Proteomic Analysis? (pdf, 509kb)
• caBig Vocabularies & Common Data Elements (pdf, 404kb)
• Low-level processing of proteomic spectra (pdf, 808kb)
• Permutation Achieved Classification Error (PACE): A Significance Test for Assessing the Statistical Significance of Classifiers for Peptide Profiling via MALDI/SELDI-TOF Mass Spectrometry (pdf, 1.5mb)
• Reproducability of SELDI/MALDI Spectra (pdf, 3.3mb)
• Over Viewing SELDI Data to Determine Quality: what are the statistical and pre-analytical considerations? (pdf, 1.5mb)
• caBIG Architecture Kickoff Meeting Presentation (pdf, 321kb)

• caBIG CDE/V Kickoff Meeting Presentation (pdf, 539kb)
• Proteomics: Finding the Needle in the Haystack (pdf, 1.3mb)
• The Need for the Review and Understanding of SELDI/MALDI Data Prior to Analysis (Analyzer Beware) (pdf, 583kb)

• Design of Early Validation Trials of Biomarkers (pdf, 65kb)
• Object Oriented Data Technology (OODT) (pdf, 1.8mb)
• Peak identification and alignment (pdf, 818kb)
• A critical view of spectral analysis (pdf, 721kb)
• Signal and Noise: Garbage in Garbage out (pdf, 2.4mb)
• Peak versus AUC to compare SELDI data (pdf, 133kb)
• The Knowledge Discovery Engine™ (pdf, 1.44mb)
• Issues in the Analysis of SELDI-TOF-MS Data (pdf, 1.5mb)