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Comparative Proteogenomics: Lessons learned from the excercise

Discover lessons learned from a proteogenomics exercise by Samuel H. Payne at J. Craig Venter Institute. Explore the practice of working with 30 proteomes in 3 years and the benefits of comparative proteogenomics. Learn about resolving conflicts in ORF filtering, leveraging peptide uniqueness, minimum peptide and protein considerations, length clustering for GC-rich genomes, understanding tryptic content of peptide sets, and unraveling sequence complexity with GA-rich peptides. Special thanks to Eli Venter, Dick Smith from PNNL, and NSF for their contributions.

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Comparative Proteogenomics: Lessons learned from the excercise

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  1. Comparative Proteogenomics:Lessons learned from the excercise Samuel H Payne J Craig Venter Institute

  2. Proteogenomics Protocol

  3. Practice Makes Perfect • 30 proteomes in 3 years

  4. Future • Comparative Proteogenomics • What can be learned with multiple datasets?

  5. Practice Reveals Flaws • Conflict resolution

  6. ORF Filtering • Peptide uniqueness • Min peptide/protein • Length clustering (GC rich genomes) • Tryptic content of peptide set • Sequence complexity (GA rich peptides)

  7. Acknowledgements • Eli Venter • Dick Smith, PNNL • NSF

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