Comparative Proteogenomics: Lessons learned from the excercise
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Comparative Proteogenomics: Lessons learned from the excercise Samuel H Payne J Craig Venter Institute
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Comparative Proteogenomics: Lessons learned from the excercise. Samuel H Payne J Craig Venter Institute. Proteogenomics Protocol. Practice Makes Perfect. 30 proteomes in 3 years. Future. Comparative Proteogenomics What can be learned with multiple datasets?. Practice Reveals Flaws. - PowerPoint PPT Presentation
Transcript of Comparative Proteogenomics: Lessons learned from the excercise
Comparative Proteogenomics:Lessons learned from the
excercise
Samuel H Payne
J Craig Venter Institute
Proteogenomics Protocol
Practice Makes Perfect
• 30 proteomes in 3 yearsNovel New Start
Y. pestis 4 5
B. anthracis 4 6
D. radiodurans 86 50
D. vulgaris 40 75
L. interrogans 18 26
C. crescentus 65 105
C. synechocystis 7 18
Arthrobacter 12 65
Pelagibacter 4 29
Future
• Comparative Proteogenomics What can be learned with multiple
datasets?
Practice Reveals Flaws
• Conflict resolution
ORF Filtering
• Peptide uniqueness• Min peptide/protein• Length clustering (GC rich genomes)• Tryptic content of peptide set• Sequence complexity (GA rich peptides)
Caulobacter 67% GC ORF FiltersSpectrum FDR
True Peptides
Decoy Peptides
Peptide FDR
Old New
p < 0.05 74291 16979 0.22 2128 1716p < 0.01 51463 2176 0.04 249 169p < 0.005 35627 736 0.02 98 79p < 0.001 17687 66 0.003 45p < 0.0005 16537 32 0.002 44p < 0.0001 12959 4 0.0003 36
Acknowledgements
• Eli Venter
• Dick Smith, PNNL
• NSF
