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