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Protein bioinformatics and systems biology

Protein bioinformatics and systems biology. Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center. Unannotated Splice Isoform. Unannotated Splice Isoform. Halobacterium sp. NRC-1 ORF: GdhA1. K-score E -value vs PepArML @ 10% FDR

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Protein bioinformatics and systems biology

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  1. Protein bioinformatics and systems biology Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center

  2. Unannotated Splice Isoform

  3. Unannotated Splice Isoform

  4. Halobacterium sp. NRC-1ORF: GdhA1 • K-score E-valuevsPepArML @ 10% FDR • Many peptides inconsistent with annotated translation start site of NP_279651

  5. PepArML Meta-Search Engine X!Tandem, KScore, OMSSA, MyriMatch, Mascot (1 core). NSF TeraGrid 1000+ CPUs Heterogeneous compute resources X!Tandem, KScore, OMSSA, MyriMatch. Secure communication Edwards Lab Scheduler & 80+ CPUs Amazon AWS Scales easily to 250+ simultaneoussearches Single, simplesearch request

  6. False-Discovery-Rate Curves

  7. PeptideMapper Web Service I’m Feeling Lucky

  8. PeptideMapper Web Service I’m Feeling Lucky

  9. If a tree falls in the forest…

  10. Nascent polypeptide-associated complex subunit alpha • Long form is "muscle-specific" • Exon 3 is missing from short form • Peptide identifications provide evidence for long form only • 9 peptides are specific to long form • 6 peptides are found in both isoforms • Urn with balls of 15 different colors • p-value of observed spectral counts: 7.3E-8

  11. Top-down CID Protein Fragmentation from Y. rohdei Match to Y. pestis 50S Ribosomal Protein L32

  12. Phyloproteomics of Y. rohdei Protein Sequence 16S-rRNA Sequence

  13. Example Glycopeptide CID Fragmentation Spectrum

  14. Haptoglobin standard • N-glycosylation motif (NX/ST) * Site of GluC cleavage Pompach et al. Journal of Proteome Research 11.3 (2012): 1728–1740. Haptoglobin (HPT_HUMAN) NLFLNHSE*NATAK VVLHPNYSQVDIGLIK MVSHHNLTTGATLINE

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