Novel Peptide Identification using ESTs and Genomic Sequence

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Novel Peptide Identification using ESTs and
Genomic Sequence

• Nathan Edwards
• Center for Bioinformatics and Computational
  Biology
• University of Maryland, College Park

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Novel Protein

• HEQASNVLSDISEFR
• Evidence
• log10(E-value) -9.6
• 100s of ESTs
• Full length mRNA sequence
• Details
• Peptide Atlas A8_IP (Resing et al.)

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Novel Protein
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Novel Protein
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Novel Protein
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Novel Splice Isoform

• LQGSATAAEAQVGHQTAR
• Evidence
• log10(E-value) -6.8
• 10s of ESTs
• Full length mRNA sequence
• Details
• Peptide Atlas raftflow (von Haller, et al.)
• LIME1 gene

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Novel Splice Isoform
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Novel Splice Isoform
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Novel Mutation

• KADDTWEPFASGK
• Evidence
• log10(E-value) -7.6
• 2 EST from same clone library
• Ala2 Deletion
• Details
• HUPO PPP 29_b1-EDTA_1 (Qian/He Omenn et al.)
• TTR gene
• Known Mutation Ala2-to-Pro associated with
  familial amyloidotic polyneuropathy.

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Novel Mutation
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Novel Mutation
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Novel Mutation
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Novel Mutation
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Known Coding SNP

• LQHLEVNELTHDIITK
• Evidence
• log10(E-value) -6.7/-10.9
• 4 ESTs, same clone library
• Known dbSNP (coding) Glu5-to-Val
• Wildtype also observed
• Details
• HUPO PPP 28_b2-CIT (Pounds/Adkins/Rodland/Anderson
  Omenn et al.)
• SERPINA1 gene

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Wildtype
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Known Coding SNP
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Known Coding SNP
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Known Coding SNP

• DTEEEDFHVDQVATTVK
• Evidence
• log10(E-value) -9.5 / -9.4
• Known dbSNP (coding) Val12-to-Ala
• Wildtype also observed
• Details
• HUPO PPP 40 (Wang Omenn et al.)
• SERPINA1 gene

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Wildtype
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Known Coding SNP
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Known Coding SNP
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IPI Common Variant Elimination

• YYGGGYGSTQATFMVFQALAQYQK
• Evidence
• log10(E-value) -5.9
• 100s ESTs, mRNA sequence
• IPI has (rare) variant (Insertion of AS_at_10)
• Differ in 5 splice site.
• Details
• HUPO PPP 29_b1-CIT_win1 (Qian/He Omenn et al.)
  
• C3 gene

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IPI Common Variant Elimination
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IPI Common Variant Elimination