Cyclopeptide Sequencing

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Presentation transcript:

Cyclopeptide Sequencing Obyanamide, a non-ribosomally produced antitumor. From Norine database. Tayla Isensee

Problem: Antibiotics are not in the genome Solution: Mass Spectrometry Coding Problem: Brute force takes too long Solution: Branch and bound Candidates: ['PG', 'PA', 'PS', 'PP', 'PV', 'PT', 'PC', 'PI', 'PL', 'PN', 'PD', 'PK', 'PQ', 'PE', 'PM', 'PH', 'PF', 'PR', 'PY', 'PW', 'PG', 'PA', 'PS', 'PP', 'PV', 'PT', 'PC', 'PI', 'PL', 'PN', 'PD', 'PK', 'PQ', 'PE', 'PM', 'PH', 'PF', 'PR', 'PY', 'PW', 'VG', 'VA', 'VS', 'VP', 'VV', 'VT‘...] Peptides Kept: ['PV', 'PT', 'PC', 'VP', 'VV', 'VT', 'VC', 'TP', 'TV', 'TT', 'CP', 'CV']

Data Spectrum = [0, 97, 97, 99, 101, 103, 196, 198, 198, 200, 202, 295, 297, 299, 299, 301, 394, 396, 398, 400, 400, 497]

High Level Steps CyclopeptideSequencing(Spectrum) Peptides ← a list while Final Peptides is empty: Peptides ← Expand(Peptides) for each peptide Peptide in Peptides if Mass(Peptide) is in Spectrum KeptPeps = KeptPeps + peptide if Cyclospectrum(Peptide) = Spectrum Final Peptides + Peptide output Final Peptide Peptides = KeptPeps clear KeptPeps CyclopeptideSequencing(Spectrum) Peptides ← a set containing only the empty peptide while Peptides is nonempty Peptides ← Expand(Peptides) for each peptide Peptide in Peptides if Mass(Peptide) = ParentMass(Spectrum) if Cyclospectrum(Peptide) = Spectrum output Peptide remove Peptide from Peptides else if Peptide is not consistent with Spectrum remove Peptide from Peptides

Results Program can sequence cyclic peptides! But…runtime limits the length of peptide (no leaderboard) And…LOTS of assumptions about the fidelity of the data Spectrum = [0, 97, 97, 99, 101, 103, 196, 198, 198, 200, 202, 295, 297, 299, 299, 301, 394, 396, 398, 400, 400, 497] Possible Amino Acid Sequence = PVCPT Mass Sequence = 97-99-103-97-101

Conclusion Program works on highly improbable, perfect datasets Improving runtime, either with more expansive bounding or implementing a leaderboard But… NRPs can contain more than 20 aa’s (100s), It isn’t science unless you find a cool database =