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Quick and clean: Cracking E.coli’s code by LC-MS/MS, de novo sequencing, and dictionary search

ABSTRACT: In this study, we faced the challenge of deciphering a protein that has been designed and expressed by E.coli in such a way that the amino acid sequence encodes two concatenated English sentences. The sequence carried unknown modifications and cannot be found online. The letters ‘O’ and ‘U’ are both replaced by ‘K’ in the protein. To solve the challenge, we developped a workflow consisting of shotgun proteomics, de novo sequencing and a bioinformatic tool to search for words from the identified sequences. By using this workflow, we assembled the first complete English sentence and validated by searching against a customized sequence database.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Lili Niu

LAB HEAD: Matthias Mann

PROVIDER: PXD012015 | Pride | 2020-05-26

REPOSITORIES: Pride

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Quick and clean: Cracking sentences encoded in <i>E. coli</i> by LC-MS/MS, de novo sequencing, and dictionary search.

Niu Lili L Mann Matthias M

EuPA open proteomics 20190301

In this study, we faced the challenge of deciphering a protein that has been designed and expressed by <i>E. coli</i> in such a way that the amino acid sequence encodes two concatenated English sentences. The letters 'O' and 'U' in the sentence are both replaced by 'K' in the protein. The sequence cannot be found online and carried to-be-discovered modifications. With limited information in hand, to solve the challenge, we developed a workflow consisting of bottom-up proteomics, de novo sequenci ...[more]

PMID: 31890553

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