PXD012015 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Quick and clean: Cracking E.coli’s code by LC-MS/MS, de novo sequencing, and dictionary search |
Description | 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. |
HostingRepository | PRIDE |
AnnounceDate | 2020-05-26 |
AnnouncementXML | Submission_2020-05-26_12:49:14.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Lili Niu |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos; Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-12-11 08:28:21 | ID requested | |
⏵ 1 | 2020-05-26 12:49:15 | announced | |
Publication List
Niu L, Mann M, by LC-MS/MS, de novo sequencing, and dictionary search. EuPA Open Proteom, 22-23():30-35(2019) [pubmed] |
Keyword List
curator keyword: Technical, Biological |
submitter keyword: E.Coli, proteomics, de novo sequencing |
Contact List
Matthias Mann |
contact affiliation | Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany |
contact email | mmann@biochem.mpg.de |
lab head | |
Lili Niu |
contact affiliation | University of Copenhagen |
contact email | lili.niu@cpr.ku.dk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/05/PXD012015 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD012015
- Label: PRIDE project
- Name: Quick and clean: Cracking E.coli’s code by LC-MS/MS, de novo sequencing, and dictionary search