PXD012015

PXD012015 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-11 08:28:21	ID requested
⏵ 1	2020-05-26 12:49:15	announced

Niu L, Mann M, by LC-MS/MS, de novo sequencing, and dictionary search. EuPA Open Proteom, 22-23():30-35(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: E.Coli, proteomics, de novo sequencing

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

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

• PRIDE
  1. PXD012015
     1. Label: PRIDE project
     2. Name: Quick and clean: Cracking E.coli’s code by LC-MS/MS, de novo sequencing, and dictionary search