PXD003342

PXD003342 is an original dataset announced via ProteomeXchange.

Title	C-terminomics E. coli
Description	The identification of protein C-termini in complex proteomes is challenging due to the poor ionization efficiency of the carboxyl group. Amidating the negatively charged C-termini with ethanolamine (EA) has been suggested to improve detection of C-terminal peptides and allows for a directed depletion of internal peptides after proteolysis using carboxyl reactive polymers. In the present study the derivatization with N,N-dimethylethylenediamine (DMEDA) and (4-aminobutyl)guanidine (AG) leading to a positively charged C-terminus was investigated. C-terminal charge-reversed peptides showed improved coverage of b- and y-ion series in the MS/MS spectra compared to their non-charged counterparts. DMEDA-derivatized peptides resulted in many peptides with charge states of 3+ which benefited from ETD-fragmentation. This makes the charge reversal strategy particularly useful for the analysis of protein C-termini which may also be posttranslationally modified. The labeling strategy and the indirect enrichment of C-termini worked with similar efficiency for both DMEDA and EA and their applicability was demonstrated on an E. coli proteome. Utilizing two proteases and different MS/MS activation mechanisms allowed for the identification of >400 C-termini, encompassing both canonical and truncated C-termini.
HostingRepository	PRIDE
AnnounceDate	2016-03-11
AnnouncementXML	Submission_2016-03-11_04:36:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Tholey
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-12-14 07:33:42	ID requested
⏵ 1	2016-03-11 04:36:59	announced

Somasundaram P, Koudelka T, Linke D, Tholey A, C-Terminal Charge-Reversal Derivatization and Parallel Use of Multiple Proteases Facilitates Identification of Protein C-Termini by C-Terminomics. J Proteome Res, 15(4):1369-78(2016) [pubmed]

curator keyword: Technical

submitter keyword: C-terminus, Derivatization, ETD, HCD, CID

Andreas Tholey
contact affiliation	Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Niemannsweg 11, 24105 Kiel, Germany
contact email	a.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, University of Kiel
contact email	a.tholey@iem.uni-kiel.de
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/2016/03/PXD003342

PRIDE project URI

• PRIDE
  1. PXD003342
     1. Label: PRIDE project
     2. Name: C-terminomics E. coli