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Selecting protein N-terminal peptides by combined fractional diagonal chromatography

An Staes UGent, Francis Impens UGent, Petra Van Damme UGent, Bart Ruttens UGent, Marc Goethals UGent, Hans Demol UGent, Evy Timmerman UGent, Joël Vandekerckhove UGent and Kris Gevaert UGent (2011) NATURE PROTOCOLS. 6(8). p.1130-1141
abstract
In recent years, procedures for selecting the N-terminal peptides of proteins with analysis by mass spectrometry have been established to characterize protease-mediated cleavage and protein alpha-N-acetylation on a proteomic level. As a pioneering technology, N-terminal combined fractional diagonal chromatography (COFRADIC) has been used in numerous studies in which these protein modifications were investigated. Derivatization of primary amines-which can include stable isotope labeling-occurs before trypsin digestion so that cleavage occurs after arginine residues. Strong cation exchange (SCX) chromatography results in the removal of most of the internal peptides. Diagonal, reversed-phase peptide chromatography, in which the two runs are separated by reaction with 2,4,6-trinitrobenzenesulfonic acid, results in the removal of the C-terminal peptides and remaining internal peptides and the fractionation of the sample. We describe here the fully matured N-terminal COFRADIC protocol as it is currently routinely used, including the most substantial improvements (including treatment with glutamine cyclotransferase and pyroglutamyl aminopeptidase to remove pyroglutamate before SCX, and a sample pooling scheme to reduce the overall number of liquid chromatography-tandem mass spectrometry analyses) that were made since its original publication. Completion of the N-terminal COFRADIC procedure takes similar to 5 d.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PROTEOLYTIC CLEAVAGE SITES, QUANTITATIVE PROTEOMICS, DEGRADOMICS, CELL-DEATH, POSITIONAL PROTEOMICS, SUBSTRATE, STRATEGY, IDENTIFICATION, IN-VIVO, APOPTOSIS
journal title
NATURE PROTOCOLS
Nat. Protoc.
volume
6
issue
8
pages
1130 - 1141
Web of Science type
Article
Web of Science id
000294480300004
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
9.924 (2011)
JCR rank
3/72 (2011)
JCR quartile
1 (2011)
ISSN
1754-2189
DOI
10.1038/nprot.2011.355
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1907040
handle
http://hdl.handle.net/1854/LU-1907040
date created
2011-09-22 16:07:29
date last changed
2013-02-27 09:11:21
@article{1907040,
  abstract     = {In recent years, procedures for selecting the N-terminal peptides of proteins with analysis by mass spectrometry have been established to characterize protease-mediated cleavage and protein alpha-N-acetylation on a proteomic level. As a pioneering technology, N-terminal combined fractional diagonal chromatography (COFRADIC) has been used in numerous studies in which these protein modifications were investigated. Derivatization of primary amines-which can include stable isotope labeling-occurs before trypsin digestion so that cleavage occurs after arginine residues. Strong cation exchange (SCX) chromatography results in the removal of most of the internal peptides. Diagonal, reversed-phase peptide chromatography, in which the two runs are separated by reaction with 2,4,6-trinitrobenzenesulfonic acid, results in the removal of the C-terminal peptides and remaining internal peptides and the fractionation of the sample. We describe here the fully matured N-terminal COFRADIC protocol as it is currently routinely used, including the most substantial improvements (including treatment with glutamine cyclotransferase and pyroglutamyl aminopeptidase to remove pyroglutamate before SCX, and a sample pooling scheme to reduce the overall number of liquid chromatography-tandem mass spectrometry analyses) that were made since its original publication. Completion of the N-terminal COFRADIC procedure takes similar to 5 d.},
  author       = {Staes, An and Impens, Francis and Van Damme, Petra and Ruttens, Bart and Goethals, Marc and Demol, Hans and Timmerman, Evy and Vandekerckhove, Jo{\"e}l and Gevaert, Kris},
  issn         = {1754-2189},
  journal      = {NATURE PROTOCOLS},
  keyword      = {PROTEOLYTIC CLEAVAGE SITES,QUANTITATIVE PROTEOMICS,DEGRADOMICS,CELL-DEATH,POSITIONAL PROTEOMICS,SUBSTRATE,STRATEGY,IDENTIFICATION,IN-VIVO,APOPTOSIS},
  language     = {eng},
  number       = {8},
  pages        = {1130--1141},
  title        = {Selecting protein N-terminal peptides by combined fractional diagonal chromatography},
  url          = {http://dx.doi.org/10.1038/nprot.2011.355},
  volume       = {6},
  year         = {2011},
}

Chicago
Staes, An, Francis Impens, Petra Van Damme, Bart Ruttens, Marc Goethals, Hans Demol, Evy Timmerman, Joël Vandekerckhove, and Kris Gevaert. 2011. “Selecting Protein N-terminal Peptides by Combined Fractional Diagonal Chromatography.” Nature Protocols 6 (8): 1130–1141.
APA
Staes, A., Impens, F., Van Damme, P., Ruttens, B., Goethals, M., Demol, H., Timmerman, E., et al. (2011). Selecting protein N-terminal peptides by combined fractional diagonal chromatography. NATURE PROTOCOLS, 6(8), 1130–1141.
Vancouver
1.
Staes A, Impens F, Van Damme P, Ruttens B, Goethals M, Demol H, et al. Selecting protein N-terminal peptides by combined fractional diagonal chromatography. NATURE PROTOCOLS. 2011;6(8):1130–41.
MLA
Staes, An, Francis Impens, Petra Van Damme, et al. “Selecting Protein N-terminal Peptides by Combined Fractional Diagonal Chromatography.” NATURE PROTOCOLS 6.8 (2011): 1130–1141. Print.