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Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS

Granlund, Irene; Kieselbach, Thomas; Alm, Rikard LU ; Schroder, Wolfgang P. and Emanuelsson, Cecilia LU (2011) In Journal of Proteomics 74(8). p.1190-1200
Abstract
It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program (http://bioinfo.theplu.se/speclust.html). The tool can also be used to remove peaks of contaminating proteins and to improve protein... (More)
It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program (http://bioinfo.theplu.se/speclust.html). The tool can also be used to remove peaks of contaminating proteins and to improve protein identification, especially for species without a fully sequenced genome. Mutually exclusive peptide peaks within a cluster provide a good starting point for MS/MS investigation of modified peptides, here exemplified by the identification of an A to E substitution that accounts for the isoelectric heterogeneity in protein isoforms. (C) 2011 Elsevier B.V. All rights reserved. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
2-DE PAGE, Hierarchical clustering, MALDI-TOF mass spectrometry, MS/MS, Post-translational modification, Proteomics
in
Journal of Proteomics
volume
74
issue
8
pages
1190 - 1200
publisher
Elsevier
external identifiers
  • wos:000294591500004
  • scopus:79961005037
ISSN
1874-3919
DOI
10.1016/j.jprot.2011.04.008
language
English
LU publication?
yes
id
28cd982d-4ed1-4f24-8fcb-805e5182ce35 (old id 2186872)
date added to LUP
2011-10-24 12:48:22
date last changed
2017-01-01 04:02:46
@article{28cd982d-4ed1-4f24-8fcb-805e5182ce35,
  abstract     = {It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program (http://bioinfo.theplu.se/speclust.html). The tool can also be used to remove peaks of contaminating proteins and to improve protein identification, especially for species without a fully sequenced genome. Mutually exclusive peptide peaks within a cluster provide a good starting point for MS/MS investigation of modified peptides, here exemplified by the identification of an A to E substitution that accounts for the isoelectric heterogeneity in protein isoforms. (C) 2011 Elsevier B.V. All rights reserved.},
  author       = {Granlund, Irene and Kieselbach, Thomas and Alm, Rikard and Schroder, Wolfgang P. and Emanuelsson, Cecilia},
  issn         = {1874-3919},
  keyword      = {2-DE PAGE,Hierarchical clustering,MALDI-TOF mass spectrometry,MS/MS,Post-translational modification,Proteomics},
  language     = {eng},
  number       = {8},
  pages        = {1190--1200},
  publisher    = {Elsevier},
  series       = {Journal of Proteomics},
  title        = {Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS},
  url          = {http://dx.doi.org/10.1016/j.jprot.2011.04.008},
  volume       = {74},
  year         = {2011},
}