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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 orcid (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
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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
  • pmid:21539947
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
2016-04-01 10:57:40
date last changed
2022-01-26 04:14:32
@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}},
  keywords     = {{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}},
  doi          = {{10.1016/j.jprot.2011.04.008}},
  volume       = {{74}},
  year         = {{2011}},
}