Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/2186872
- author
- Granlund, Irene ; Kieselbach, Thomas ; Alm, Rikard LU ; Schroder, Wolfgang P. and Emanuelsson, Cecilia LU
- organization
- publishing date
- 2011
- 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}}, }