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Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra

Alm, Rikard LU ; Johansson, Peter LU ; Hjerno, K ; Emanuelsson, Cecilia LU orcid ; Ringnér, Markus LU orcid and Häkkinen, Jari LU orcid (2006) In Journal of Proteome Research 5(4). p.785-792
Abstract
We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different sample sets, dates, and instruments, revealed similarities between mass spectra, and was a useful tool to highlight peptide peaks of interest for further investigation. Shared peak masses in a cluster could be identified and were used to create novel peak mass lists suitable for protein identification using peptide mass fingerprinting. Complex mass... (More)
We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different sample sets, dates, and instruments, revealed similarities between mass spectra, and was a useful tool to highlight peptide peaks of interest for further investigation. Shared peak masses in a cluster could be identified and were used to create novel peak mass lists suitable for protein identification using peptide mass fingerprinting. Complex mass spectra consisting of more than one protein were deconvoluted using information from other mass spectra in the same cluster. The number of peptide peaks shared between mass spectra in a cluster was typically found to be larger than the number of peaks that matched to calculated peak masses in databases, thus modified peaks are probably among the shared peptides. Clustering increased the number of peaks associated with a given protein. (Less)
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author
; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
proteomics, protein, hierarchical clustering, identification, isoforms, mass spectra
in
Journal of Proteome Research
volume
5
issue
4
pages
785 - 792
publisher
The American Chemical Society (ACS)
external identifiers
  • pmid:16602684
  • wos:000236816100006
  • scopus:33645779007
  • pmid:16602684
ISSN
1535-3893
DOI
10.1021/pr050354v
language
English
LU publication?
yes
id
b7f31d5c-c018-47b0-b2c2-d0d213391824 (old id 414012)
date added to LUP
2016-04-01 12:07:56
date last changed
2021-06-08 05:44:26
@article{b7f31d5c-c018-47b0-b2c2-d0d213391824,
  abstract     = {We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different sample sets, dates, and instruments, revealed similarities between mass spectra, and was a useful tool to highlight peptide peaks of interest for further investigation. Shared peak masses in a cluster could be identified and were used to create novel peak mass lists suitable for protein identification using peptide mass fingerprinting. Complex mass spectra consisting of more than one protein were deconvoluted using information from other mass spectra in the same cluster. The number of peptide peaks shared between mass spectra in a cluster was typically found to be larger than the number of peaks that matched to calculated peak masses in databases, thus modified peaks are probably among the shared peptides. Clustering increased the number of peaks associated with a given protein.},
  author       = {Alm, Rikard and Johansson, Peter and Hjerno, K and Emanuelsson, Cecilia and Ringnér, Markus and Häkkinen, Jari},
  issn         = {1535-3893},
  language     = {eng},
  number       = {4},
  pages        = {785--792},
  publisher    = {The American Chemical Society (ACS)},
  series       = {Journal of Proteome Research},
  title        = {Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra},
  url          = {http://dx.doi.org/10.1021/pr050354v},
  doi          = {10.1021/pr050354v},
  volume       = {5},
  year         = {2006},
}