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
; Ringnér, Markus
LU
and Häkkinen, Jari
LU
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/414012
- author
- Alm, Rikard
LU
; Johansson, Peter
LU
; Hjerno, K
; Emanuelsson, Cecilia
LU
; Ringnér, Markus
LU
and Häkkinen, Jari
LU
- organization
- publishing date
- 2006-03-16
- 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
- 2022-12-10 23:09:08
@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}},
keywords = {{proteomics; protein; hierarchical clustering; identification; isoforms; mass spectra}},
language = {{eng}},
month = {{03}},
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}},
}