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Clustering of MS sp...
Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS
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- Granlund, Irene (author)
- Umeå universitet,Kemiska institutionen
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- Kieselbach, Thomas (author)
- Umeå universitet,Kemiska institutionen
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- Alm, Rikard (author)
- Lund University,Lunds universitet,Biokemi och Strukturbiologi,Centrum för Molekylär Proteinvetenskap,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Biochemistry and Structural Biology,Center for Molecular Protein Science,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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- Schröder, Wolfgang P (author)
- Umeå universitet,Kemiska institutionen
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- Emanuelsson, Cecilia (author)
- Lund University,Lunds universitet,Biokemi och Strukturbiologi,Centrum för Molekylär Proteinvetenskap,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Biochemistry and Structural Biology,Center for Molecular Protein Science,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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(creator_code:org_t)
- Elsevier BV, 2011
- 2011
- English.
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In: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 74:8, s. 1190-1200
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences (hsv//eng)
Keyword
- 2-DE PAGE
- Hierarchical clustering
- MALDI-TOF mass spectrometry
- MS/MS
- Post-translational modification
- Proteomics
- 2-DE PAGE; Hierarchical clustering; MALDI-TOF mass spectrometry
Publication and Content Type
- art (subject category)
- ref (subject category)
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