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Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases

BACKGROUND: Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two main approaches for characterization: (i) using a predefined set of possible mod...

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Autores principales: Barsnes, Harald, Mikalsen, Svein-Ole, Eidhammer, Ingvar
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653020/
https://www.ncbi.nlm.nih.gov/pubmed/19099572
http://dx.doi.org/10.1186/1756-0500-1-130
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author Barsnes, Harald
Mikalsen, Svein-Ole
Eidhammer, Ingvar
author_facet Barsnes, Harald
Mikalsen, Svein-Ole
Eidhammer, Ingvar
author_sort Barsnes, Harald
collection PubMed
description BACKGROUND: Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two main approaches for characterization: (i) using a predefined set of possible modifications and substitutions or (ii) performing a blind search. The first option is straightforward, but can not detect modifications or substitutions outside the predefined set. A blind search does not have this limitation, and therefore has the potential of detecting both known and unknown modifications and substitutions. Combining the peptide mass fingerprints from two proteases result in overlapping sequence coverage of the protein, thereby offering alternative views of the protein and a novel way of indicating post-translational modifications and amino acid substitutions. RESULTS: We have developed an algorithm and a software tool, MassShiftFinder, that performs a blind search using peptide mass fingerprints from two proteases with different cleavage specificities. The algorithm is based on equal mass shifts for overlapping peptides from the two proteases used, and can indicate both post-translational modifications and amino acid substitutions. In most cases it is possible to suggest a restricted area within the overlapping peptides where the mass shift can occur. The program is available at . CONCLUSION: Without any prior assumptions on their presence the described algorithm is able to indicate post-translational modifications or amino acid substitutions in MALDI-TOF experiments on identified proteins, and can thereby direct the involved peptides to subsequent TOF-TOF analysis. The algorithm is designed for detailed and low-throughput characterization of single proteins.
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spelling pubmed-26530202009-03-10 Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases Barsnes, Harald Mikalsen, Svein-Ole Eidhammer, Ingvar BMC Res Notes Short Report BACKGROUND: Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two main approaches for characterization: (i) using a predefined set of possible modifications and substitutions or (ii) performing a blind search. The first option is straightforward, but can not detect modifications or substitutions outside the predefined set. A blind search does not have this limitation, and therefore has the potential of detecting both known and unknown modifications and substitutions. Combining the peptide mass fingerprints from two proteases result in overlapping sequence coverage of the protein, thereby offering alternative views of the protein and a novel way of indicating post-translational modifications and amino acid substitutions. RESULTS: We have developed an algorithm and a software tool, MassShiftFinder, that performs a blind search using peptide mass fingerprints from two proteases with different cleavage specificities. The algorithm is based on equal mass shifts for overlapping peptides from the two proteases used, and can indicate both post-translational modifications and amino acid substitutions. In most cases it is possible to suggest a restricted area within the overlapping peptides where the mass shift can occur. The program is available at . CONCLUSION: Without any prior assumptions on their presence the described algorithm is able to indicate post-translational modifications or amino acid substitutions in MALDI-TOF experiments on identified proteins, and can thereby direct the involved peptides to subsequent TOF-TOF analysis. The algorithm is designed for detailed and low-throughput characterization of single proteins. BioMed Central 2008-12-19 /pmc/articles/PMC2653020/ /pubmed/19099572 http://dx.doi.org/10.1186/1756-0500-1-130 Text en Copyright © 2008 Barsnes et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Report
Barsnes, Harald
Mikalsen, Svein-Ole
Eidhammer, Ingvar
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
title Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
title_full Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
title_fullStr Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
title_full_unstemmed Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
title_short Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
title_sort blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653020/
https://www.ncbi.nlm.nih.gov/pubmed/19099572
http://dx.doi.org/10.1186/1756-0500-1-130
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