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PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data

BACKGROUND: We have created a software implementation of a published and verified method for assigning probabilities to potential phosphorylation sites on peptides using mass spectrometric data. Our tool, named PhosCalc, determines the number of possible phosphorylation sites and calculates the theo...

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Autores principales: MacLean, Daniel, Burrell, Michael A, Studholme, David J, Jones, Alexandra ME
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518918/
https://www.ncbi.nlm.nih.gov/pubmed/18710483
http://dx.doi.org/10.1186/1756-0500-1-30
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author MacLean, Daniel
Burrell, Michael A
Studholme, David J
Jones, Alexandra ME
author_facet MacLean, Daniel
Burrell, Michael A
Studholme, David J
Jones, Alexandra ME
author_sort MacLean, Daniel
collection PubMed
description BACKGROUND: We have created a software implementation of a published and verified method for assigning probabilities to potential phosphorylation sites on peptides using mass spectrometric data. Our tool, named PhosCalc, determines the number of possible phosphorylation sites and calculates the theoretical masses for the b and y fragment ions of a user-provided peptide sequence. A corresponding user-provided mass spectrum is examined to determine which putative b and y ions have support in the spectrum and a probability score is calculated for each combination of phosphorylation sites. FINDINGS: We test the implementation using spectra of phosphopeptides from bovine beta-casein and we compare the results from the implementation to those from manually curated and verified phosphopeptides from our own experiments. We find that the PhosCalc scores are capable of helping a user to identify phosphorylated sites and can remove a bottleneck in high throughput proteomics analyses. CONCLUSION: PhosCalc is available as a web-based interface for examining up to 100 peptides and as a downloadable tool for examining larger numbers of peptides. PhosCalc can be used to speed up identification of phosphorylation sites and can be easily integrated into data handling pipelines making it a very useful tool for those involved in phosphoproteomic research.
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spelling pubmed-25189182008-08-22 PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data MacLean, Daniel Burrell, Michael A Studholme, David J Jones, Alexandra ME BMC Res Notes Technical Note BACKGROUND: We have created a software implementation of a published and verified method for assigning probabilities to potential phosphorylation sites on peptides using mass spectrometric data. Our tool, named PhosCalc, determines the number of possible phosphorylation sites and calculates the theoretical masses for the b and y fragment ions of a user-provided peptide sequence. A corresponding user-provided mass spectrum is examined to determine which putative b and y ions have support in the spectrum and a probability score is calculated for each combination of phosphorylation sites. FINDINGS: We test the implementation using spectra of phosphopeptides from bovine beta-casein and we compare the results from the implementation to those from manually curated and verified phosphopeptides from our own experiments. We find that the PhosCalc scores are capable of helping a user to identify phosphorylated sites and can remove a bottleneck in high throughput proteomics analyses. CONCLUSION: PhosCalc is available as a web-based interface for examining up to 100 peptides and as a downloadable tool for examining larger numbers of peptides. PhosCalc can be used to speed up identification of phosphorylation sites and can be easily integrated into data handling pipelines making it a very useful tool for those involved in phosphoproteomic research. BioMed Central 2008-06-23 /pmc/articles/PMC2518918/ /pubmed/18710483 http://dx.doi.org/10.1186/1756-0500-1-30 Text en Copyright © 2008 MacLean et al; licensee BioMed Central Ltd. 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 Technical Note
MacLean, Daniel
Burrell, Michael A
Studholme, David J
Jones, Alexandra ME
PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
title PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
title_full PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
title_fullStr PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
title_full_unstemmed PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
title_short PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
title_sort phoscalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518918/
https://www.ncbi.nlm.nih.gov/pubmed/18710483
http://dx.doi.org/10.1186/1756-0500-1-30
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