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Accurate peak list extraction from proteomic mass spectra for identification and profiling studies

BACKGROUND: Mass spectrometry is an essential technique in proteomics both to identify the proteins of a biological sample and to compare proteomic profiles of different samples. In both cases, the main phase of the data analysis is the procedure to extract the significant features from a mass spect...

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Detalles Bibliográficos
Autores principales: Barbarini, Nicola, Magni, Paolo
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2967564/
https://www.ncbi.nlm.nih.gov/pubmed/20950483
http://dx.doi.org/10.1186/1471-2105-11-518
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author Barbarini, Nicola
Magni, Paolo
author_facet Barbarini, Nicola
Magni, Paolo
author_sort Barbarini, Nicola
collection PubMed
description BACKGROUND: Mass spectrometry is an essential technique in proteomics both to identify the proteins of a biological sample and to compare proteomic profiles of different samples. In both cases, the main phase of the data analysis is the procedure to extract the significant features from a mass spectrum. Its final output is the so-called peak list which contains the mass, the charge and the intensity of every detected biomolecule. The main steps of the peak list extraction procedure are usually preprocessing, peak detection, peak selection, charge determination and monoisotoping operation. RESULTS: This paper describes an original algorithm for peak list extraction from low and high resolution mass spectra. It has been developed principally to improve the precision of peak extraction in comparison to other reference algorithms. It contains many innovative features among which a sophisticated method for managing the overlapping isotopic distributions. CONCLUSIONS: The performances of the basic version of the algorithm and of its optional functionalities have been evaluated in this paper on both SELDI-TOF, MALDI-TOF and ESI-FTICR ECD mass spectra. Executable files of MassSpec, a MATLAB implementation of the peak list extraction procedure for Windows and Linux systems, can be downloaded free of charge for nonprofit institutions from the following web site: http://aimed11.unipv.it/MassSpec
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spelling pubmed-29675642010-11-03 Accurate peak list extraction from proteomic mass spectra for identification and profiling studies Barbarini, Nicola Magni, Paolo BMC Bioinformatics Methodology Article BACKGROUND: Mass spectrometry is an essential technique in proteomics both to identify the proteins of a biological sample and to compare proteomic profiles of different samples. In both cases, the main phase of the data analysis is the procedure to extract the significant features from a mass spectrum. Its final output is the so-called peak list which contains the mass, the charge and the intensity of every detected biomolecule. The main steps of the peak list extraction procedure are usually preprocessing, peak detection, peak selection, charge determination and monoisotoping operation. RESULTS: This paper describes an original algorithm for peak list extraction from low and high resolution mass spectra. It has been developed principally to improve the precision of peak extraction in comparison to other reference algorithms. It contains many innovative features among which a sophisticated method for managing the overlapping isotopic distributions. CONCLUSIONS: The performances of the basic version of the algorithm and of its optional functionalities have been evaluated in this paper on both SELDI-TOF, MALDI-TOF and ESI-FTICR ECD mass spectra. Executable files of MassSpec, a MATLAB implementation of the peak list extraction procedure for Windows and Linux systems, can be downloaded free of charge for nonprofit institutions from the following web site: http://aimed11.unipv.it/MassSpec BioMed Central 2010-10-16 /pmc/articles/PMC2967564/ /pubmed/20950483 http://dx.doi.org/10.1186/1471-2105-11-518 Text en Copyright ©2010 Barbarini and Magni; 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 Methodology Article
Barbarini, Nicola
Magni, Paolo
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
title Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
title_full Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
title_fullStr Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
title_full_unstemmed Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
title_short Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
title_sort accurate peak list extraction from proteomic mass spectra for identification and profiling studies
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2967564/
https://www.ncbi.nlm.nih.gov/pubmed/20950483
http://dx.doi.org/10.1186/1471-2105-11-518
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