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Title

PICarver: a software tool and strategy for peptides isoelectric focusing
Authors
Vaezzadeh, Alireza
Hernandez, Céline
Vadas, Oscar
Deshusses, Jacques
Lescuyer, Pierre
Lisacek, Frédérique
Hochstrasser, Denis
Published in Journal of Proteome Research. 2008, vol. 7, no. 10, p. 4336-45
Abstract The use of isoelectric focusing as first dimension of separation is a new trend in shotgun proteomics. In all applications using this approach, peptides are separated into equitable fractions, whereas theoretical distribution of peptides according to p I is heterogeneous. We present the development of a new tool and strategy that generates a fractionation scheme resulting in almost even distribution of peptides per fraction, based on theoretical and experimental data. The "pICarver" software tool also increases the throughput of the approach by reducing the number of fractions and merging the peptide-poor regions. A set of isoelectric point fluorescent peptide markers was also developed in combination with the pICarver program to calibrate the pH gradient of commercially available strips. These markers enhanced the precision of pICarver predications. The overall strategy allowed detecting false positive identification and post-translational modifications. The software tool is freely available on www.expasy.org/tools/pICarver.
Keywords Bacterial Proteins/analysis — Fluorescent Dyes/metabolism — Isoelectric Focusing/instrumentation/methods — Peptides/analysis — Proteome/analysis — Proteomics/methods — Software — Staphylococcus aureus/chemistry
Identifiers
PMID: 18783261
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Structures
Faculté de médecine / Section de médecine fondamentale / Département de biologie structurale et bioinformatique
Research group La protéomique au service de la clinique (270)
Citation
(ISO format) 		VAEZZADEH, Alireza et al. PICarver: a software tool and strategy for peptides isoelectric focusing. In: Journal of Proteome Research, 2008, vol. 7, n° 10, p. 4336-45. https://archive-ouverte.unige.ch/unige:1306

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Deposited on : 2009-04-02

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