PICarver: a software tool and strategy for peptides isoelectric focusing

Vaezzadeh, Alireza; Hernandez, Céline; Vadas, Oscar; Deshusses, Jacques; Lescuyer, Pierre; Lisacek, Frédérique; Hochstrasser, Denis

doi:10.1021/pr8002672

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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		DOI: 10.1021/pr8002672 PMID: 18783261
Full text		Article (Accepted version) (629 Kb) - Limited access to UNIGE Supplemental data - I (11 Kb) - Limited access to UNIGE Supplemental data - II (18 Kb) - Limited access to UNIGE Supplemental data - III (140 Kb) - Limited access to UNIGE Supplemental data - IV (276 Kb) - Limited access to UNIGE Supplemental data - V (250 Kb) - Limited access to UNIGE Supplemental data - VI (252 Kb) - Limited access to UNIGE Supplemental data - VII (262 Kb) - Limited access to UNIGE Supplemental data - VIII (1.8 MB) - Limited access to UNIGE Supplemental data - IX (1.6 MB) - Limited access to UNIGE Supplemental data - X (2.3 MB) - Limited access to UNIGE
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. doi: 10.1021/pr8002672 https://archive-ouverte.unige.ch/unige:1306