title: PICarver: a software tool and strategy for peptides isoelectric focusing.
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.
authors.affiliation: Biomedical Proteomics Research Group, Department of Bioinformatics and Structural Biology, Geneva University, 1 Michel Servet, 1211 Geneva, Switzerland.
authors.forename: Ali R
authors.initials: AR
authors.lastname: Vaezzadeh
authors.forename: Céline
authors.initials: C
authors.lastname: Hernandez
authors.forename: Oscar
authors.initials: O
authors.lastname: Vadas
authors.forename: Jacques J M
authors.initials: JJ
authors.lastname: Deshusses
authors.forename: Pierre
authors.initials: P
authors.lastname: Lescuyer
authors.forename: Frédérique
authors.initials: F
authors.lastname: Lisacek
authors.forename: Denis F
authors.initials: DF
authors.lastname: Hochstrasser
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis; D005456:Fluorescent Dyes / Q000378:metabolism; D007525:Isoelectric Focusing / Q000295:instrumentation / Q000379:methods; D010455:Peptides / Q000032:analysis*; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D012984:Software; D013211:Staphylococcus aureus / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D005456:Fluorescent Dyes; D010455:Peptides; D020543:Proteome