PICarver: a software tool and strategy for peptides isoelectric focusing.
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.
Vaezzadeh
Ali R
AR
Biomedical Proteomics Research Group, Department of Bioinformatics and Structural Biology, Geneva University, 1 Michel Servet, 1211 Geneva, Switzerland.
Hernandez
Céline
C
Vadas
Oscar
O
Deshusses
Jacques J M
JJ
Lescuyer
Pierre
P
Lisacek
Frédérique
F
Hochstrasser
Denis F
DF
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
D001426:Bacterial Proteins; D005456:Fluorescent Dyes; D010455:Peptides; D020543:Proteome