10.1021/pr8002672.s009 Ali R. Vaezzadeh Ali R. Vaezzadeh Céline Hernandez Céline Hernandez Oscar Vadas Oscar Vadas Jacques J. M. Deshusses Jacques J. M. Deshusses Pierre Lescuyer Pierre Lescuyer Frédérique Lisacek Frédérique Lisacek Denis F. Hochstrasser Denis F. Hochstrasser pICarver: A Software Tool and Strategy for Peptides Isoelectric Focusing American Chemical Society 2008 shotgun proteomics peptide markers pICarver program isoelectric point strategy approach Software Tool pH gradient fractionation scheme pICarver predications software tool Peptides Isoelectric FocusingThe use 2008-10-03 00:00:00 Journal contribution https://acs.figshare.com/articles/journal_contribution/pICarver_A_Software_Tool_and_Strategy_for_Peptides_Isoelectric_Focusing/2910148 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>I</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.