The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments

Background: Isotope-coded affinity tags (ICAT) is a method for quantitative proteomics based on differential isotopic labeling, sample digestion and mass spectrometry (MS). The method allows the identification and relative quantification of proteins present in two samples and consists of the following phases. First, cysteine residues are either labeled using the ICAT Light or ICAT Heavy reagent (having identical chemical properties but different masses). Then, after whole sample digestion, the labeled peptides are captured selectively using the biotin tag contained in both ICAT reagents. Finally, the simplified peptide mixture is analyzed by nanoscale liquid chromatography-tandem mass spectrometry (LC-MS/MS). Nevertheless, the ICAT LC-MS/MS method still suffers from insufficient sample-to-sample reproducibility on peptide identification. In particular, the number and the type of peptides identified in different experiments can vary considerably and, thus, the statistical (comparative)...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Mario Cannataro, Giovanni Cuda, Marco Gaspari, Sergio Greco, Giuseppe Tradigo, Pierangelo Veltri
• Keywords: BMCBI 2007, ICAT, Mass Spectrometry, Peptides