Software development for improved analysis and data-handling of high-throughput MS data

General info

Date from - to

01 Jun 2005 - 01 Jan 2009

Project leader(s)

Breukelen, van Bas Dr. ir.

Prof. dr. ir. Henk G. Stunnenberg

Abstract

This project harmonizes the various software efforts in the field of early data handling and analysis. A generic pipeline framework is developed (in Java) for mass spectrometric data that will aid in processing of proteomic data. The framework will support the large size of mass spectrometric data files, which is likely to only further increase. Furthermore, a novel technology in mass spectrometry (Electron transfer dissociation - ETD) is investigated. A particular area of interest concerns peptide fragmentation rules, scoring filters for peptide identification and complementary data generated by collision induced dissociation (CID). In collaboration with the European Bioinformatics Institute EBI, a data repository (Pride) and a database for annotated MSMS spectra are created.

Link to the end report of this project

Publications

• A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing
• Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster
• Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo
• Targeted SCX Based Peptide Fractionation for Optimal Sequencing by Collision Induced, and Electron Transfer Dissociation
• All-inclusive proteomics mapping of yeast RNA polymerase II and III reveals several novel phosphorylation sites
• Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes
• Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites