Seattle Proteome Center (SPC) - Proteomics Tools
NHLBI Proteomics Center at the Institute for Systems Biology

Prequips

Prequips is a software environment for integration, visualization and analysis of LC-MS/MS data.

Integration: The software is capable of integrating mass spectrometry data at the raw data, peptide and protein level. Furthermore, this data can be linked to other data types such as microarray data or sequence information. Currently data can be read from mzXML, pepXML, Bioworks (tabular), and protXML files.

Visualization: Prequips includes tabular data viewers as well as spectrum and chromatogram plots. It also provides an overview of the data as a 2-D gel-like image, which is a essential tool for quality control. All visualizations are interactive and linked to each other, making visual data exploration straightforward.

Analysis: Through implementation of the Gaggle interface [http://gaggle.systemsbiology.net] mass spectrometry data can be exchanged with programs such as Cytoscape, TIGR MeV, R and Firefox. This enables analysis and interactive exploration of large heterogeneous data sets without manual data conversion.

Prequips is written in Java and based on the Eclipse Rich Client platform. It runs on all operating systems supporting Java 1.5 or later.

Please see the Prequips wiki page on the SPCTools wiki for addition information.

Inclusion List Builder Extension

The Inclusion List Builder plug-in for Prequips implements the computational aspects of a directed LC-MS/MS approach based on inclusion lists. The approach is described in detail in Schmidt A, Gehlenborg N, Bodenmiller B, Mueller L, Domon B and Aebersold R, "An integrated, directed mass spectrometric approach for in depth characterization of complex peptide mixtures." (submitted).

Please see the Prequips Inclusion List Builder wiki page on the SPCTools wiki for addition information.