Data Analysis

We apply the open-source quantitative proteomics software MaxQuant for analyzing large-scale mass-spectrometric data. It includes the Andromeda search engine and supports label-free quantification of proteomes as well as all main labeling techniques like SILAC, Di-methyl, TMT, and iTRAQ. We further offer a standard analysis of the raw data as well as case to case oriented bioinformatics service. For this we use the Perseus framework as well as R and Python for further statistical and bioinformatics analyses, data annotation and visualization.

Data and Experiment Information Storage

The raw and result data are archived on servers of the computing center of the University of Cologne (RRZK) using a Network-attached storage (NAS) system. The data-synchronization between the hard disc of the measuring instruments with the NAS is performed by the facility personnel and will be automatized in the future. Users obtain the result data via email.  
A web-based sample submission portal connected to a SQL-database will be available soon. It provides an interface between users and the facility as well as an electronic system for the collection and storage of experiment metadata. It allows members of CECAD and collaborators to submit information on the performed experiments and samples, which are necessary for the MS-measurements and the subsequent data analysis. It furthermore shows the status of the sample processing.

Dr. Christian Frese
Head of Proteomics Facility CECAD
Tel.  +49 221 478 84013

CECAD Research Institute
Universität zu Köln
Joseph-Stelzmann-Str. 26
50931 Köln

Dr. Christian Frese