P.L. (Peter) Horvatovich, Prof

Proteogenomics data integration of human lung tissue of COPD patients and controls.

Collaboration with Victor Guryev (ERIBA/UMCG), Maarten van den Berge, Corry-Anke Brandsma, Wim Timens (Pulmonary Diseases, Pathology and Medical Biology departments of UMCG) and the laboratory of Gyorgy Marko Varga (Lund University).

Chronic obstructive pulmonary disease (COPD) is a common disease characterized by chronic progressive airflow obstruction. The prevalence of COPD increases with age to > 10% of adults over 65 years old. With no effective treatments, COPD has significant personal and economic impact which is expected to rise further. The ultimate goal of the project is to integrate data on the genomic, transcriptomic and proteomic levels, to identify the causal genetic variants, genes, and proteins responsible for the aberrant extracellular matrix turnover driving COPD development. In this project, we have developed a proteogenomics data integration pipeline for comprehensive data processing and analysis.

Determining Head and Neck Cancer protein profile difference between elderly and young patients.

This project is realized in collaboration with György Halmos and Renee Verhoeven at the Head and Neck Department, UMCG.

Aging of the Western society challenges health care professionals. Head and neck cancer is the sixth most common solid malignancy, with annual half million new cases worldwide, and almost 3000 new cases in the Netherlands. The aims of the study are (1) to develop an optimized tissue sample preparation protocol for larynx cancer tumors; (2) to identify protein profile differences between head and neck cancers of young and elderly patients and (3) to analyze differences between protein interaction network in cancer and healthy tissue between elderly and young head and neck cancer patients.

Identifying missing proteins and protein forms in Chromosome 5.

The project is performed in collaboration with the HUPO Chromosome Centric Human Proteome Project (Young-Ki Paik, Chris Overall and others).

The goals of the Chromosome 5 project are to identify the protein part list of Chromosome 5 including missing proteins (proteins which were not detected until today by mass spectrometry or other proteomics techniques) in biological samples, and to detect all possible genetic variants and post-translational modifications of proteins encoded in human chromosome 5. See further details at C-HPP Wiki: http://c-hpp.webhosting.rug.nl.

Pipelines and Systems for Threshold-Avoiding Quantification (PASTAQ).

The project is performed by Alejandro Sanchez Brotons PhD student as main developer and in collaboration with Frank Suits (Melbourne, Australia). Ido Kema, Stephan Bakker and Folkert Kuipers are supporting the project.

This project has the aim to develop a comprehensive single-stage data-dependent LC-MS(/MS) data processing pipeline for accurate quantification of all mass spectrometry signal independent of the identification status. The pipeline can be applied to any separation technology (LC, CE, GC) coupled to mass spectrometry data, which deliver non-fragmented single-stage MS data. Source code and other details are available at https://pastaq.horvatovichlab.com/.

Cancer Moonshot for personalised diagnostic and treatment of melanoma patients.

Proteins are the key biomolecules actively involved biology. Cancer Moonshot project has the goal to integrate proteomics data into clinical cancer research to provide breakthrough in cancer diagnosis and treatment. Gyorgy Marko-Varga at the Centre of Excellence in Biological and Medical Mass Spectrometry (CEBMMS) at Lund University (Sweden) is leading a Cancer Moonshot project for melanoma, where Peter Horvatovich has received an honorary position. Cancer Moonshot project at CEBMMS received in 2016 aims to profile more than 4 000 samples from melanoma patients over the next 5 years. The role of our group is to support the high-throughput data analysis of LC-MS/MS proteomics data, proteogenomics data integration, to perform statistical analysis of the collected molecular profiles and clinical metadata and participation in the supervision of the PhD candidate Jonatan Erikson.

A chemoproteomic approach to study advanced glycation end-products

Saskia Sokoliova is a PhD student working on this project, which is performed in collaboration with Martin Witte (Stratingh Institute for Chemistry).

Glycolysis is one of the fundamental molecular cell processes, and dysfunctioning of this process leads to unregulated glycation of, among others, proteins. Glycation altered proteins are involved in multiple complex diseases such as cancer and COPD. In this project, we aim to develop a novel chemical tool and bioinformatic approach that identifies and quantifies advanced glycation end (AGE)-products of proteins produced by the methylglyoxal reaction at endogenously relevant concentrations. This project was recently funded by the FSE Faculty Theme of Molecular Life And Health and is a joint project with Martin Witte, leader of Chemical Biology research group at the Stratingh Institute (RUG).