* 1. What is Biomarker?

Theory: Definition of proteomic biomarkers, discovery, and validation of biomarkers

Practical: Sample preparation and pre-analytical factors

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 2. Biomarker Pipeline-Part I

Theory: Methodologies used to identify novel proteomic biomarkers

Practical: Protein extraction from cells and tissues

Roman Viták, Mgr., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 3. Biomarker Pipeline-Part II

Theory: Identification of candidate biomarker, qualification, verification, validation, and clinical assay development

Practical: Protein quantification, sample preparation, enzyme digestion

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 4. Harnessing the Power of Multiparameter Flow Cytometry in Biomarker Discovery (Invited Lecture)

Practical: Gel-based proteomics, one-dimensional electrophoresis, staining and de-staining

Suhail Tahir, Ph.D., Former researcher (Harvard Medical School), Scientist at BD Biosciences, USA.

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 5. Role of Biomarker in Personalised Medicine

Theory: Use of biomarkers to improve patient outcomes, application of biomarkers, Plasma proteomics, Affinity-based technologies, future perspectives

Practical: Analysis of digestion efficiency by electrophoresis

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 6. Introduction to Mass Spectrometry

Theory: History, principles, mass spectral interpretation, electron ionization, detection, and quantitation, data analysis

Practical: A raw data file from the proteomics experiment will be used for analysis. Participants will go through MS spectra to identify and quantify peptides thereby obtaining lists of protein identifiers that can be analyzed further using a wide range of resources.

Ing. Tůma Zdeněk, Ph.D., Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Czech Republic

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 7. Recent Advancements in Mass Spectrometry

What is targeted proteomics? Selected ion monitoring, extracted ion chromatograms, Multiple Reaction Monitoring, Skyline Software

Practical: Raw data from a proteomics experiment will be used for analysis to develop MRM assay. Participants will be able to go through MS spectra to identify and quantify peptides (same line as above)

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

Ing. Tůma Zdeněk, Ph.D., Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 8. FDA-approved Proteomic Markers: Issues & Challenges

Theory: Proteomic biomarkers in Cancer, Diabetes, Heart, Neurological disease, and other diseases.

Practical: Gel electrophoresis, Immunoblotting.

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 9. The cutting-edge Research on Peptides

Theory: Basic concepts of chemical biology, peptide synthesis, post-translational modification

Practical: Immunoblot data analysis

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic

* 10. In Vitro Diagnostics and Peptide Biomarkers (Invited Lecture)

Theory: Peptide chemistry, microwave-assisted peptide synthesis, usage of synthetic peptides in diagnostics

Elisa Peroni, Ph.D., Director of the Platform PeptLab@CY of the CY Cergy Paris Université-France

Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic