An optional course is designed on “Proteomic Biomarker Discovery”. In this course, students will focus on topics related
to Proteomics which is a rapidly growing field and does not fit into basic pharmacology. In this course, students will not
only acquire basic theoretical and practical training on routine techniques used in proteomics but also will acquire good
knowledge in proteomic biomarker discovery and its use in clinical settings. In order to achieve a better understanding
of this field, a special course will be also developed in MOODLE.
Proteomic Biomarker Discovery
A proteomic biomarker usually refers to disease-related proteins that can be used as an indicator of a specific biological
state. Biomarkers are not only used in the clinic to diagnose and monitor the disease but also used to guide the
molecular target treatment or evaluation of the therapeutic response. The potential use of proteomic biomarkers has
been increased in basic and clinical research in last 2-3 decades. During the course, students will have a chance to
learn basic routine techniques used in proteomic laboratories.
Last update: Dr. Shashank Pandey, Ph.D. (13.02.2024)
An optional course is designed on “Proteomic Biomarker Discovery”. In this course, students will focus on topics related
to Proteomics which is a rapidly growing field and does not fit into basic pharmacology. In this course, students will not
only acquire basic theoretical and practical training on routine techniques used in proteomics but also will acquire good
knowledge in proteomic biomarker discovery and its use in clinical settings. In order to achieve a better understanding
of this field, a special course will be also developed in MOODLE.
Proteomic Biomarker Discovery
A proteomic biomarker usually refers to disease-related proteins that can be used as an indicator of a specific biological
state. Biomarkers are not only used in the clinic to diagnose and monitor the disease but also used to guide the
molecular target treatment or evaluation of the therapeutic response. The potential use of proteomic biomarkers has
been increased in basic and clinical research in last 2-3 decades. During the course, students will have a chance to
learn basic routine techniques used in proteomic laboratories.
Course completion requirements
Last update: Ing. Lenka Křikavová (03.05.2022)
Requirements for credit
1) 15-minute scientific discussion
2) Attendance
Literature -
Last update: Dr. Shashank Pandey, Ph.D. (15.02.2024)
* Recommended literature 1. Nelson, D. L., & Cox, M. M. (2017). Lehninger principles of biochemistry (7th ed.). W.H. Freeman. 2. Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman. 3. MATOUŠ, Bohuslav. Základy lékařské chemie a biochemie. Praha: Galén, 2010, ISBN 978-80-7262-702-8. 4. WALKER, John M. The proteomics protocols handbook. Totowa: Humana Press, 2005, ISBN 1-58829-343-2. 5. Scientific literature published in high impact journals- Analytical Biochemistry, Journals in clinical pharmacology, Clinical Proteomics, Pharmaceutical Research, International Journal of Molecular Sciences, Molecular & Cellular Proteomics, Nature Biotechnology, etc.
Last update: Dr. Shashank Pandey, Ph.D. (15.02.2024)
* Recommended literature 1. Nelson, D. L., & Cox, M. M. (2017). Lehninger principles of biochemistry (7th ed.). W.H. Freeman. 2. Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman. 3. MATOUŠ, Bohuslav. Základy lékařské chemie a biochemie. Praha: Galén, 2010, ISBN 978-80-7262-702-8. 4. WALKER, John M. The proteomics protocols handbook. Totowa: Humana Press, 2005, ISBN 1-58829-343-2. 5. Scientific literature published in high impact journals- Analytical Biochemistry, Journals in clinical pharmacology, Clinical Proteomics, Pharmaceutical Research, International Journal of Molecular Sciences, Molecular & Cellular Proteomics, Nature Biotechnology, etc.
Requirements to the exam - Czech
Last update: Ing. Lenka Křikavová (03.05.2022)
Participation in seminars and elaboration of case studies.
Syllabus -
Last update: Dr. Shashank Pandey, Ph.D. (19.02.2024)
* 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
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
Last update: Dr. Shashank Pandey, Ph.D. (19.02.2024)
* 1. What is Biomarker?
Theory: Definition of proteomic biomarkers, discovery, and validation of biomarkers
Practical: Polymerization of SDS–PAGE
Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic
Roman Viták, Mgr., 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
* 2. Biomarker Pipeline-Part I
Theory: Methodologies used to identify novel proteomic 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
Roman Viták, Mgr., 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
Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic
Roman Viták, Mgr., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic
* 4. 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: Gel-based proteomics, one-dimensional electrophoresis, staining and de-staining
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
* 5. Harnessing the Power of Multiparameter Flow Cytometry in Biomarker Discovery (Invited Lecture)
Dr. Suhail Tahir, Ph.D., Former researcher (Harvard Medical School), Scientist at BD Biosciences, USA.
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)
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
