The course is focused on the methods of identification and quantitative analysis of proteins, which are mainly based on the utilization of low-flow liquid chromatography and mass spectrometry. After discussing methods of analysis and the labeling of proteins for their quantification, we will introduce you to the structure of proteomic data, methods of its preprocessing and the use of available tools supporting data processing. The course is designed for people who are just beginning their adventure in the field of biochemistry and bioinformatics, as well as for those who want to use their knowledge to explore the world of proteomic analysis at a higher level by learning secrets of the structure of data acquired experimentally, for biochemical or biomedical analysis. The training is a live workshop, with the possibility of mutual interaction between participants and the instructor,the opportunity to ask questions and check the progress of knowledge.

Date: : to be agreed with the client (2-days online workshop).

Time: 10 hours (5 hours each day with a coffee break).

Location: online.

Group: for a group larger than 3 persons.

Teacher: Łukasz Marczak, Ph.D.

Price: 390 EUR (plus VAT if applicable).

Topics:

• Fundamentals of mass spectrometry and chromatography in the context of proteomic analytics
• Structure and processing of raw proteomic data, methods of protein identification and methods of quantitative data analysis
• Working on amino acid sequences, building and managing sequence databases, analysis of post-translational modifications, etc.
• Interpretation and preprocessing of LC-MS data: deconvolution, data normalization, scaling, sample alignment
• Statistical methods used in proteomic analyses; univariate analysis – ANOVA, t-test, fold change, data correlations, etc.; multivariate analysis – PCA, PLS-DA, OPLS-DA, clustering, heatmaps, etc.
• Biomarker analysis to identify differential proteomic features, e.g. ROC curves, classifiers, model building, etc.
• Available web-based platforms for proteomic data processing and analysis
• Functional analysis of proteomic data, integration with omics data obtained on other levels

Learning Outcomes

By the end of the workshop, participants will:

1. Possess extensive knowledge of proteomics research and be able to select appropriate analytical methods for a given research problem.
2. Understand what mass spectrometry is and its importance in proteomics research.
3. Know how to identify proteins using PMF methods and tandem mass spectrometry.
4. Be familiar with different approaches to quantitative proteomics analysis (stable isotope labeling, label-free) and be able to select the appropriate technique for their needs.
5. Be capable of designing and conducting proteomics experiments using modern analytical techniques, including:
1. Peptide mapping (PMF),
2. DDA (Data-Dependent Acquisition) analysis,
3. DIA (Data-Independent Acquisition) analysis,
4. Targeted analysis such as MRM and PRM.
6. Understand how to perform de novo protein sequencing.
7. Know what ion mobility is in mass spectrometry and how to use it in proteomics research.
8. Be familiar with and understand the structure of data in result files obtained through major analytical techniques.
9. Be proficient in processing raw data obtained from PMF (peptide mapping) and LC-MS (bottom-up proteomics) techniques.
10. Know bioinformatics tools used for protein identification and quantitative protein analysis.
11. Be able to select appropriate statistical methods for processing the obtained data.

Łukasz Marczak, Ph.D.

Head of Mass Spectrometry Laboratory at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznan. Author and co-author of over 100 scientific publications, during his 20-year career he has been PI and researcher in numerous projects in the field of mass spectrometry, proteomics and metabolomics. Organizer of many national and international scientific conferences. Experienced trainer and recognized expert in the field of analytics. Former secretary of the Polish Society of Mass Spectrometry and long-time president of the Polish Proteomics Society. He gained experience in Poland and abroad, including a fellowship at the University of Toulouse and an internship at the INRA Institute in Versailles, France. He has collaborated with the University of Life Sciences in Poznań, Poznań University of Technology, Institute of Plant Genetics, Institute of Oncology in Gliwice and University of Pittsburgh.