Challenges And Opportunities In Proteomics Data Analysis Assignment 

Assignment Task

Description

Each week during the proteomics section of the unit, you will learn about a different aspect of the proteomics data processing workflow. The section will focus on three aspects of proteomics data analysis, namely data-dependent acquisition (DDA) and protein identification,targeted quantitative analysis (MRM) and dataindependent acquisition (DIA). You will receive datasets of a human protein extract mixed with a yeast protein extract. You will need to setup a search for protein identification and report on the obtained results using dedicated proteomics data analysis tools. For the targeted analysis you will receive a list of protein families. You will need to develop a method and report on the quantitative results. Using DIA data analysis, you will need to explore the number of quantified proteins and peptides. You will be provided tasks to facilitate your practical skills development, thus complementing your theoretical learning. During this time, you will gain an understanding and appreciation for the challenges and flexibility associated with this process. You will be expected to extend your understanding of the content and challenges by examining the literature and other relevant resources.

Questions 

1. What parameter settings should be considered for the protein database search step using the Paragon method?

2. Which criteria and thresholds did you use for peptide and protein identification, FDR reporting?

3. Which criteria did you use for peptide and transition selection during targeted method development?

4. Which criteria did you use in your targeted data analysis (data interpretation)?

5. Which criteria did you use in your DIA data analysis?

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