Teaching for the Heidelberg Biosciences International Graduate School (HBIGS). The course focused on the presenting step-by-step analysis of Proteomics data as well as the integrative analysis of Proteomics and Transcriptomics. The lecture was organized over an the EGF-driven protein synthesis case-study date from this paper.

Proteomics Analysis

Ste-bystep tutorials of analysis from raw proteomics data to differential protein analysis: i) Data preparation (reformatting of the raw peptide data, QC, dealing with duplicated peptides, etc.). ii) Data filtering. iii) Data transformation/normalization. iv) Data imputation techniques. v) Dimensionality reduction/PCA analysis for interpretation of samples. vi) Identification and removal of bathc effects. vii) Differential analysis of data.

Integrative Analysis

Step-by-step tutorials for integrative analysis of proteomics & transcriptomics data. This part focused on covering the following aspects: i) Data preparation and pre-processing. ii) Correlation analysis. iii) Data clustering. iv) Pathway analysis. v) Identification of functional protein interaction modules.