Summary
Phase 1: Before Normalization
Phase 2: After Normalization
PeptidomeR
An integrated workflow for preprocessing, exploratory analysis, differential analysis, multivariate analysis, and proteolytic motif analysis of peptidomics data.
1 Quality control
Filter missing values, normalize, impute, and export intermediate datasets.
2 Exploratory analysis
Summarize experiment coverage, peptide overlap, and length distributions.
3 Differential peptides
Compare peptide abundance between two selected experimental groups.
4 Differential proteins
Compare peptide abundance between two selected experimental groups.
5 Multivariate analysis
Select PCA, t-SNE, or UMAP, and visualize the top PCA-loading peptides in a heatmap.
6 Proteolytic motifs
Generate N- and C-terminal motif analyses from peptides based on either binomial probability distribution with a backgroumd of top proteins or frequenct counts.