Proteomics Results Landscape

This chapter introduces common proteomics result types and how they fit into downstream analysis.

Common Files

Proteomics projects may produce:

• raw mass spectrometry files
• peptide-level tables
• protein-level abundance tables
• differential abundance result tables
• sample metadata
• quality control summaries
• annotation files

Results-First Entry Point

This system begins with the files most researchers commonly receive after core facility processing:

protein_id
gene_symbol
protein_name
log2FC
pvalue
padj
comparison