Identification tells you what was detected
Protein identification is a starting point. Interpret a detected-protein list in the context of sample type, controls and methodology. Biological conclusions should remain tied to the design.
Quantitative differences depend on design
When comparing groups, consider sample comparability, replication and processing strategy. Differential enrichment or abundance is an observation under experimental conditions, not direct proof of a functional change.
Pathway analysis offers research leads
GO and KEGG analyses help organize relevant functions and pathways. They provide leads for follow-up research; interpretation should consider the background set, statistical approach and context.
Move from association to validation
Protein enrichment, modification-site identification and functional validation are different evidence levels. Key findings may require targeted validation, site analysis or functional experiments.