Affinity-purification mass-spectrometry (AP-MS) is a powerful tool for the identifying components of protein complexes. We previously used AP-MS to perform a large-scale analysis of the human protein interactome (Ewing et al, 2007. Molecular Systems Biology). In this module, we analyze some of the data from this study. For each protein of interest, an epitope-tagged bait was expressed in human cells, and an antibody used to purify the interacting proteins. A challenge of AP-MS is to ensure that genuine interacting proteins can be distinguished from non-specific proteins. Control experiments are performed using cells with no epitope-tag.


The goal of this module is to demonstrate how AP-MS experiments can rapidly identify many components of protein complexes. Search the provided mass-spectrometry data and analyze the resulting proteins to map EIF and proteasome protein complexes and networks. Use the control data to identify non-specific interacting proteins in the data




Raw Data

EIF4EBP1 (EIF) as bait

EIF3S10 (EIF) as bait

PSMD13 (proteasome) as bait

No bait (control)

Search Results

Identified proteins from EIF4EBP1 experiment

Identified proteins from EIF3S10 experiment

Identified proteins from PSMD13 experiment

Identified proteins from No bait (control) experiment

Taxonomy: Homo sapiens


Ewing et al. Large-scale mapping of human protein-protein interactions by mass-spectrometry (PubMed).