Identification of protein-protein interaction partners

APMS (affinity purification coupled to mass spectrometry)

Using affinity purification methods such as immunoprecipitation enables the isolation of whole protein complexes from a cell or tissue extract. In the old days, or in workflows where knowing the identity of only one protein is needed, the immunoprecipitated proteins would be resolved by SDS-PAGE, stained, and individual bands were cut and analyzed by LC-MS/MS. With modern instruments, the whole protein complex can be subjected to proteolytic digestion and analyzed by LC-MS/MS. The result of such experiment is a list of proteins that were co-immunoprecipitated alongside the bait.

Do you need more than just a list of protein?

Interestingly, our APMS workflow is compatible with label-free quantitative proteomics. Therefore, if needed, we can provide quantitative information on every IPed protein relative to a control condition. This experiment would be ideal to compare the affinity of interaction partners to your protein of interest in two or more conditions.

Data reports

• For data reports where only protein identification is required, a spreadsheet with a list of probable IDs, as well as a score and the number of peptides associated with every ID will be provided.
• For quantitative APMS workflows, an interactive data report with relative quantification for every detected protein will be generated. Basic statistical analyses will also be included in the report. Optional advanced statistics (PCA, heatmap clustering, GO) can be added.