Identification of protein-protein interaction partners

Identify and quantify the interaction partners of your protein of interest. Because the days when you had to cut a band out of a gel to identify an interaction partner are over.

Graphical representation of known protein-protein interactions with Cytoscape

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.

Contact us for your needs in APMS

My personal experience of collaborating with PhenoSwitch Bioscience was really amazing and great. Ribosomal protein paralogs have very limited number of amino acid differences. If it were not for PhenoSwitch, it would not have been possible to get such a high quality identification and quantification of duplicated ribosomal proteins in yeast. I am highly indebted and thankful for their perseverance, commitment, help and guidance during the tough times of optimization. If you you need to use MS for identification and quantification of your molecules, I strongly recommend you to talk to these guys!
Mustafa Malik Ghulam, Post Doctoral Fellow, RNA Therapeutic Institute, Umass Medical School, Worcester, Massachussetts

"PhenoSwitch Bioscience Inc has provided us with outstanding efficacious service, high quality data and exemplary data analysis over the past three years."

Stephen Naylor, Ph.D., CEO at ReNeuroGen LCC, Milwaukee, USA
"They have provided excellent data in a timely manner on a number of metabolism and protein studies ongoing in my group"
Klaus Klarskov, Ph.D., Professor at Université de Sherbrooke, Canada
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