Synopsis

The human meiotic recombination 11 homolog (MRE11A) gene encodes a protein with a central role in DNA double-stranded repair. Several proteins form a complex with MRE11A, such as NBN and RAD50. We used MRE11A as a bait protein in affinity purification-mass spectrometry (AP-MS) experiments as a proof of principle for using endogenously-epitope tagged cell lines for AP-MS.

Tasks & Questions

• Count the number of spectra in the MGF files
• Search the MRE11 and Control MS/MS spectra using Tandem
  • How many unique proteins are identified?
  • Using the Control data, which proteins are most likely background or contaminant proteins?
  • (This question can also be addressed by comparing MRE11 and Control spectral counts using the Scaffold software)

• Use GORilla to analyze the set of identified proteins
• What is the most significantly enriched Gene Ontology term?
• Use STRING to analyze the set of identiied proteins
• Does this identify any other known MRE11-NBN-RAD50 associated proteins?

Data	Notes
Raw Data MS/MS spectra from MRE11 experiment MS/MS spectra from Control experiment Scaffold file comparing 2 MRE11 samples and 1 control sample Search Results Identified proteins from MRE11 experiment Identified proteins from Control experiment	Taxonomy=Homo sapiens

References

Song et al, Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry. Journal Proteome Research, 2012 (PubMed).