Abstract: Methods and reagents for high throughput analysis of protein-protein interaction networks using mass spectrometry.

Abstract: The instant invention relates to improved methods and systems for proteomic analysis using MS (mass spectrometry) data, particularly tandem mass spectrometry (MS/MS) data. The method comprises searching a first level database using sequence information generated by MS/MS obtained from a peptide selected from a digested protein sample. A second level database (which is smaller and contains only the candidate proteins) is then searched to identify the identity of the protein containing the selected peptide. More levels of even smaller databases can be generated for successive rounds of searches if the previous round of search does not unequivocally identify the protein containing the selected peptide(s). The method may be carried out on a range of mass spectrometers including a tandem mass spectrometer (MS/MS), an ion trap mass spectrometer or others capable of generating MS and MS/MS data.