Patent Document ID: 9612246
Application ID: 14283902
Patent Flag: 1

Claim One:
1. A method for identifying at least two different interacting peptide pairs within a biological system comprising: (a) obtaining a sample comprising a population of cross-linked precursor peptides produced by digestion of a population of proteins cross-linked with a cleavable protein interaction reporter (PIR) cross-linker; (b) subjecting the sample to mass spectrometry (MS) to: (i) produce a population of precursor ions, and (ii) generate a 1° mass spectrum used to determine the charge states and masses of precursor ions within the population of precursor ions; (c) selecting, from within the 1° mass spectrum, a precursor ion with a charge state equal to or greater than a cutoff charge state; subjecting the selected precursor ion-to conditions under which the cleavable PIR cross-linker, if present in the selected precursor ion, is cleaved, thereby producing a population of released peptides and, if present in the selected precursor ion, cleaved reporter ions; and determining the masses of the released peptides and, if present in the selected precursor ion, cleaved reporter ions by tandem mass spectrometry (MS 2 ); (d) analyzing the population of released peptides to identify one or more pairs of interacting peptides, where a pair of released peptides is identified as an interacting peptide pair if the combined mass of the pair of released peptides and cleaved reporter ion, as determined by MS 2 in step (c), is equal to the mass of the selected precursor ion, as determined by MS in step (b)(ii); and (e) repeating steps (b)-(d) at least once, and until at least two different interacting peptide pairs are identified within the biological system, wherein the same cutoff charge state is used for each repetition.