Methods and systems of detecting protein-protein interaction and probing protein structures

A system for detecting protein-protein interaction and probing protein structures, comprising:

• a receptacle for receiving a cross-linked precursor peptide produced by digestion of a protein cross-linked with a cleavable or a non-cleavable crosslinker;
• a mass spectrometer for producing precursor ions and generating MS1 spectrum so as to determine the mass spectrum of the ions with their charge states and masses;
• and processing at least one precursor ion to undergo a fragmentation treatment to generate an interested MS2 spectrum;
• a precursor mass refinement module for analyzing an elution profile generated by the mass spectrometer and extracting and merging MS1 spectra obtained before and after the interested MS2 spectrum in the elution profile to form a complete isotope cluster of the precursor ion;
• a MS2 spectrum scoring module for matching the interested MS2 spectrum with the complete isotope cluster utilizing a scoring function S(x) and detecting and storing top p hits of the MS2 spectrum and their scores, wherein the MS2 spectrum scoring module further retrieves the top a peptide and β peptide hit of the MS2 spectrum as significant peptides and generates a scoring histogram;
• a protein score database constructed based on the scoring histogram and significant peptides for providing global information to connect peptides to proteins, comprising protein sequences in a biological system;
• a feedback mechanism processor for retrieving the stored top p hits in the protein score database and identifying at least one peptide candidate in the protein score database, wherein a peptide candidate having the largest protein score among the at least one peptide candidate is identified as a matching result for the interested MS2 spectrum;
• identifying the peptide interaction or protein structure from the matching result;
• and
• a cross-linking dataset, comprising cleavable cross-linker data or non-cleavable cross-linker data, both obtained from proteins in a biological system cross-linked by a cleavable or non-cleavable crosslinking reagent.