Systems and Methods for Multipart Molecule Fragment Determination and Scoring

A mass spectrometry system, comprising

• a predictive system comprising at least one digital data processor configured to determine cleavage products of a putative macromolecule, which comprises a plurality of residues coupled to one another by one or more chemical bonds and in which at least one of said residues is defined as having a core and at least one linker, wherein said at least one linker is defined as an assembly of two or more structural units,
• an ion source for receiving a target macromolecule and ionizing said target macromolecule so as to generate a plurality of precursor ions,
• at least one ion guide for receiving said precursor ions and providing focusing thereof,
• a first mass analyzer positioned downstream of said at least one ion guide for selecting precursor ions having a target m/z ratio,
• a collision cell positioned downstream of said mass analyzer for causing fragmentation of at least a portion of said selected precursor ions into a plurality of product ions,
• a second mass analyzer for selecting at least a portion of the product ions having a target m/z ratio,
• a detector for detecting said selected product ions and generating one or more detection signals in response to the detection of said product ions, and
• an analysis module configured to receive said detection signals and to generate an experimentally-observed MS/MS spectrum of said target macromolecule,
• wherein said analysis module is configured to transmit said experimentally-observed MS/MS spectrum to said predictive system and said predictive system is configured to compare said experimentally-observed MS/MS spectrum with a spectrum corresponding to said theoretically determined cleavage products so as to determine a degree of correspondence between said putative macromolecule and said target macromolecule.