Goal: Annotate MS2 spectra of small molecules with chemical compositions.
Data: Orbi, QstAR, QTOF spectra of ~200 known compounds (<1KDa) with different CID energies
Build consensus spectra from different energies
- Calculate chemical formula of parent mass from MS1 spectrum (given)
- Guild graph (DAG) of possible formulas to explain peaks
- Node for each possible chem formula for a single peak (usually 3-4 nodes per peak)
- Color nodes from the same peak with the same color
- Edge between nodes if they could be generated by a plausible neutral loss
- Score nodes based on likelihood of that formula
- Score edges according to known probabilities of various neutral losses
- Want a 'colorful' graph, ie explains most peaks ("colors") in the spectrum, and few peaks have multiple formula associated
Solve 3 formally:
Input: DAG + edge weights + set of colors
Output: Directed tree with maximal edge weight containing a unique set of colors
Solved by dynamic programming.
- Fragment tree is alternate representation of spectra
- Helps experts with manual peak annotation (somehow).
- Better than existing greedy solution and other tools for predicting spectra from structure (Mass Frontier)
- Could be used for comparing fragmentation trees to a library, but this isn't well developed.
- No clear progress towards goal of determining structure from MS2
- Not very systematic in the analysis
- Poor paper organization
- Are fragment trees useful?