Table 2.
Conditional Probability Table a
|
PCID(Ij|Iπ(j), S, Pj) |
|||
|---|---|---|---|
| Iπ(j) intensity | Ij intensity |
Ij = b − H3PO4 Iπ(j) = b |
Ij = y − H3PO4 Iπ(j) = y |
| strong | strong | 22.5% | 9.5% |
| strong | medium | 20.4% | 15.2% |
| strong | weak | 3.8% | 4.8% |
| strong | absent | 53.3% | 70.5% |
| medium | strong | 8.1% | 1.7% |
| medium | medium | 25.1% | 11.4% |
| medium | weak | 10.8% | 8.6% |
| medium | absent | 55.9% | 78.4% |
| weak | strong | 3.1% | 0.4% |
| weak | medium | 12.9% | 4.0% |
| weak | weak | 14.5% | 9.4% |
| weak | absent | 69.5% | 86.3% |
| absent | strong | 5.4% | 1.5% |
| absent | medium | 15.9% | 4.1% |
| absent | weak | 9.3% | 4.4% |
| absent | absent | 69.4% | 90.0% |
Using the observed intensity for Ij and Iπ(j), we look up the learned conditional probability and score the peak assignment Ij accordingly. This table shows two conditional probabilities: the third column for b − H3PO4 given b, the fourth column for y − H3PO4 given y. Notice the distinct propensities for fragment neutral loss of a b ion compared to a y ion. For example, a strong b peak produces a medium/strong b − H3PO4 43% of the time. Remembering that on average only 50% of b ions contain the phosphate moiety, almost all phosphorylated b peaks are accompanied by a neutral phosphate loss. In contrast, a strong y peak produces a medium/strong y − H3PO4 only 25% of the time, or roughly half of the fragments containing a phosphate.