Charge state determination

CREATED: 200701200833 ** Definition

• Given an MS/MS spectrum, determine the charge of the parent peptide
• Increases throughput and accuracy of sequencing algorithms

** Related Work

• score function based approach (Sadygov et al 2001) ** detect complementary ion pairs ** state with higher count is taken (Colinge et al 2003)
• probabilistic approach
• machine learning (Klammer et al 2005)

** Approach

• score each charge state using

count of no of complimentary peaks

effect of charge state, higher charge state produced more complementary peaks

effect of intensity, large sum of intensities, small difference in intensities

• final score function is $\frac{1}{z+1} (h_i + h_j)(1 - |\frac{h_i - h_j}{h_i + h_j}|^\alpha)$

** Algorithm

• $z_1 + z_2 = z$, so brute force over all possible $z_1$ and $z_2$, for each one use a linear time algorithm to find complimentary peaks, similar to find i, j such that a[i] + a[j] = X

** Issues

• use $\delta$ as error in m/z ratios, leads to excessive error amplification
• degenerate cases where complimentary peaks are closer than $\epsilon$
• try log intensities
• effect of tolerance
• modification of fragments