Coursera Week 3

How do I expand the list of candidate peptides in CyclopeptideSequencing?

One of the students in the first session of our class, John Cloutier, provided the following example that illustrates how CyclopeptideSequencing works. Consider a strange amino acid alphabet consisting of just two amino acids with masses 1 and 3. The figure below shows the peptides generated at each step by CyclopeptideSequencing with respect to a sample experimental spectrum {0, 1, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 5, 6}. Consistent peptides are shown in black, and inconsistent peptides are shown in red. In step 4, CyclopeptideSequencing produces the blue peptides 1-1-1-3, 1-1-3-1, 1-3-1-1, and 3-1-1-1; these four linear peptides all represent the same cyclic peptide, whose spectrum is equal to the experimental spectrum.

I've noticed a discrepancy between the mass of an amino acid cited in the book and in other sources. Why is this?

For example book suggests that glycine has elemental composition C2H3ON (integer mass 24+3+16+14=57 Da), whereas Wikipedia suggests that it is C2H5ON2 (integer mass 24+5+16+28=75 Da). We should use the former formula in analyzing mass spectra, since when an amino acid forms a peptide bond, it loses a water molecule (H2O).

Coursera Week 4

How can I improve the performance of LeaderboardCyclopeptideSequencing?

You should not need to optimize your implementation for LeaderboardCyclopeptideSequencing in order to pass its Code Challenge. However, various optimization approaches can be applied. To take one example, if the leaderboard has a peptide with mass smaller than ParentMass(Spectrum) but exceeding ParentMass(Spectrum) - 57 (recall that 57 is the mass of the lightest amino acid, glycine), this peptide can be safely removed from the leaderboard.

How can I trim the peptide leaderboard without sorting?

To trim a peptide leaderboard without using sorting, we will first compute an array ScoreHistogram, where ScoreHistogram(i) holds the number of peptides in Leaderboard with score i. For example, if we are trimming the leaderboard from Charging Station: Trimming the Peptide Leaderboard to N = 5 peptides (including ties), then ScoreHistogram = ScoreHistogram = (0, 0, 2, 1, 3, 2, 2).

As a result, 2 + 2 + 3 = 7 peptides will be retained and the remaining 0 + 0 + 2 + 1 = 3 peptides will be trimmed. Here, the minimum score that a peptide can have without being cut is denoted ScoreThresholdN(Spectrum).

Assuming that N is smaller than the number of elements on Leaderboard, note that the number of peptides cut is at most |Leaderboard| - N. In order to compute ScoreThresholdN(Spectrum), we need to find the index i such that the sum of the first i elements in ScoreHistogram is at most |Leaderboard| - N and the sum of the first i + 1 elements in ScoreHistogram exceeds |Leaderboard| - N. To find this index, we will compute CumulativeHistogram, where CumulativeHistogram(i) holds the number of peptides in Leaderboard with score below i.

For our ongoing example, CumulativeHistogram = (0, 0, 2, 3, 6, 8, 10). This leads us to the following pseudocode.

AnotherTrim(Leaderboard, Spectrum, N, AminoAcid, AminoAcidMass) for i ← 0 to |Spectrum| ScoreHistogram(i) ← 0 for j ← 1 to |Leaderboard| Peptide ← j-th peptide in Leaderboard LinearSpectrum ← LinearSpectrum(Peptide, AminoAcid, AminoAcidMass) LinearScore ← Score(Peptide, LinearSpectrum) LinearScore(j) ← LinearScore ScoreHistogram(LinearScore) ← ScoreHistogram(LinearScore) + 1 sum ← 0 for i ← 0 to |Spectrum| sum ← sum + ScoreHistogram(i) if sum > |Leaderboard| - N ScoreThreshold ← i - 1 for j ← 1 to |Leaderboard| Peptide ← j-th peptide in Leaderboard if LinearScores(j) < ScoreThreshold remove Peptide from Leaderboard return Leaderboard

FAQ Chapter 4

How Do We Sequence Antibiotics?