Question In mass spectrometry, what is a precursor ion and what is a product ion?
Question Explain the fragmentation of peptides in the second stage of a tandem mass spectrometry experiment, and the measurements we'd expect to see for a given fragmentation event. What is a b-ion and y-ion, and where do they show up on the m/z axis for a given fragmentation?
Approach to …. The C_n score is defined as a difference between two terms. What is the first term of this score, and why would we expect it to be high if we are guessing the correct peptide? What is the second term of the score, and why might we expect it to be high if we are guessing the wrong peptide?
Significance … What is the difference between p-values and q-values? In the tandem mass spec experiment, what is the null hypothesis and how is it generated?
Peptide … What are the two Dynamic Bayesian Networks (DBNs), and how are they used to discriminate correct peptide-spectrum matches (PSMs) from incorrect PSMs?