Why do we include only masses of prefix and suffix subpeptides in the ideal spectrum of a peptide (e.g., RED or DCA for REDCA)? Why don't we include masses of other subpeptides (like EDC)?
How do we infer the charges of annotated peaks in a spectrum?
How does the use of rounded (integer) masses of amino acids diminish our ability to accurately sequence peptides?
Why do the heights of some peaks in DinosaurSpectrum correlate so poorly with the corresponding amplitudes in the spectral vector?
If we know the proteome, isn’t it always better to use peptide identification instead of peptide sequencing?
Why do we generate the decoy database by assuming that all amino acids have the same frequency (1/20), despite the fact that many proteomes have widely varying amino acid frequencies?
What is the running time of the dynamic programming algorithm for computing the size of a spectral dictionary?