Created a visualizer for MSMS data. My next step is to pair that with a visualization of where fragment lines *should* appear given the known amino acid sequence. Here’s the output for CheZ_MS_1_Combo.pkl

UPDATE: I added code to include demarcation of amino acid boundaries of the correct amino acid sequence (as determined by GFS and marked with green lines). (NOTE: Some of the spectrum values had very low intensities, so for ease of visualization I bumped up the base intensity from 0 to 50%.):

Another note: You’ll notice that each of these graphics is the same width. Each spectrum has been scaled to fit a certain width.

The 5 amino acid sequences:
MMDVIQEIER
LYYVVQMTAQAAER
ALNSVEASQPHQDQMEK
ELGLDQAIAEAAEAIPDAR
QLLMVLLENIPEQESRPK

UPDATE: I scaled the GFS output amino acid sequence to match the length of the spectrum data. Perhaps this will compensate some for added ion weights: