Creating a mzLib method to calculate the stoichiometry (or site-occupancy) of PTMs using the intensity of each quantified peak. The current inputs are the protein database(s) file(.xml) paths and the AllQuantifiedPeaks.tsv file path. The output, occupancyDict, is currently a dictionary of nested dictionaries with the following structure:

{{string PROTEIN1, {{int MAA1, {{string MODNAME1, double INTENSITY}, 
                                {string MODNAME2, double INTENSITY},
                                ...,
                                {string "Total", double INTENSITY}}} 
                    {int MAA2, {...}}, 
                   ...}},
 {string PROTEIN2, {...}},
 ...}

where PROTEINX is the protein accession, MAAX is the modified amino acid at protein position X, and MODNAME1 is the full label of the modification. For each MAAX, there is a "Total" key (instead of a modification name) that holds the total intensity of that amino acid measured in the quantified peaks file, including modified and unmodified peptides with that specific residue.

The general approach is to first get all of the modification intensities and record those in occupancyDict while storing in proteinSeqRangesSeen a dictionary with protein accession keys and values stored as a list of (STARTINDEX, ENDINDEX, INTENSITY) tuples. This helps keep track of the index ranges seen for each protein. Once we have parsed all of the mods, for every amino acid falling into any of those ranges, we increase its "Total" intensity by that amount.

From our discussion, I've added below some of the items I'd like to get some opinions about. Imade them a task list primarily for me to keep track of what I've figured out.

• Where should this code live in mzLib. The most reasonable suggestions so far are in FlashLFQResults and Readers/QuantificationResults.
• To interface this nicely with MetaMorpheus, what should the inputs be? My goal now is to look into how/where this will be integrated into MM, but any suggestions on places to look to figure this out are appreciated.
• I have some ideas on making the code more efficient/succinct, especially foreseeing a lot more information about the peaks being readily available in MM (like the exact protein index for a peptide/peak). Any new ideas are welcomed.

Thanks in advance!