Big changes to MATCH BETWEEN RUNS

What's Changed

1. Transcriptomics Digestion and Fragmentation by @nbollis in #801

• Introduced support for handling RNA data within the UsefulProteomicsDatabases project.
• Add new properties and caching to oligo digestion
• Add RNA sequence and database handling and related test cases
• Refactor and enhance RNA and oligo handling in tests

2. Neutral Mass Spectrum by @nbollis in #806

• Created a 'NeutralMassSpectrum' class to represent a spectrum read off of a deconvoluted file by deriving the MzSpectrum.

3. Scan Filter in Averaged Spectra by @nbollis in #808

• This change ensures that the ScanFilter property is properly set, improving the accuracy and completeness of the scan data

4. MSFragger Results Folder Reader by @mzhastings in #792

• efficiently access MsFragger results using the full results folder rather than accessing each psm.tsv file within the folder individually

5. Get Modifications from Full Sequence by @nbollis in #796

• Added two methods in IBiopolymerWithSetModifications allowing one to get out a list or dictionary of modifications from the full sequence and a dictionary of all known modifications

6. Changes to MBR within FlashLFQ by @Alexander-Sol in #802

• attempt to locate a decoy peak for each acceptor peak
• All MBR peaks are fed into a binary classifier
• For each file, Q-Values are calculated for each MBR peak by ranking them in PEP order and performing target-decoy competition

7. Fixed decoy order by @Alexander-Sol in #809

• decoys are sorted before they are returned to ensure that the list of Proteins is ordered the same way every time.