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.

Stabilized Decoy Scrambling

What's Changed

• Modified decoy scrambler to no longer use static Random generator by @Alexander-Sol in #798. Previously, calling the ScrambledDecoyProteinSequence would report different results depending on how many times it had been called previously. This was unintended, and has been reverted.
• • Quantifiable interfaces for results reading in FlashLFQ by @mzhastings in #793

New Contributors

• @mzhastings made their first contribution in #793

Full Changelog: 1.0.551...1.0.552

1.0.551

What's Changed

• DecoyScrambler now accounts for modifications by @Alexander-Sol in #795
• Updated SpectraFileInfo, changed fields to properties by @Alexander-Sol in #794

Full Changelog: 1.0.550...1.0.551

1.0.550

• Update to .NET 8.0
• Added external results readers for MsPathFinder, Crux, and FlashLFQ
• Changed MBR scoring functions within FlashLFQ, refactored FlashLfqEngine
• Added new function for generating decoy proteins, ScrambleDecoyProteinSequence

What's Changed

• Update nearly all nuget packages and .Net to 8.0 by @trishorts in #783
• Added support for crux output by @nbollis in #774
• MsPathFinderT result reading by @nbollis in #775
• All Quantified Peaks Reader by @nbollis in #788
• Refactored FlashLFQEngine and updated scoring functions for MBR by @Alexander-Sol in #777
• Pwsm target decoy by @Alexander-Sol in #769
• Updated package versions in nuspec by @Alexander-Sol in #790
• Added scramble method in Protein class that enables generation of decoy proteins that aren't homologous to target proteins, associated tests by @Alexander-Sol in #789

Full Changelog: 1.0.549...1.0.550

Revert Determination of Intensity Pairs for Spectrum Similarity

What's Changed

• Revert intensity pairs pr765 by @trishorts in #784

Full Changelog: 1.0.548...1.0.549

1.0.548 - Bug Fixes and QoL Improvements

What's Changed

• Handled edge case with digestion product having a null parent by @nbollis in #763
• Test fixed mod gptmd mod competition during digestion by @trishorts in #764
• Update dotnet.yml by @Alexander-Sol in #767
• Improved intensity pairs trying to make spectrum library comparisons faster by @trishorts in #765
• Fragger Result reading by @nbollis in #770
• Update dotnet.yml by @Alexander-Sol in #778
• Allow SSRCalc to be called from just base sequence without constructing PeptideWithSetModifications by @nbollis in #773
• Allow multiple custom fragmentations by @nbollis in #780
• FlashLFQ now enables selection of peptides to be quantified by @Alexander-Sol in #779

Full Changelog: 1.0.547...1.0.548

1.0.547 - Nucleotides, bug fixes, and refactoring

What's Changed

• Nucleotide, Rnase, Digestion Params Clone Method, and Interface Modificaiton by @nbollis in #757
• Add leucine to chymo cleavage motif by @trishorts in #759
• Changed Deconvoluter to have a static call by @nbollis in #760
• Mbr refactor by @Alexander-Sol in #758
• Edited the MatchedFramgentIon Equals method by @Alexander-Sol in #751

Full Changelog: 1.0.546...1.0.547

Minor Tweak to Digestion Parameters

What's Changed

• Changed behavior of masked members in Digestionparams by @nbollis in #756
  Enables toml reading and writing in MetaMorpheus

Full Changelog: 1.0.545...1.0.546

1.0.545 fix bugs in flashLFQ output

What's Changed

• Eliminate extra tab from chromatographic peak by @trishorts in #749
• Create CODE_OF_CONDUCT.md by @trishorts in #741
• Create CONTRIBUTING.md by @trishorts in #742

Full Changelog: 1.0.544...1.0.545

Update classes and class arrangment to accommodate both peptides and oligos

What's Changed

• Eliminate extra tab from chromatographic peak by @trishorts in #747
• Rearranging classes to fit within the Transcriptomics Structure by @nbollis in #743

Full Changelog: 1.0.543...1.0.544