Made updates pertaining to PIP-ECHO

[Alexander-Sol]

The current version of mzLib has had some significant changes made to MBR in FlashLFQ.

This update supports those changes.

• Added property to SearchParameters - MbrFdrThreshold. This controls the FDR of MBR identifications

  • Added text box in Search Task to allow users to set this parameter

• Call to the FlashLFQ engine in PostSearchAnalysisTask receives additional argument - PeptidesToQuantify

  • This ensures that only peptides with a peptide-level Q-value <0.01 are written to the output and used to calculate protein intensities

• Identifications passed in to FlashLFQ now have additional information: Score, Q-value, and bool isDecoy.

[codecov]

Codecov Report

Attention: Patch coverage is 97.36842% with 1 line in your changes missing coverage. Please review.

Project coverage is 93.95%. Comparing base (9766001) to head (2e2cf5d).

Files with missing lines	Patch %	Lines
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs	95.83%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2468      +/-   ##
==========================================
+ Coverage   93.93%   93.95%   +0.01%     
==========================================
  Files         149      149              
  Lines       22474    22497      +23     
  Branches     3090     3093       +3     
==========================================
+ Hits        21111    21137      +26     
+ Misses        911      908       -3     
  Partials      452      452              

Files with missing lines	Coverage Δ
MetaMorpheus/TaskLayer/FilteredPsms.cs	96.84% <100.00%> (+0.03%)	⬆️
...aMorpheus/TaskLayer/SearchTask/SearchParameters.cs	100.00% <100.00%> (ø)
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs	94.15% <95.83%> (+0.27%)	⬆️

[trishorts]

Should say that this is the q-value cut-off to select peptides used for label free quant. Could say that there may be some PSMs with q-value below cut-off that from peptides at greater than q-value cut-off and these will not be quantified. Also, all psms with q-value below cut-off will be used to mark a peptide as MSMS identified

[Alexander-Sol]

Should say that this is the q-value cut-off to select peptides used for label free quant.

This controls the q-value for PIP, determining which PIP Events/MBR transfers are reported in the AllQuantifiedPeptides/ProteinGroups output. I've updated the text to make this more clear