Fragger and xcorr modules

[trishorts]

Here I add two candidate modules for use in the PEP analysis engine. These should be investigated for efficacy in discrimination between correct and incorrect identifications.

MSFragger computes a hyperscore similar to that of X!:
hyperscore=log(Nb!Ny!∑i=1NbIb,i∑i=1NyIy,i)

where Nb is the number of matched b-ions, Ny is the number of matched y-ions, Ib,i are the intensities of matched b-ions, and Iy,i are the intensities of matched b-ions. While the theoretical fragment index can be adapted to include other fragment ion types, only b and y ions are included and used for scoring at this time. Expectation calculation is also performed in a similar manner as X! Tandem through linear regression of the survival function to estimate the expectation of a given hyperscore 51.

Nat Methods. Author manuscript; available in PMC 2017 Oct 10.
Published in final edited form as:
Nat Methods. 2017 May; 14(5): 513–520.
Published online 2017 Apr 10. doi: 10.1038/nmeth.4256
PMCID: PMC5409104
NIHMSID: NIHMS861287
PMID: 28394336
MSFragger: ultrafast and comprehensive peptide identification in shotgun proteomics

XCorr -
///

/// https://willfondrie.com/2019/02/an-intuitive-look-at-the-xcorr-score-function-in-proteomics/
///
/// A mass spectrum can be preprocessed by subtracting the mean intensities at all of the offsets.
/// Then a single dot product between the preprocessed mass spectrum and the theoretical peptide
/// mass spectrum yields the xcorr score, which is made possible because of the distributive
/// property of the dot product.
///
/// Since we have already chosen the match for this scan, we can use the matched ions to calculate the
/// xcorr and skip the dot product step.

[codecov]

Codecov Report

Attention: Patch coverage is 91.93548% with 5 lines in your changes missing coverage. Please review.

Project coverage is 93.64%. Comparing base (14ef43d) to head (abd8da9).
Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
...pheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs	91.93%	0 Missing and 5 partials ⚠️

Additional details and impacted files

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+ Hits        20528    20585      +57     
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Files with missing lines	Coverage Δ
...pheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs	94.74% <91.93%> (-0.22%)	⬇️