Add fragger hyper score #2407
Open
Add fragger hyper score #2407
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2407 +/- ##
==========================================
+ Coverage 93.67% 93.69% +0.01%
==========================================
Files 141 141
Lines 21925 21977 +52
Branches 3007 3014 +7
==========================================
+ Hits 20539 20591 +52
Misses 934 934
Partials 452 452
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
(5) Scoring and results reporting
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
Andy T. Kong,1,2 Felipe V. Leprevost,2 Dmitry M. Avtonomov,2 Dattatreya Mellacheruvu,2 and Alexey I. Nesvizhskii1,2,*