Decoy on the fly And Searching Match Ions with All Charges for decoy library generation #2059
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zrolfs
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May 18, 2021
This was referenced May 24, 2021
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rmillikin
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Jun 21, 2021
EngineLayer/SpectralLibrarySearch/SpectralLibrarySearchFunction.cs
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Test/TestData/2021-06-08-19-48-32/Task Settings/Task1-SearchTaskconfig.toml
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…ub.com/smith-chem-wisc/MetaMorpheus into DecoyOnTheFlyAndMatchedIonsWithAllCharges
rmillikin
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Jun 24, 2021
zrolfs
requested changes
Jun 28, 2021
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| // this is thread-safe because even if the score improves from another thread writing to this PSM, | ||
| // the lock combined with AddOrReplace method will ensure thread safety | ||
| if (meetsScoreCutoff) |
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Can we keep this conditional outside of the method?
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We can do it but if keep it outside, then we will have to add one line to calculate the "meetsScoreCutOff" every time we call this method.
…ub.com/smith-chem-wisc/MetaMorpheus into DecoyOnTheFlyAndMatchedIonsWithAllCharges
…ub.com/smith-chem-wisc/MetaMorpheus into DecoyOnTheFlyAndMatchedIonsWithAllCharges
zrolfs
approved these changes
Jun 29, 2021
rmmiller22
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Jul 15, 2021
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There are 2 main parts which have been changed:
1st one is decoy-on-the-fly method which generates decoy sequence by reversing target sequence. This is useful for decoy spectral library generation from target spectral library.
2nd one is looking for match ions with all charges. The original one finds a fragment with the theoretical mass, and if it accepts it and doesn't try to look for different charge states of that same fragment. This is not good for spectral library generation.
I added a check box in Search task GUI and added the Boolean value "write spectral library" to classic search engine parameters. The new decoy and matched ions searching methods would only work under the condition that you check the write spectral library box.