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Extend Tutorial on other FeatureFinders

1

https://github.com/OpenMS/OpenMS/issues/5697

timosachsenberg

Add example how to filter ConsensusMap and move more C++ code from FileFiltering to library (and expose to python)

1

timosachsenberg

Add branch generation to release job in OpenMS repo

2

I.e. in OpenMS jenkins release job trigger creation of "release/X.Y.Z" and use rules in ReadTheDocs. So that a new version of the documentation is generated on each release.

jpfeuffer

algo parameter documentation

2

add to https://pyopenms.readthedocs.io/en/latest/parameter_handling.html how to getDescription in a nice way

timosachsenberg

iPyNB conversion for code in Notes not working

4

see Chemistry

jpfeuffer

Code that should be wrapped in PyOpenMS

4

Wrapping: - [ ] ./src/openms/include/OpenMS/METADATA/IonSource.h ``` static const std::string NamesOfPolarity[SIZE_OF_POLARITY]; static const std::string NamesOfInletType[SIZE_OF_INLETTYPE]; static const std::string NamesOfIonizationMethod[SIZE_OF_IONIZATIONMETHOD]; ``` - [ ] ./src/openms/include/OpenMS/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.h: ``` static const std::string NamesOfDerivatizationAgent[static_cast(DerivatizationAgent::SIZE_OF_DERIVATIZATIONAGENT)]; static const...

oliveralka

Add basic protein inference example

4

Add target / decoy creation, PeptideIndexer, FDR, filtering https://pyopenms.readthedocs.io/en/latest/peptide_search.html#simplesearch also protein inference at the end

timosachsenberg

Targeted proteomics Targeted proteomics/metabolomics is based on a list of known analytes (proteins, metabolites). Targeted methods are in contrast to so-­called discovery mode or shotgun proteomics, where proteins/metabolites are identified...

timosachsenberg

Potential useful information to review and add to the readthedocs page - from learning unit 5

3

Label-free quantification Label-free quantification is a method that aims to determine the relative amount of proteins in two or more biological samples. It may be based on precursor signal intensity...

timosachsenberg

This material is from a past lecture and can be reused. It should nevertheless be reviewed. ------------------ Types of chromatography (TLC, LC, GC) Chromatography is used to separate a mixture,...

timosachsenberg