# Conflicts:
# src/openms/source/APPLICATIONS/ToolHandler.cpp
# src/utils/executables.cmake

[REFACTOR] some cleanup of PeptideIndexing...

[FEATURE] FileFilter flag to remove empty spectra / chromatograms

[FIX] empty hits

now no empty hit is added on resize

[FEATURE] some memory fixes for ProteomicsLFQ

[FIX] make decoy estimation more robust

[FIX] wrong loop variable

[DOC] Fix broken PDF creation

"
! Undefined control sequence.
\DoxyCode ...}{0ex plus 0ex minus 0ex}\ifthenelse
...

"l.173 \end{longtabu}

?
! Emergency stop.
\multispan ->\omit
...

[FIX] only write protein ids once in assay generation. remove decoys

from targeted extraction

[INTERNAL] consistent parameter name between header and definition in…

Very few fragment annotations were removed and some scores changed slightly.
Although the change...

[STYLE] Improve EmgGradientDescent's methods names

changed the same parameter name in the corresponding pxd as well

[FEATURE] New features in Deisotoper

QualityControl TOPP tool

style: Move some methods from protected to public

There was a slight error in summing up intensities in the old code.

Removed the old deisotoping function that was used exclusively by OpenPepXL.
OpenPepXL now uses ...

The Deisotoper can now annotate the number of peaks in each isotopic pattern. The averagine mode...

Feature/osw cleanup

[FIX] ChromeleonFile can handle commas as thousands separator