fasta2speclib: Improved workflow for generating spectral libraries starting from a FASTA file, with new configuration options. ⚠️ These changes break compatibility with the previous configuration files. ⚠️
Support for C-terminal modifications
Differentiate between peptide and protein termini for variable modifications
Allow filtering of peptides based on precursor m/z
Allow semi-specific cleavage
Allow non-specific cleavage
Allow setting of a maximum of variable modifications per peptide
Add tests for modification assignment
Changed
Change logging of model configuration to debug level
Removed
fasta2speclib: Removed support for Elude-based RT predictions, RT predictions file, PEPREC filter, saving temporary PEPREC files
Fixed
Remove unsupported argument for mzml.read
spectrum_output: Fix CSV output to always use \n line terminators
spectrum_output: Use semi-colon for spectronaut CSV output
DeepLC integration: Disable PyGAM for default calibration on iRT peptides (led to poor calibration)
Added
fasta2speclib: Improved workflow for generating spectral libraries starting from a FASTA file, with new configuration options. ⚠️ These changes break compatibility with the previous configuration files. ⚠️Changed
Removed
fasta2speclib: Removed support for Elude-based RT predictions, RT predictions file, PEPREC filter, saving temporary PEPREC filesFixed
mzml.readspectrum_output: Fix CSV output to always use\nline terminatorsspectrum_output: Use semi-colon for spectronaut CSV output