3.11.0

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. ⚠️ (PR #193, fixes #188)
  • 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
• Add figures for 2023 manuscript (PR #194)

Changed

• Change logging of model configuration to debug level (PR #193)

Removed

• fasta2speclib: Removed support for Elude-based RT predictions, RT predictions file, PEPREC filter, saving temporary PEPREC files (PR #193)

Fixed

• Remove unsupported argument for mzml.read (PR #193)
• spectrum_output: Fix CSV output to always use \n line terminators (PR #193)
• spectrum_output: Use semi-colon for spectronaut CSV output (PR #193)
• DeepLC integration: Disable PyGAM for default calibration on iRT peptides (led to poor calibration) (PR #193)