v3.13.0

Added

• New timsTOF 2024 model added (now alias for timsTOF) by @ArthurDeclercq in #211

Full Changelog: v3.12.0...v3.13.0

v3.12.0

What's Changed

• Add code and figures for 2023 NAR manuscript @ArthurDeclercq in #196 and #197
• Backport timsTOF model from 4.0 dev release to 3.12 release by @RalfG in #206

Full Changelog: v3.11.0...v3.12.0

v4.0.0-dev6

Full Changelog: v4.0.0-dev5...v4.0.0-dev6

v4.0.0-dev5

Full Changelog: v4.0.0-dev4...v4.0.0-dev5

v4.0.0-dev4

Full Changelog: v4.0.0-dev3...v4.0.0-dev4

v4.0.0-dev3

What's Changed

• Timstof models by @ArthurDeclercq in #203

Full Changelog: v4.0.0-dev2...v4.0.0-dev3

v4.0.0-dev2

Full Changelog: v4.0.0-dev1...v4.0.0-dev2

v4.0.0-dev1

Full Changelog: v4.0.0-dev0...v4.0.0-dev1

v4.0.0-dev0

Early development release of v4.0.0, which includes:

• Fully refactored Python API
• New command-line interface
• Support for all file formats readable by psm_utils
• Support for both MGF and mzML spectrum files
• Support for ProForma 2.0 peptide notation (no modification configuration required anymore)
• Support for multiple peptides/PSMs per spectrum
• ...

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)