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@RalfG RalfG released this 12 Mar 20:00
· 265 commits to releases since this release
v3.9.0
7c95af1

New and improved 🚀

  • New prediction model for CID-TMT: TMT-labelled peptide spectra acquired on ion trap (trap-type CID), often used for "MultiNotch MS3" (https://dx.doi.org/10.1021/ac502040v) (PR #157)
  • Support for Python 3.9 and 3.10; dropped support for end-of-life Python 3.6 (PR #156, fixes #126)
  • Support for alternative cleavage rules (digestion enzymes) in fasta2speclib (PR #166, fixes #96)

Bugfixes 🐛

  • Fixed missing support for XGBoost models in single-prediction mode (PR #157, fixes #155)
  • Use oldest-supported-numpy for build in CI testing (PR #157)

Refactoring and minor changes 🔧

  • Replaced C models files with their XGBoost counterpart (except for HCD2019 and TMT): Faster compilation, smaller Python package (PR #157)
  • Add model_dir option to set custom directory for model downloads (CLI, single-prediction CLI, Python API) (PR #169, fixes #165)
  • Add docstring to MS2PIP class and add example to README.md (PR #167, fixes #131)
  • Relaxed click version requirements (PR #157, fixes #158)
  • Removed XGBoost warnings from the CLI output (PR #157)
  • Various fasta2speclib improvements (PR #166)
    • Add deeplc option to default config
    • Suppress tensorflow warnings
    • Replace deprecated pandas append with concat
  • Add missing sptm and gptm to example config.toml (#167)

New prediction models

Model Current version Train-test dataset (unique peptides) Evaluation dataset (unique peptides) Median Pearson correlation on evaluation dataset
CID-TMT v20220104 [in-house dataset] (72 138) PXD005890 (69 768) 0.851085
Assets 2
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