CHANGELOG.md

Changelog

All notable changes to this project are documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[4.2.0] - 2026-07-13

Added

• All prediction, m/z calculation, and spectrum annotation now use ms2rescore-rs (Rust); replaces C/Cython backend
• ms2_tolerance_mode parameter ("Da" or "ppm") on all correlation/annotation functions and CLI
• correlate now accepts preloaded spectra on PSMs (MS2Spectrum / AnnotatedMS2Spectrum)
• read_psms accepts list[PSM] in addition to PSMList, str, and Path
• Replaced remaining C-based model files with native XGBoost models (HCD2019, TMT, and HCDch2)
• XGBoost models are now pre-loaded across predict_library batches for improved efficiency
• rt and im optional dependency groups for DeepLC and IM2Deep
• Min/max length validators on ProteomeSearchSpace
• CUDA_VISIBLE_DEVICES workaround on XGBoost model load (dmlc/xgboost#11283)
• API docs for ms2pip.result and ms2pip.spectrum

Changed

• Minimum Python version raised to 3.11
• Package is now a pure-Python wheel (no compiled extensions)
• Batch processing uses Rayon-parallelized Rust calls instead of Python multiprocessing
• DeepLC integration uses deeplc.predict() functional API (replaces class-based DeepLC wrapper)
• IM2Deep integration uses im2deep.predict() functional API (replaces legacy im2deep.im2deep.predict_ccs)
• predict_library now runs RT/IM predictions once on the full filtered PSMList before batching (closes #243)
• Invalid peptidoforms (unsupported amino acids, length outside 4–100, missing charge) are skipped with a summarized warning instead of raising
• Bumped ms2rescore-rs requirement to >=0.5.0a3,<2
• Bumped psm_utils requirement to >=1.5

Removed

• C/Cython components: _cython_modules/, _models_c/, setup.py, MANIFEST.in
• All Python-based multiprocessing (_Parallelized class)
• _utils/retention_time.py and _utils/ion_mobility.py (inlined into core.py)
• iRT calibration peptides (DeepLC v4 handles calibration internally)
• Minor breaking change: ms2pip.constants.MODELS entries no longer contain id, peaks_version, or features_version keys (C/Cython routing metadata); replaced by fragmentation. Code accessing these keys directly will break.

Fixed

• annotate-spectra CLI crash (.with_suffix() called with no argument)
• write_correlations now accepts Path objects
• _peptidoform_spaces empty check uses is None instead of truthiness
• Spectrum model: deprecated model_validator/classmethod combination, missing serializers for np.ndarray fields (broke model_dump_json()), and equality comparison crashing on array fields

[4.1.2] - 2026-02-10

Fixed

• Prefer (faster) Genesis for model downloads, with a fallback to Zenodo
• CI: Update build runners for macOS (see actions/runner-images#13046)
• Fix logging for spectral library prediction (by @paretje in #257)

[4.1.1] - 2026-01-07

Fixed

• Fix support for SQLAlchemy v2, keeping backwards compatibility with v1.4 (#249, fixes #250)
• Fix typo of max_length in search_space documentation (#245 by @paretje)
• CI: Do not build dependencies like pyarrow from source, which can cause failed build workflows

[4.1.0] - 2025-01-20

Added

• Support for Thermo raw (requiring dotnet runtime) and gzipped spectrum files, through mobiusklein/mzdata (#226, by @paretje)
• New Python API usage mode correlate-single to correlate a single ObservedSpectrum object with predictions (#232)
• Support for Python 3.12 and 3.13, NumPy v2, and newer pandas and XGBoost versions (#228)
• CI: Add integration test for predict-single (#228)

Changed

• Ion mobility is now returned instead of collisional cross section when IM2Deep is used through the add_ion_mobility option (#236, by @rodvrees)
• Model files are now downloaded from Zenodo instead of Genesis (#225, by @paretje, fixes #229)
• Docs: Updated README to include correlate-single; moved webserver API docs from old Wiki (#239)

Removed

• Removed support for Python 3.8 (EOL) and for musllinux distributions (#228, #237)
• Removed old conversion scripts, mostly implemented in psm_utils (#239)
• Removed old train script, to be replaced with a page in docs (#239)

[4.0.0] - 2024-07-17

Fully refactored and substantially more user-friendly version of MS²PIP:

• More modular Python API
• One consolidated command-line interface with subcommands
• Support for all file formats readable by psm_utils
• Support for MGF, mzML, and Bruker raw spectrum files
• Support for ProForma 2.0 peptide notation (no modification configuration required)
• Support for multiple peptides/PSMs per spectrum
• Detailed documentation on ms2pip.readthedocs.io

[3.13.0] - 2024-03-05

Added

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

[3.12.0] - 2024-02-01

Added

• 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)

[3.11.0] - 2023-02-27

Added

• fasta2speclib: Improved workflow for generating spectral libraries from a FASTA file, with new configuration options (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, and 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 semicolon separator for Spectronaut CSV output (PR #193)
• DeepLC integration: Disable PyGAM for default calibration on iRT peptides (PR #193)

[3.10.1] - 2023-02-15

Added

• If precursor charge is not found in the MGF file, the charge from the PeptideRecord file is used instead (#189)
• Add tests for fasta2speclib modification generation (#190)

Fixed

• Fixed issue in fasta2speclib where fixed modifications were added one residue to the left of the actual site; bug introduced in v3.10.0 (#190)

[3.10.0] - 2023-02-01

Added

• Support for mzML spectrum files, both for evaluating models and for extracting feature vectors
• New argument spectrum_id_pattern: regular expression applied to spectrum titles before matching to peptide file entries
• When using MS²PIP as a class instance, the pred_and_emp dataframe can be returned instead of written to file by setting return_results=True
• If requested, retention time prediction with DeepLC is now also enabled when a spectrum file is provided

Changed

• Improved logging: use Rich library for logging with timestamps and message log levels
• MS²PIP now shows a progress bar instead of verbose output during prediction
• fasta2speclib: Improved variable modification assignment algorithm; combinatorial explosion is now reduced by setting a maximum number of modified residues per peptide
• Switch to Pyteomics MGF reader
• Avoid SciPy dependency
• More optimal use of NumPy in calc_correlations

Removed

• Removed unsupported Tableau output format

Fixed

• Vastly improved computational speed and reduced memory usage when using XGBoost model files with a spectrum file input
• fasta2speclib: Fixed issue where modified versions of peptides were duplicated
• spectrum_output: Various fixes in MSP spectral library file writing for DIA-NN compatibility (m/z error of 0.0 per peak, modifications sorted by position, use RetentionTime instead of RTINSECONDS)
• Fixed spectrum_utils modification off-by-one bug (fixes #170)
• Updated python_requires to minimum 3.7

[3.9.0] - 2022-03-12

Added

• New CID-TMT prediction model for TMT-labelled peptide spectra acquired on ion trap (trap-type CID), for use in MultiNotch MS3 workflows (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)
• model_dir option to set a custom directory for model downloads (CLI and Python API) (PR #169, fixes #165)
• Add docstring to MS2PIP class and example to README.md (PR #167)

Changed

• Replaced C model files with XGBoost counterparts (except for HCD2019 and TMT): faster compilation, smaller package (PR #157)
• Various fasta2speclib improvements: add DeepLC option to default config, suppress TensorFlow warnings, replace deprecated pandas.DataFrame.append with concat (PR #166)
• Relaxed click version requirements (PR #157)
• Removed XGBoost warnings from CLI output (PR #157)

Fixed

• Fixed missing support for XGBoost models in single-prediction mode (PR #157, fixes #155)

[3.8.0] - 2021-11-14

Added

• New models for non-tryptic peptides and immunopeptides (PR #137); see https://doi.org/10.1101/2021.11.02.466886
• Windows support (PR #151)
• Direct support for .xgboost model files; no dump to C and compilation required (PR #137)

Fixed

• In DLIB output, a value is now written to the isDecoy column (#140, PR #152)

[3.7.1] - 2021-09-13

Fixed

• Pin NumPy version used during build to fix compatibility with older NumPy versions (PR #148)

[3.7.0] - 2021-09-09

Added

• New command to predict and plot a single spectrum (PR #136)

Changed

• fasta2speclib: Pass through options from config file to DeepLC (PR #135, fixes #138)
• fasta2speclib: Pass num_cpu to DeepLC from the config

Fixed

• Parse modifications on residue L (#144, PR #145)

[3.6.3] - 2021-01-25

Added

• Python 3.9 support (PR #122)
• bioconda package and biocontainers Docker image
• macOS support (PR #95, PR #127); not yet for Python 3.9 (#126)

Fixed

• MS²PIP now exits on incorrectly configured or unknown modifications, instead of only showing a warning (#100, PR #101)
• Parsing of C-terminal modifications from a txt config file was broken in v3.6.2; now fixed (PR #109)
• Example fasta2speclib configuration erroneously contained average mass shifts; updated to monoisotopic mass shifts (PR #121)
• MS²PIP now exits with status code 1 on critical error (#102, PR #123)
• Supported config file extensions are now described in help and error messages (#125, PR #129)

[3.6.2] - 2020-05-08

Fixed

• Fixes in logging formatting (#64, #65)
• Use float formatting in CSV output
• Retention time predictions can be added without writing output to file
• When MS²PIP runs in a daemon process, it will not attempt to use multiprocessing
• Various improvements in match_spectra functionality (e.g. SQLite backend, output handling)
• General cleanup of repository (e.g. unused models)

[3.6.1] - 2020-04-01

Added

• New option save_peprec in fasta2speclib to save PEPREC files (including DeepLC predictions, if present)

Fixed

• Small fix in fasta2speclib parameter handling

[3.6.0] - 2020-03-30

Added

• DeepLC integration for accurate LC retention time prediction, including for modified peptides; enable with the -r flag or "add_retention_time": true in fasta2speclib config
• Support for TOML-based configuration files
• New Skyline .blib to PEPREC and MGF converter script in conversion_tools

[3.5.1] - 2020-03-04

Fixed

• Add header files to manifest (hotfix)

[3.5.0] - 2020-03-04

Added

• ProteinId column added to Spectronaut CSV output

Changed

• Major code refactoring
• Improved logging
• Improved exception handling
• Faster compilation

[3.4.2] - 2019-12-31

Added

• MS²PIP is now installable from PyPI with pip install ms2pip (no compilation step)
• MS²PIP now uses all available CPUs by default
• Moved to semantic versioning

Changed

• Speed improvements after the multiprocessing step, especially for large numbers of predictions

[v20191029] - 2019-10-29

Added

• MS²PIP is now locally installable with pip and conda
• New Spectronaut CSV and Bibliospec/Skyline output formats
• Output formats can now be specified in the config file (e.g. out=csv,msp,spectronaut)
• Slightly faster model compilation

[v20190624] - 2019-06-24

Added

• Add RetentionTimeMins to MSP output when an ELUDE model file is provided

[v20190312] - 2019-03-12

Added

• Models for charge 2 fragment ions (CID and HCD)

[v20190130] - 2019-01-30

Fixed

• Bugfixes
• Updated requirements.txt

[v20190120] - 2019-01-20

First official GitHub release of MS2PIPc (third iteration of MS2PIP).