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RalfGRalfG
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Merge branch 'main' of https://github.com/compomics/psm_utils into pepxml-fixes
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‎.github/workflows/publish.yml‎

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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.9"
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python-version: "3.10"
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- name: Install dependencies
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run: |

‎.github/workflows/test.yml‎

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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.9
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.9"
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python-version: "3.10"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ruff
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- name: Lint with Ruff
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uses: astral-sh/ruff-action@v3
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with:
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args: check --exclude docs,tests
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- name: Check with Ruff
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run: ruff check --output-format=github .
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- name: Check formatting with Ruff
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uses: astral-sh/ruff-action@v3
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with:
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args: format --check --diff --exclude docs,tests
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- name: Install package and its dependencies
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run: pip install --editable .[dev,idxml]
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run: pip install --editable .[dev,io]
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- name: Static type checking with mypy
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run: mypy --non-interactive
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- name: Test with pytest and codecov
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run: |
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pytest --cov=psm_utils --cov-report=xml tests/
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pytest --cov=psm_utils --cov-report=xml tests/
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v3
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@v4
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- name: Install optional dependencies that might not be available
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continue-on-error: true
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run: pip install .[idxml]
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run: pip install .[io]
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- name: Test imports
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run: python -c "import psm_utils"

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.5.0] - 2025-10-27
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### Added
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- ✨ `io`: Read/write support for **JSON** and **CBOR** formats. (#125)
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- ✨ `io.percolator`: Added support for Comet-style N- and C-terminal modifications (#121 and #131 by @ATPs)
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### Changed
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- ♻️ `stats.qvalues`: Set the **regular target–decoy formula** explicitly in Pyteomics when `remove_decoy=False` and apply the **+1 correction** (probability that the first excluded decoy out-scores the threshold PSM). This produces less overly conservative q-values (e.g., on `example_files/msms.txt`). (#128)
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- 🏷️ **Typing**: Adopted full **MyPy** typing across the codebase. (#125)
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- 👷 **CI**: Replaced file-hash–based tests for `io.idxml` with unit tests; added formatting checks. (#125)
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### Removed
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- 💥 Dropped support for **Python 3.9**. (#125)
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### Fixed
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- 🐛 `io.mzid`: Treat **MS:1001460 “unknown modification”** as a **delta-mass–designated** modification in peptidoforms so mass calculations remain possible. Previously rendered as `[unknown modification]`. (#126 by @levitsky)
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- 🐛 `io.fragpipe`: Build more comprehensive **ProForma** strings using “Assigned Modifications” from FragPipe output. (fixes #123; #124 by @levitsky)
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- 🐛 `peptidoform`: Allow **residue `X` with a MassModification** to indicate a **gap of known mass** per ProForma §4.2.7; resolves failures computing theoretical mass for non-natural residues (fixes #127). (#130)
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## [1.4.1] - 2025-04-15
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### Fixed
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- Restored compatibility with older Sage versions that have no ion mobility columns (introduced in v1.4.0) (by @rodvrees in #120)
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## [1.4.0] - 2025-03-06
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### Added
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- ✨ `io.sage`: Add parsing of ion mobility values (PR #113)
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### Fixed
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- 🐛 `io.percolator`: Fix bug in `PercolatorTabWriter` where style parameter was not propagated (fixes #114, PR #117)
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- 📝 Docs: Explicitly set Sphinx configuration path for Read the Docs (fixes #115, PR #118)
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## [1.3.0] - 2025-01-20
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### Added
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- ✨ `io.idxml`: Parse ion mobility from idXML files if present.
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- 🐍 Added support for Python 3.12 and 3.13
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### Removed
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- 🐍 Removed support for Python 3.7
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### Fixed
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- 🐛 Fix bug introduced in #102 where dtypes were not coerced anymore by Numpy, which lead to unexpected behavior downstream (e.g., `psm_list["is_decoy"]` would return an array of objects instead of bools)
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- 🩹 Fix potential downstream issues because pepxml-read PSM had `rescoring_features=None` (partially fixes #108)
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## [1.2.0] - 2024-11-19
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### Added

‎README.rst‎

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File format psm_utils tag Read support Write support Comments
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===================================================================================================================== ======================== =============== =============== ==========
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`AlphaDIA precursors TSV <https://alphadia.readthedocs.io/en/latest/quickstart.html#output-files>`_ ``alphadia`` ✅ ❌
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`CBOR <https://psm-utils.readthedocs.io/en/stable/api/psm_utils.io#module-psm_utils.io.cbor>`_ ``cbor`` ✅ ✅
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`DIA-NN TSV <https://github.com/vdemichev/DiaNN#output>`_ ``diann`` ✅ ❌
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`FlashLFQ generic TSV <https://github.com/smith-chem-wisc/FlashLFQ/wiki/Identification-Input-Formats>`_ ``flashlfq`` ✅ ✅
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`FragPipe PSM TSV <https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#psmtsv/>`_ ``fragpipe`` ✅ ❌
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`ionbot CSV <https://ionbot.cloud/>`_ ``ionbot`` ✅ ❌
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`JSON <https://psm-utils.readthedocs.io/en/stable/api/psm_utils.io#module-psm_utils.io.json>`_ ``json`` ✅ ✅
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`OpenMS idXML <https://www.openms.de/>`_ ``idxml`` ✅ ✅ Requires the optional ``openms`` dependency (``pip install psm-utils[idxml]``)
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`MaxQuant msms.txt <https://www.maxquant.org/>`_ ``msms`` ✅ ❌
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`MS Amanda CSV <https://ms.imp.ac.at/?goto=msamanda>`_ ``msamanda`` ✅ ❌

‎docs/source/api/psm_utils.io.rst‎

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psm_utils.io.alphapept
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##################
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psm_utils.io.alphadia
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#####################
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.. automodule:: psm_utils.io.alphapept
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.. automodule:: psm_utils.io.alphadia
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:members:
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:inherited-members:
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psm_utils.io.cbor
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#################
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.. automodule:: psm_utils.io.cbor
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:inherited-members:
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##################
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#####################
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psm_utils.io.json
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#################
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.. automodule:: psm_utils.io.json
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:members:
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:inherited-members:
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psm_utils.io.maxquant
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#####################
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‎example_files/example.psm_utils.cbor‎

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‎example_files/example.psm_utils.json‎

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[
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{
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"peptidoform": "SSYGSSSNDDSYGSSNNDDSYGSSNK/3",
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"spectrum_id": "71876",
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"run": "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01",
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"spectrum": "71876",
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"is_decoy": false,
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"score": 136.160126,
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"qvalue": 0.0,
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"pep": 0.0,
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"precursor_mz": 894.33783,
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"retention_time": 2800.518555,
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"ion_mobility": 1e-06,
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"protein_list": [
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"P18899"
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],
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"rank": 1,
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"source": "AlphaDIA",
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"provenance_data": {
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"alphadia_filename": "C:\\Users\\ralfg\\git\\psm_utils\\example_files\\alphadia.precursors.tsv"
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},
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"metadata": {},
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"rescoring_features": {
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"rt_observed": 2800.518555,
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"mobility_observed": 1e-06,
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"mz_observed": 894.33783,
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"charge": 3.0,
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"delta_rt": 452.909424
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}
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},
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{
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"peptidoform": "SSQGSSSSTQSAPSETASASK/2",
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"spectrum_id": "41978",
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"run": "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01",
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"spectrum": "41978",
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"is_decoy": false,
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"score": 122.27832,
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"qvalue": 0.0,
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"pep": 0.0,
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"precursor_mz": 986.440491,
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"retention_time": 1647.208252,
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"ion_mobility": 1e-06,
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"protein_list": [
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"Q9ULU4"
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],
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"rank": 1,
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"source": "AlphaDIA",
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"provenance_data": {
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"alphadia_filename": "C:\\Users\\ralfg\\git\\psm_utils\\example_files\\alphadia.precursors.tsv"
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},
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"metadata": {},
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"rescoring_features": {
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"rt_observed": 1647.208252,
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"mobility_observed": 1e-06,
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"mz_observed": 986.440491,
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"charge": 2.0,
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"delta_rt": -23.25415
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}
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},
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{
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"peptidoform": "SSQTSGTNEQSSAIVSAR/2",
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"spectrum_id": "68554",
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"run": "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01",
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"spectrum": "68554",
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"is_decoy": false,
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"score": 152.012512,
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"qvalue": 0.0,
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"pep": 0.0,
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"precursor_mz": 905.432312,
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"retention_time": 2678.317139,
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"ion_mobility": 1e-06,
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"protein_list": [
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"O60763"
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],
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"rank": 1,
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"source": "AlphaDIA",
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"provenance_data": {
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"alphadia_filename": "C:\\Users\\ralfg\\git\\psm_utils\\example_files\\alphadia.precursors.tsv"
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},
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"metadata": {},
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"rescoring_features": {
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"rt_observed": 2678.317139,
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"mobility_observed": 1e-06,
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"mz_observed": 905.432312,
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"charge": 2.0,
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"delta_rt": 31.525879
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}
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}
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]

‎example_files/example.psm_utils.tsv‎

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peptidoform spectrum_id run collection is_decoy score qvalue pep precursor_mz retention_time ion_mobility protein_list rank source provenance:alphadia_filename rescoring:rt_observed rescoring:mobility_observed rescoring:mz_observed rescoring:charge rescoring:delta_rt
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SSYGSSSNDDSYGSSNNDDSYGSSNK/3 71876 LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 False 136.160126 0.0 0.0 894.33783 2800.518555 1e-06 ['P18899'] 1 AlphaDIA C:\Users\ralfg\git\psm_utils\example_files\alphadia.precursors.tsv 2800.518555 1e-06 894.33783 3.0 452.909424
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SSQGSSSSTQSAPSETASASK/2 41978 LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 False 122.27832 0.0 0.0 986.440491 1647.208252 1e-06 ['Q9ULU4'] 1 AlphaDIA C:\Users\ralfg\git\psm_utils\example_files\alphadia.precursors.tsv 1647.208252 1e-06 986.440491 2.0 -23.25415
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SSQTSGTNEQSSAIVSAR/2 68554 LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 False 152.012512 0.0 0.0 905.432312 2678.317139 1e-06 ['O60763'] 1 AlphaDIA C:\Users\ralfg\git\psm_utils\example_files\alphadia.precursors.tsv 2678.317139 1e-06 905.432312 2.0 31.525879

‎online/Home.py‎

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class StreamlitPageHome(StreamlitPage):
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"""Streamlit page for the home section."""
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pass
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‎online/_utils.py‎

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----------
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def fdr_plot(psm_df, fdr_threshold):
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"""Plot number of identifications in function of FDR threshold."""
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psm_df[~psm_df["is_decoy"]]
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