Merge pull request #1 from hgb-bin-proteomics/develop

release version

.github/workflows/python-app.yml

@@ -0,0 +1,46 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# Reference workflow provided by (c) GitHub
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: msannika_spectral_library
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Copy scripts and data to "/tests"
+      run: |
+        cp create_spectral_library.py tests
+        cp config.py tests
+        cp data/20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.mgf .
+        cp data/20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.xlsx .
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest tests/tests.py

CITATION.cff

@@ -0,0 +1,28 @@
+cff-version: 1.2.0
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Birklbauer"
+    given-names: "Micha J."
+    orcid: "https://orcid.org/0009-0005-1051-179X"
+  - family-names: "Matzinger"
+    given-names: "Manuel"
+    orcid: "https://orcid.org/0000-0002-9765-7951"
+  - family-names: "Müller"
+    given-names: "Fränze"
+    orcid: "https://orcid.org/0000-0003-3764-3547"
+  - family-names: "Mechtler"
+    given-names: "Karl"
+    orcid: "https://orcid.org/0000-0002-3392-9946"
+  - family-names: "Dorfer"
+    given-names: "Viktoria"
+    orcid: "https://orcid.org/0000-0002-5332-5701"
+  doi: "10.1021/acs.jproteome.3c00325"
+  journal: "Journal of Proteome Research"
+  month: 9
+  start: 3009
+  end: 3021
+  title: "MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity"
+  issue: 9
+  volume: 22
+  year: 2023

README.md

@@ -1 +1,90 @@
-# MSAnnika_Spectral_Library_exporter
+# MS Annika Spectral Library exporter
+
+Generate a spectral library for [Spectronaut](https://biognosys.com/software/spectronaut/) from [MS Annika](https://github.com/hgb-bin-proteomics/MSAnnika) results.
+
+![Screenshot](screenshot.png)
+
+## Usage
+
+- Install python 3.7+: [https://www.python.org/downloads/](https://www.python.org/downloads/)
+- Install requirements: `pip install -r requirements.txt`
+- Export MS Annika CSMs from Proteome Discoverer to Microsoft Excel format. Filter out decoys beforehand and filter for high-confidence CSMs (see below).
+- Convert any RAW files to *.mgf format.
+- Set your desired parameters in `config.py` (see below).
+- Run `python create_spectral_library.py`.
+- If the script successfully finishes, the spectral library should be generated with the extension `_spectralLibrary.csv`.
+
+## Exporting MS Annika results to Microsoft Excel
+
+The script uses a Micrsoft Excel files as input, for that MS Annika results need to be exported from Proteome Discoverer. It is recommended to first filter results according to your needs, e.g. filter for high-confidence crosslinks and filter out decoy crosslinks as depicted below.
+
+![PDFilter](filter.png)
+
+Results can then be exported by selecting `File > Export > To Microsoft Excel… > Level 1: Crosslinks > Export` in Proteome Discoverer.
+
+## Parameters
+
+The following parameters need to be adjusted for your needs in the `config.py` file:
+
+```python
+##### PARAMETERS #####
+
+# name of the mgf file containing the MS2 spectra
+SPECTRA_FILE = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.mgf"
+# name of the CSM file exported from Proteome Discoverer
+CSMS_FILE = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.xlsx"
+# name of the experiment / run (any descriptive text is allowed)
+RUN_NAME = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001-(1)"
+# name of the crosslink modification
+CROSSLINKER = "DSSO"
+# possible modifications and their monoisotopic masses
+MODIFICATIONS = \
+    {"Oxidation": [15.994915],
+     "Carbamidomethyl": [57.021464],
+     "DSSO": [54.01056, 85.98264, 103.99320]}
+# expected ion types (any of a, b, c, x, y, z)
+ION_TYPES = ("b", "y")
+# maximum expected charge of fragment ions
+MAX_CHARGE = 4
+# tolerance for matching peaks
+MATCH_TOLERANCE = 0.02
+# parameters for calculating iRT
+iRT_PARAMS = {"iRT_m": 1.3066, "iRT_t": 29.502}
+```
+
+## Known Issues
+
+[List of known issues](https://github.com/hgb-bin-proteomics/MSAnnika_Spectral_Library_exporter/issues)
+
+## Citing
+
+If you are using the MS Annika CSM Annotation script please cite:
+```
+MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity
+Micha J. Birklbauer, Manuel Matzinger, Fränze Müller, Karl Mechtler, and Viktoria Dorfer
+Journal of Proteome Research 2023 22 (9), 3009-3021
+DOI: 10.1021/acs.jproteome.3c00325
+```
+
+If you are using MS Annika please cite:
+```
+MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity
+Micha J. Birklbauer, Manuel Matzinger, Fränze Müller, Karl Mechtler, and Viktoria Dorfer
+Journal of Proteome Research 2023 22 (9), 3009-3021
+DOI: 10.1021/acs.jproteome.3c00325
+```
+or
+```
+MS Annika: A New Cross-Linking Search Engine
+Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, and Viktoria Dorfer
+Journal of Proteome Research 2021 20 (5), 2560-2569
+DOI: 10.1021/acs.jproteome.0c01000
+```
+
+## License
+
+- [MIT](https://github.com/hgb-bin-proteomics/MSAnnika_Spectral_Library_exporter/blob/master/LICENSE)
+
+## Contact
+
+- [micha.birklbauer@fh-hagenberg.at](mailto:micha.birklbauer@fh-hagenberg.at)

config.py

@@ -0,0 +1,23 @@
+##### PARAMETERS #####
+
+# name of the mgf file containing the MS2 spectra
+SPECTRA_FILE = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.mgf"
+# name of the CSM file exported from Proteome Discoverer
+CSMS_FILE = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.xlsx"
+# name of the experiment / run (any descriptive text is allowed)
+RUN_NAME = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001-(1)"
+# name of the crosslink modification
+CROSSLINKER = "DSSO"
+# possible modifications and their monoisotopic masses
+MODIFICATIONS = \
+    {"Oxidation": [15.994915],
+     "Carbamidomethyl": [57.021464],
+     "DSSO": [54.01056, 85.98264, 103.99320]}
+# expected ion types (any of a, b, c, x, y, z)
+ION_TYPES = ("b", "y")
+# maximum expected charge of fragment ions
+MAX_CHARGE = 4
+# tolerance for matching peaks
+MATCH_TOLERANCE = 0.02
+# parameters for calculating iRT
+iRT_PARAMS = {"iRT_m": 1.3066, "iRT_t": 29.502}