FHOOE Hagenberg Bioinformatics/Proteomics Research Group

All

23 repositories

MSAnnika_MS1_Error
Public
Calculation of the MS1 Error for CSMs from MS Annika
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Jan 29, 2025Jan 29, 2025
MSAnnika_exporters
Public
Export MS Annika crosslink results to different formats.
visualization python proteomics mass-spectrometry spectrometry mass cross-linking ms2 ms3 crosslinking
Python
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MIT License
•0•4•2•0•Updated Jan 21, 2025Jan 21, 2025
SCOmics-Proof-of-Concept
Public
A proof-of-concept implementation for automated analysis of (single cell) multi-omic proteomics and transcriptomics data.
R
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GNU General Public License v3.0
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
MSAnnika_Combine_Results
Public
A script to merge and optionally validate several MS Annika search results.
python merge join proteomics mass-spectrometry spectrometry combine mass cross-linking crosslinking
Python
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MIT License
•0•0•0•0•Updated Dec 19, 2024Dec 19, 2024
MSAnnika_CSM_Annotation
Public
Calculates Intensities of Cross-linked Peptides from MS Annika CSMs.
python annotation proteomics mass-spectrometry spectrometry mass cross-linking ms2 ms3 fragment-ions
Python
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MIT License
•0•1•1•0•Updated Dec 19, 2024Dec 19, 2024
MSAnnika_FDR
Public
A script and functions to group and validate MS Annika results.
python validation discovery rate proteomics mass-spectrometry spectrometry false mass false-discovery-rate
Python
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MIT License
•0•0•0•0•Updated Dec 19, 2024Dec 19, 2024
MSAnnika_Spectral_Library_exporter
Public
Generate a spectral library for Spectronaut from MS Annika results.
fragments library spectral proteomics mass-spectrometry spectrometry mass cross-linking ms2 spectral-library
Python
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MIT License
•0•0•0•0•Updated Dec 19, 2024Dec 19, 2024
CandidateVectorSearch_template
Public template
Template repository for custom backends in MS Annika.
search search-engine engine psm sparse identification row proteomics csr mass-spectrometry
C++
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MIT License
•0•0•4•0•Updated Dec 19, 2024Dec 19, 2024
CandidateVectorSearch
Public
Searching for peptide candidates using sparse matrix + matrix/vector multiplication.
search search-engine gpu engine eigen cuda psm sparse identification proteomics
C++
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MIT License
•1•1•1•0•Updated Dec 19, 2024Dec 19, 2024
CandidateSearch
Public
Proof-of-concept implementation of a search engine that uses sparse matrix multiplication to identify the best peptide candidates for a given mass spectrum.
search search-engine gpu engine eigen cuda psm sparse identification proteomics
C#
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MIT License
•1•1•0•0•Updated Dec 19, 2024Dec 19, 2024
MSAnnika_NC_Results
Public archive
Repository containing scripts used for the analysis and visualization of the results of the MS Annika 3.0 non-cleavable crosslink search.
proteomics mass-spectrometry spectrometry mass crosslinking xlms crosslinker non-cleavable
HTML
•0•0•0•0•Updated Dec 19, 2024Dec 19, 2024
MSAnnika
Public
MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra.
search-engine proteomics mass-spectrometry spectrometry mass cross-linking ms2 ms3 crosslinking xlms
Other
•0•6•7•0•Updated Dec 19, 2024Dec 19, 2024
pdResult_Reader
Public
Proteome Discoverer Result File Reader
proteomics mass-spectrometry proteome spectrometry mass filereader discoverer proteome-discoverer
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Dec 4, 2024Dec 4, 2024
python_template
Public template
A template repository for linting, testing, GUI building and dockerizing python scripts.
Python
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MIT License
•1•0•0•0•Updated Nov 20, 2024Nov 20, 2024
MSAmanda
Public
MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.
search-engine proteomics mass-spectrometry spectrometry peptide-identification mass ms2 tandem-ms
Other
•0•3•0•0•Updated Sep 26, 2024Sep 26, 2024
.github
Public
GitHub Profile
0•0•0•0•Updated Jul 2, 2024Jul 2, 2024
dotnet_template
Public template
A template repository for building and testing .NET commandline applications.
C#
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MIT License
•1•0•0•0•Updated Jun 30, 2024Jun 30, 2024
MSAnnika_Extensions
Public
List of all available extensions for our cross-linking search engine MS Annika.
search-engine extension proteomics mass-spectrometry spectrometry mass cross-linking ms2 ms3 crosslinking
MIT License
•0•0•0•0•Updated Jun 21, 2024Jun 21, 2024
Proteome_Discoverer_MGF_Scan_Number_Repair_Tool
Public
A simple python script to fix scan numbers in result files generated by Proteome Discoverer.
proteomics mass-spectrometry spectrometry mass mgf proteome-discoverer
Python
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MIT License
•0•0•0•0•Updated Jun 19, 2024Jun 19, 2024
peptide_matching_game
Public
Peptide Matching Game
Python
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MIT License
•1•0•0•0•Updated Feb 26, 2024Feb 26, 2024
MSAnnika_MS3_Results
Public archive
Results and Evaluation of the MS3 Search Algorithm of MS Annika.
search-engine mass-spectrometry spectrometry mass cross-linking ms3 crosslinking xlms crosslinker tandem-ms
Jupyter Notebook
•0•0•0•0•Updated Oct 2, 2023Oct 2, 2023
MaXLinker_extensions
Public
Extensions for better usability of the cross-linking tool MaXLinker.
proteomics mass-spectrometry spectrometry mass cross-linking ms2 ms3 crosslinking xlms crosslinker
Python
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MIT License
•1•1•0•0•Updated Sep 4, 2023Sep 4, 2023
Crosslink_Utils
Public
Helper scripts for crosslink analysis.
python proteomics mass-spectrometry spectrometry mass cross-linking crosslinking xlms crosslinker
Python
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MIT License
•0•0•0•0•Updated Sep 4, 2023Sep 4, 2023