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Merge pull request #35 from hgb-bin-proteomics/develop
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update readme
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michabirklbauer authored Apr 16, 2024
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![test_state_windows](https://github.com/hgb-bin-proteomics/CandidateSearch/workflows/Test%20for%20Windows/badge.svg)
![test_state_ubuntu](https://github.com/hgb-bin-proteomics/CandidateSearch/workflows/Test%20for%20Ubuntu%2022.04/badge.svg)
![test_state_macos](https://github.com/hgb-bin-proteomics/CandidateSearch/workflows/Test%20for%20macOS/badge.svg)

# CandidateSearch

Proof-of-concept implementation of a search engine that uses [CandidateVectorSearch](https://github.com/hgb-bin-proteomics/CandidateVectorSearch)
to identify the best peptide candidates for a given mass spectrum. *CandidateSearch* creates the vector encodings of peptides and spectra that are
to identify the best peptide candidates for a given mass spectrum. *CandidateSearch* is also the computational backend of the non-cleavable crosslink
search in [MS Annika](https://github.com/hgb-bin-proteomics/MSAnnika). *CandidateSearch* creates the vector encodings of peptides and spectra that are
needed for the sparse matrix search of *CandidateVectorSearch*.

*CandidateSearch* can identify peptide candidates from a given mass spectrum without any precursor ion/mass information and no previous knowledge about
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## Downloads

Compiled DLLs and an executable for Windows 10/11 (x86, 64-bit) are available in the `exe` folder or in
Compiled DLLs and and executables are available in the `exe` folder or in
[Releases](https://github.com/hgb-bin-proteomics/CandidateSearch/releases).

We supply compiled executables and DLLs for:
- Windows 10/11 (x86, 64-bit)
- Ubuntu 22.04 (x86, 64-bit)
- macOS 14.4 (arm, 64-bit)

For other operating systems/architectures please compile the source code yourself!
You will also need to compile [CandidateVectorSearch](https://github.com/hgb-bin-proteomics/CandidateVectorSearch)!

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## Results

Example results of *CandidateSearch* and results analysis are given in `tests`.
Example results of *CandidateSearch* and results analysis are given in `tests`. An extensive report is given in [results.md](results.md).

![Results on a HeLa dataset](tests/v1.0.0/results.svg)

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