Exhaustive cross-linking search with protein feedback
About ECL-PF |
Sensitively probing protein-protein interactions and protein structure is a principal challenge in cross-linking mass spectrometry (XL-MS). We describe an exhaustive crosslinking search with protein feedback mechanism (ECL-PF) for cleavable XL-MS data. ECL-PF adopts optimized α/β mass detection scheme and establishes protein-peptide association that enable identification in a sensitive way. We proved that different scoring functions can all benefit from the ECL-PF pipeline to a great extent.
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Related Publication |
C. Zhou*, S. Dai*, Y. Lin*, S. Lin, X. Fan, N. Li and W. Yu. *These authors contributed equally to this work.
"Exhaustive cross-linking search with protein feedback", bioRXiv, doi: https://doi.org/10.1101/2022.03.03.482813. |
Where to download ECL-PF |
The source code is available at: (updated Feb. 25, 2022)
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How to use it? |
Tutorial.pdf is attached in the source code for detailed instructions.
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Test data |
Synthetic BSA dataset and corresponding FASTA file is provided for testing purpose. BSA is Dimethyl labeled by light/heavy hydrogens and cross-linked by CBDPS. Parameters are provided in configuration.py by default setting.
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