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.

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)
Source code:       ECL_PF_source.zip

How to use it?

Tutorial.pdf is attached in the source code for detailed instructions.

For any enquiry, please contact ZHOU, Chen ( czhouau@connect.ust.hk).

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.

Data and FASTA file can be downloaded here Test_example.zip.