Fig. 2: Benchmarking of BFPA cross-linkers on BSA protein. | Communications Biology

Fig. 2: Benchmarking of BFPA cross-linkers on BSA protein.

From: Towards a universal cross-linking mass spectrometry approach for protein structure analysis with homo-bi-functional photo-activatable cross-linkers

Fig. 2

A, B Cross-links on BSA sequence for DSSO (blue), SDA (purple), EBDA (green) and BBDA (orange) cross-links. Lysine amino acids are marked in red. C, D Cross-links mapped to BSA structure (PDB: 4F5S). E Cross-link Cα-Cα distance constraint should be adjusted to account for different amino acid side-chain lengths. F Distribution of Cα-Cα distances of identified cross-links. G Percentage of cross-links mapped onto PDB: 4F5S which satisfied (blue) or violated (red) a 30 Å distance constraint or adjusted Cα-Cα distance constraint. Bars are labelled with number of satisfied/violated cross-links. H Frequency of amino acid cross-link sites by percentage (%) of all cross-link sites. I Comparison of cross-links identified by MeroX, xiSEARCH+xiFDR and Metamorpheus. Individual values from n = 3 cross-link replicates shown as dots. Mean value with standard deviation shown. J Comparison of BSA cross-links identified from non cross-linked BSA sample (false sample) across different search engines. Individual values from n = 3 cross-link replicates shown as dots. Mean value with standard deviation shown. K Comparison of non-BSA cross-links identified with Enolase sequence added (false sequence) across different search engines. Individual values from n = 3 cross-link replicates shown as dots. Mean value with standard deviation shown.

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