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  • Title: Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking.
    Author: de Jong L, Roseboom W, Kramer G.
    Journal: Biochim Biophys Acta Proteins Proteom; 2021 Jul; 1869(7):140655. PubMed ID: 33812047.
    Abstract:
    Chemical cross-linking (CX) of proteins in vivo or in cell free extracts followed by mass spectrometric (MS) identification of linked peptide pairs (CXMS) can reveal protein-protein interactions (PPIs) both at a proteome wide scale and the level of cross-linked amino acid residues. However, error estimation at the level of PPI remains challenging in large scale datasets. Here we discuss recent advances in the recognition of spurious inter-protein peptide pairs and in diminishing the FDR for these PPI-signaling cross-links, such as the use of chromatographic retention time prediction, in order to come to a more reliable reporting of PPIs.
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