Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking

• Published in: Biochimica et biophysica acta. Proteins and proteomics Vol. 1869; no. 7; p. 140655
• Main Authors: de Jong, Luitzen, Roseboom, Winfried, Kramer, Gertjan
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.07.2021
• ISSN: 1570-9639; 1878-1454
• DOI: 10.1016/j.bbapap.2021.140655

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. •Reporting of decoy identifications in results files of cross-link analysis of complex samples is important to validate the FDR of PPIs•Recent methods are discussed to recognize spurious inter-protein peptide pairs in result files of cross-link analysis•Intra-protein cross-linked peptide pairs can be used to predict retention times of SCX chromatography•Retention time prediction of SCXC can reveal part of false identifications of inter-protein cross-linked peptide pairs•Examples are shown that in vivo cross-linking reveals many novel dynamic protein-protein interactions