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• W3143795625 endingPage "140655" @default.
• W3143795625 startingPage "140655" @default.
• W3143795625 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. • 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" @default.
• W3143795625 created "2021-04-13" @default.
• W3143795625 creator A5007090283 @default.
• W3143795625 creator A5017320872 @default.
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• W3143795625 date "2021-07-01" @default.
• W3143795625 modified "2023-09-25" @default.
• W3143795625 title "Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking" @default.
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• W3143795625 doi "https://doi.org/10.1016/j.bbapap.2021.140655" @default.
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• W3143795625 hasPublicationYear "2021" @default.
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