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Mono- and Intralink Filter (Mi-Filter) To Reduce False Identifications in Cross-Linking Mass Spectrometry Data.
Anal Chem, 94(51):17751-17756.
Cross-linking mass spectrometry (XL-MS) has become an indispensable tool for theemerging field of systems structural biology over the recent years. However, theconfidence in individual protein-protein interactions (PPIs) depends on thecorrect assessment of individual inter-protein cross-links. In this article, wedescribe a mono- and intralink filter (mi-filter) that is applicable to any kindof cross-linking data and workflow. It stipulates that only proteins for which atleast one monolink or intra-protein cross-link has been identified within a givendata set are considered for an inter-protein cross-link and therefore participatein a PPI. We show that this simple and intuitive filter has a dramatic effect ondifferent types of cross-linking data ranging from individual protein complexesover medium-complexity affinity enrichments to proteome-wide cell lysates andsignificantly reduces the number of false-positive identifications forinter-protein links in all these types of XL-MS data.
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