Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification.
We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data ... analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ?1% false discovery rate. These protein interaction repositories provide meaningful structural information on many endogenous macromolecular assemblies, as we showcase on several protein complexes involved in translation, protein folding and carbohydrate metabolism.
Mesh Terms:
Algorithms, Carbohydrates, Computational Biology, DNA Fragmentation, Databases, Protein, Escherichia coli, False Positive Reactions, HeLa Cells, Humans, Models, Statistical, Protein Biosynthesis, Protein Conformation, Protein Folding, Proteome, Proteomics, Reproducibility of Results, Tandem Mass Spectrometry
Algorithms, Carbohydrates, Computational Biology, DNA Fragmentation, Databases, Protein, Escherichia coli, False Positive Reactions, HeLa Cells, Humans, Models, Statistical, Protein Biosynthesis, Protein Conformation, Protein Folding, Proteome, Proteomics, Reproducibility of Results, Tandem Mass Spectrometry
Nat Commun
Date: May. 19, 2017
PubMed ID: 28524877
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