2020
DOI: 10.1126/sciadv.aax5783
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Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions

Abstract: Synaptic transmission is the predominant form of communication in the brain. It requires functionally specialized molecular machineries constituted by thousands of interacting synaptic proteins. Here, we made use of recent advances in cross-linking mass spectrometry (XL-MS) in combination with biochemical and computational approaches to reveal the architecture and assembly of synaptic protein complexes from mouse brain hippocampus and cerebellum. We obtained 11,999 unique lysine-lysine cross-links, comprising … Show more

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Cited by 92 publications
(81 citation statements)
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“…3D). These data suggest that each experimental set identified a subset of the total PiSCES that change during homeostatic scaling, and were consistent with reproducibility rates reported for mass spectrometry (Gonzalez-Lozano et al, 2020;Tabb et al, 2010).…”
Section: Upscaling and Downscaling Induce Bidirectional And Unidirectsupporting
confidence: 85%
See 1 more Smart Citation
“…3D). These data suggest that each experimental set identified a subset of the total PiSCES that change during homeostatic scaling, and were consistent with reproducibility rates reported for mass spectrometry (Gonzalez-Lozano et al, 2020;Tabb et al, 2010).…”
Section: Upscaling and Downscaling Induce Bidirectional And Unidirectsupporting
confidence: 85%
“…QMI attempts to measure unstable protein-protein interactions within noisy and stochastic intracellular environments and thus faces reproducibility challenges similar to mass spectrometry (Gonzalez-Lozano et al, 2020;Tabb et al, 2010). While noise is inherent to all signal transduction experiments, we are uniquely able to bioinformatically sort signal from noise using CNA modules.…”
Section: Signal Vs Noise In Signal Transduction Experimentsmentioning
confidence: 99%
“…In cases where a spectral library may not be readily obtainable, for instance when only limited input samples are available, DDA could be a better analysis choice. The use of a mass spectrometer gas phase cleavable chemical crosslinker to examine proteinprotein interactions has recently been successfully applied to elucidate a global protein interactome in the synapse; around 12,000 unique lysine crosslinks from 2,362 proteins were identified (Gonzalez-Lozano et al, 2020). Given the stochastic nature of intra-and inter-protein crosslinking events at various lysine sites, a single spectral library for their identification is not favorable and therefore DDA was used.…”
Section: Alternative Methodsologies Applicable To Quantitative Proteomicsmentioning
confidence: 99%
“…Technical limitations of Co-IP include the strength of the interaction after cell lysis, quality of the antibody, and the use of appropriate controls. However, techniques such as chemical cross-linking mass spectrometry have been used to identify more transient interactors in the synaptic compartment [74]. Co-IP works well with scaffold and adherent proteins that are enriched in the synaptic compartment (e.g., SHANK or HOMER).…”
Section: Affinity Pull-down and Co-immunoprecipitationmentioning
confidence: 99%