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Open AccessAutomated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications
The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands...
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Article
Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells
The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeli...
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Article
Open AccessWorkflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and...
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Article
Open AccessRNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition
The RNF43_p.G659fs mutation occurs frequently in colorectal cancer, but its function remains poorly understood and there are no specific therapies directed against this alteration. In this study, we find that RNF...
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Article
Open AccessProteomics of protein trafficking by in vivo tissue-specific labeling
Conventional approaches to identify secreted factors that regulate homeostasis are limited in their abilities to identify the tissues/cells of origin and destination. We established a platform to identify secr...
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Article
Open AccessDual functions of SPOP and ERG dictate androgen therapy responses in prostate cancer
Driver genes with a mutually exclusive mutation pattern across tumor genomes are thought to have overlap** roles in tumorigenesis. In contrast, we show here that mutually exclusive prostate cancer driver alt...
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Article
Proximity labeling in mammalian cells with TurboID and split-TurboID
This protocol describes the use of TurboID and split-TurboID in proximity labeling applications for map** protein–protein interactions and subcellular proteomes in live mammalian cells. TurboID is an enginee...
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Article
Open AccessDiscovery of suppressors of CRMP2 phosphorylation reveals compounds that mimic the behavioral effects of lithium on amphetamine-induced hyperlocomotion
The effective treatment of bipolar disorder (BD) represents a significant unmet medical need. Although lithium remains a mainstay of treatment for BD, limited knowledge regarding how it modulates affective beh...
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Article
Open AccessRapid and deep-scale ubiquitylation profiling for biology and translational research
Protein ubiquitylation is involved in a plethora of cellular processes. While antibodies directed at ubiquitin remnants (K-ɛ-GG) have improved the ability to monitor ubiquitylation using mass spectrometry, met...
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Article
Author Correction: Efficient proximity labeling in living cells and organisms with TurboID
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Protocol
In Situ Peroxidase Labeling and Mass Spectrometry of Alpha-Synuclein in Rat Cortical Neurons
In this chapter, we describe a novel ascorbate peroxidase (APEX)-based labeling method that in combination with mass spectrometry identifies proteins in the immediate vicinity of αSyn in living rat cortical ne...
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Article
Efficient proximity labeling in living cells and organisms with TurboID
Protein–protein interactions in cells are rapidly identified with improved proximity labeling methods.
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Article
Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry
Here we present an optimized workflow for global proteome and phosphoproteome analysis of tissues or cell lines that uses isobaric tags (TMT (tandem mass tags)-10) for multiplexed analysis and relative quantif...
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Article
Antibodies to biotin enable large-scale detection of biotinylation sites on proteins
Enrichment of biotinylated peptides using an anti-biotin antibody results in substantially improved biotinylation site identifications by mass spectrometry compared to traditional streptavidin-based biotinylat...
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Article
Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors
Different mutations found in endometrial and prostate tumors affecting the substrate-recognition domain of SPOP, a component of the E3 ubiquitin ligase complex, result in opposing degradation activity of BET p...
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Article
Spatially resolved proteomic map** in living cells with the engineered peroxidase APEX2
In this protocol, Hung et al. describe a method for performing cell compartment–specific proteomics for regions of interest using the engineered ascorbate peroxidase APEX2.
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Article
Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS
Lenalidomide is a highly effective treatment for myelodysplastic syndrome (MDS) with deletion of chromosome 5q (del(5q)). Here, we demonstrate that lenalidomide induces the ubiquitination of casein kinase 1A1 ...
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Article
Large-scale identification of ubiquitination sites by mass spectrometry
Ubiquitination is essential for the regulation of cellular protein homeostasis. It also has a central role in numerous signaling events. Recent advances in the production and availability of antibodies that re...
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Article
Integrated proteomic analysis of post-translational modifications by serial enrichment
A mass spectrometry–based method using serial enrichments of different post-translational modifications (SEPTM) enables high-coverage proteomic analysis of multiple PTMs from a single biological sample.
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Article
O-GlcNAcylation of the Plum pox virus capsid protein catalyzed by SECRET AGENT: characterization of O-GlcNAc sites by electron transfer dissociation mass spectrometry
The capsid protein of Plum pox virus (PPV-CP) is modified with O-linked β-N-acetylglucosamine (O-GlcNAc). In Arabidopsis thaliana this modification is made by an O-GlcNAc transferase named SECRET AGENT (SEC). Mod...
