Featured
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Method to Watch |
Nanopores for sequencing proteins
Developments in nanopore-based peptide detection and sequencing show promise of a breakthrough.
- Arunima Singh
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Editorial |
Single-cell proteomics: challenges and prospects
Single-cell proteomics is a challenging goal and an area of rapid methods development. This Focus issue highlights the many paths toward high-throughput, high-sensitivity measurements.
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Brief Communication |
A multi-purpose, regenerable, proteome-scale, human phosphoserine resource for phosphoproteomics
Iterative Synthetically Phosphorylated Isomers (iSPI) is a proteome-scale library of human-derived phosphoserine-containing phosphopeptides with precisely known positions of phosphorylation. This multi-purpose resource is available for optimization, standardization, and benchmarking of key steps in phosphoproteomics workflows.
- Brandon M. Gassaway
- , Jiaming Li
- & Steven P. Gygi
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Technology Feature |
Diving deeper into the proteome
As new technology enables researchers to find and characterize less-common post-translational modifications that drive gene expression and cellular metabolism, the movement to catalog the entire human proteome gains momentum
- Caroline Seydel
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Article |
Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome
This article reports the cyclic immonium ion as a diagnostic fragment ion for lysine lactylation. The approach was used for identifying lactylation in various enriched and unenriched proteome databases, demonstrating prevalence of lactylation beyond histones.
- Ning Wan
- , Nian Wang
- & Hui Ye
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Brief Communication |
Histidine phosphorylation in human cells; a needle or phantom in the haystack?
Extensive analyses of mammalian phosphoproteomics datasets show that protein histidine phosphorylation in human cells may not be as prevalent as previously thought.
- Niels M. Leijten
- , Albert J. R. Heck
- & Simone Lemeer
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News & Views |
Uncovering an overlooked consequence of phosphorylation: change in cysteine reactivity
Global profiling of changes in the reactivity of cysteine residues in response to phosphorylation during mitosis identifies cysteine residues as potential regulatory and drug binding sites on proteins.
- Markus Lakemeyer
- & Matthew Bogyo
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Article |
Global profiling of phosphorylation-dependent changes in cysteine reactivity
This article describes a chemical proteomic approach to quantitatively relate serine/threonine phosphorylation to changes in the reactivity of cysteine residues, thereby affecting their potential to be post-translationally modified and/or targeted by electrophilic small molecules.
- Esther K. Kemper
- , Yuanjin Zhang
- & Benjamin F. Cravatt
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Research Highlight |
Engineered protein–protein toggle network
Sensitive synthetic protein-phosphorylation networks manifest fast bistable dynamics.
- Lin Tang
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Matters Arising |
Impact of phosphorylation on thermal stability of proteins
- Clément M. Potel
- , Nils Kurzawa
- & Mikhail M. Savitski
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Matters Arising |
Identification of phosphosites that alter protein thermal stability
- Ian R. Smith
- , Kyle N. Hess
- & Judit Villén
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Research Highlight |
Walking through chromatin modifications
The Cell-TALKING technique probes DNA modifications around a histone modification in fixed cells.
- Lei Tang
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Article |
Decoding the protein composition of whole nucleosomes with Nuc-MS
Nuc-MS makes use of top–down mass spectrometry in ‘native’ mode to quantitatively interrogate histone proteoforms and their post-translational modifications in a single experiment.
- Luis F. Schachner
- , Kevin Jooß
- & Neil L. Kelleher
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Method to Watch |
Glycoproteomics
Glycoproteomics is coming of age, thanks to advances in instrumentation, experimental methodologies and computational search algorithms.
- Arunima Singh
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Article |
Targeted deubiquitination rescues distinct trafficking-deficient ion channelopathies
Engineered deubiquitinases (enDUBs) use nanobodies to bring deubiquitinases to target proteins for selective ubiquitin chain removal. enDUBs can rescue the functional expression of mutant ion channels like those responsible for cystic fibrosis.
- Scott A. Kanner
- , Zunaira Shuja
- & Henry M. Colecraft
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Article |
O-Pair Search with MetaMorpheus for O-glycopeptide characterization
O-Pair search identifies O-glycopeptides and localizes O-glycosites using a fragment-ion-indexed open modification search combined with a graph-based approach. It also introduces a classification scheme to unify data reporting for glycoproteomics.
- Lei Lu
- , Nicholas M. Riley
- & Lloyd M. Smith
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Article |
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco
MSFragger-Glyco allows identification of N- and O-linked glycopeptides using the localization-aware open search strategy of the MSFragger search engine.
- Daniel A. Polasky
- , Fengchao Yu
- & Alexey I. Nesvizhskii
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Research Highlight |
Selective cell-surface N-glycan editing
A two-step chemoenzymatic method for N-glycan subtype-selective editing.
- Arunima Singh
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Article |
Cell-type-specific signaling networks in heterocellular organoids
Mass cytometry in combination with a thiol-reactive barcoding strategy allows analysis and comparison of cell-type-specific signaling networks in organoids.
- Xiao Qin
- , Jahangir Sufi
- & Christopher J. Tape
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Article |
An antibody for analysis of autophagy induction
A new method of autophagy measurement is based on the detection of phospho-ATG16L1, a conserved early marker of autophagy. Sensitive detection can be achieved in multiple biological systems and assays with advantages over standard methods.
- Wensheng Tian
- , Reham Alsaadi
- & Ryan C. Russell
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Article |
High throughput discovery of functional protein modifications by Hotspot Thermal Profiling
A massively parallel biophysical approach, Hotspot Thermal Profiling, analyzes the effects of phosphorylation on protein stability across the proteome in live cells.
- Jun X. Huang
- , Gihoon Lee
- & Raymond E. Moellering
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Article |
Glyco-DIA: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries
O-glycopeptides and O-glycan structures can be identified and quantified on a proteome-wide scale with Glyco-DIA, a data-independent-acquisition mass spectrometry-based method.
- Zilu Ye
- , Yang Mao
- & Sergey Y. Vakhrushev
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Brief Communication |
Thesaurus: quantifying phosphopeptide positional isomers
The search engine Thesaurus detects and quantifies phosphopeptide positional isomers from data-independent acquisition and parallel reaction monitoring mass spectrometry data, enabling studies of how neighboring phosphosites are regulated.
- Brian C. Searle
- , Robert T. Lawrence
- & Judit Villén
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Brief Communication |
Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification
Covalent linking of a histone-modification-specific antibody to MNase allows for the isolation of fragments with the desired histone mark, which can be amplified and sequenced. This approach is sensitive enough to profile histone modifications in single cells.
- Wai Lim Ku
- , Kosuke Nakamura
- & Keji Zhao
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Brief Communication |
Imaging cellular ultrastructures using expansion microscopy (U-ExM)
U-ExM enables near-native expansion microscopy of samples in vitro and in cells. The combination of U-ExM with confocal microscopy and HyVolution revealed details of centriole chirality that were previously accessible only by electron microscopy.
- Davide Gambarotto
- , Fabian U. Zwettler
- & Paul Guichard
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Brief Communication |
Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs
Fusion of a guide RNA directly to an adenosine deaminase via a SNAP-tag allows for precise and efficient RNA editing.
- Paul Vogel
- , Matin Moschref
- & Thorsten Stafforst
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Brief Communication |
Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics
A twist on a common method used for enriching phosphorylated peptides for mass spectrometry-based proteomics analysis now reveals previously undetected and widespread histidine phosphorylation in Escherichia coli.
- Clement M Potel
- , Miao-Hsia Lin
- & Simone Lemeer
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Article |
Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing
A new approach to evolve novel aminoacyl-tRNA synthetase–tRNA pairs with orthogonal substrate specificity is applied to generate a system to site-specifically incorporate phosphothreonine into proteins, enabling functional studies of this post-translational modification.
- Michael Shaofei Zhang
- , Simon F Brunner
- & Jason W Chin
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This Month |
Koraljka Husnjak
A “simple but a bit crazy idea” to tag ubiquitin and practice multilingual, multidisciplinary proteomics.
- Vivien Marx
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Article |
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
An ultrafast, fragment-ion indexing–based database search tool, MSFragger, makes open searching practical and enables comprehensive identification of modified peptides in mass spectrometry–based proteomics data sets.
- Andy T Kong
- , Felipe V Leprevost
- & Alexey I Nesvizhskii
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Article |
Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry
A lysine-less, internally affinity-tagged ubiquitin construct is deployed to discover linear polyubiquitinated substrates via a mass-spectrometry-based proteomics approach.
- Katarzyna Kliza
- , Christoph Taumer
- & Koraljka Husnjak
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Article |
Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution
New fluorescent biosensors enable the first super-resolution imaging of enzyme activity in live cells via fluorescence fluctuation increase by contact (FLINC).
- Gary C H Mo
- , Brian Ross
- & Jin Zhang
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Research Highlights |
Designer proteases for post-translational modifications
Researchers have engineered a protease specific for a post-translational modification.
- Rita Strack
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Brief Communication |
Post-translational selective intracellular silencing of acetylated proteins with de novo selected intrabodies
PISA, generates intrabodies that selectively bind and interfere with the intracellular function of an acetylated version of a target protein.
- Michele Chirichella
- , Simonetta Lisi
- & Antonino Cattaneo
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Tools in Brief |
Three steps to installing authentic protein modifications
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Research Highlights |
Extreme makeover: protein edition
Oxford scientists unleash radical chemistry to explore novel protein activities through synthetic post-translational modifications.
- Stéphane Larochelle
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Article |
A bacterial genetic selection system for ubiquitylation cascade discovery
An Escherichia coli-based genetic selection system, constructed from a split antibiotic resistance protein individually tethered to ubiquitin and a target protein, helps discover ubiquitin cascade pathway interactions.
- Olga Levin-Kravets
- , Neta Tanner
- & Gali Prag
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Brief Communication |
Enzyme-catalyzed expressed protein ligation
The enzyme subtiligase can be used to catalyze expressed protein ligation of proteins of interest with peptides lacking an N-terminal cysteine. This enables the analysis of protein modifications in the context of the native primary sequence.
- Samuel H Henager
- , Nam Chu
- & Philip A Cole
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This Month |
Judit Villén
Measuring phosphoproteins reproducibly and taking time to bike.
- Vivien Marx
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Brief Communication |
Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry
A method (and resource) demonstrating the mining of information from large-scale phosphoproteomics data sets is presented, allowing users to build targeted parallel reaction monitoring mass spectrometry assays to study phosphosites of interest.
- Robert T Lawrence
- , Brian C Searle
- & Judit Villén
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Tools in Brief |
An approach to study MARylation
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput
Nanopore-based detection of phosphorylation
Huang et al. reply
Henry Colecraft