Featured
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Technology Feature |
scRNA-seq: oh, the joys
To those who seek transcriptomic information at high resolution, scale and throughput, single-cell RNA sequencing brings the data. Scientists share tips and future plans as they reflect on the method’s rise to stardom.
- Vivien Marx
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Perspective |
Can AlphaFold’s breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?
This Perspective discusses the potential of protein structure-prediction models for exploring the structural landscape and specificity of TCR–pMHC interactions.
- Benjamin McMaster
- , Christopher Thorpe
- & Hashem Koohy
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News & Views |
LiMCA: Hi-C gets an RNA twist
A multiomics method measures both the cellular three-dimensional genome and transcriptome at the single-cell level.
- Jane Kawaoka
- & Stavros Lomvardas
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Article |
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry
Implementation of ultralong transients on an Orbitrap mass spectrometer improves mass resolution, sensitivity and accuracy of charge determination in the analysis of large macromolecular ions.
- Evolène Deslignière
- , Victor C. Yin
- & Albert J. R. Heck
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This Month |
Early-career navigation tips
In a group interview, early-career researchers in proteomics share how they plan for the future and navigate divides over methods.
- Vivien Marx
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Research Briefing |
TREX identifies region-specific protein interactors of RNA molecules
Interactions between RNA and RNA-binding proteins (RBPs) define the fate and function of every RNA molecule. We present TREX, or targeted RNase H-mediated extraction of crosslinked RBPs, an efficient and accurate method to unbiasedly reveal the protein interactors of specific regions of RNAs isolated from living cells.
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Article
| Open Access
TREX reveals proteins that bind to specific RNA regions in living cells
TREX introduces an RNA-centric tool for identifying proteins binding to specific RNA regions in living cells.
- Martin Dodel
- , Giulia Guiducci
- & Faraz K. Mardakheh
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Article
| Open Access
Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry
MEISTER is an integrative experimental and computational framework for mass spectrometry that integrates three-dimensional, organ-wide biomolecular mapping with single-cell analysis for multiscale profiling of spatial–biochemical organization.
- Yuxuan Richard Xie
- , Daniel C. Castro
- & Fan Lam
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News & Views |
Single-cell probing of RNA structure
sc-SPORT offers a way to probe RNA structure at the single-cell level. It reveals cell-to-cell heterogeneity in RNA folding.
- Elizabeth A. Jolley
- & Philip C. Bevilacqua
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This Month |
From zero to hero in budget-making
The grant deadline approaches but budget details are still missing. Experienced budget-makers share how they manage budgets and the ‘boom–bust’ cycle.
- Vivien Marx
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Technology Feature |
Inside the chase after those elusive proteoforms
Human cells contain crowds of protein variants, but, especially in a time of funding challenges, chasing these proteoforms takes dogged persistence.
- Vivien Marx
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Article |
Deep generative design of RNA family sequences
RNA family sequence generator (RfamGen) is a deep generative model for designing novel, functional RNA sequences. RfamGen is applicable to diverse RNA families and can yield ribozymes with higher enzymatic activity.
- Shunsuke Sumi
- , Michiaki Hamada
- & Hirohide Saito
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Article
| Open Access
Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
This work introduces ARTR-seq for in situ measurement of RNA-binding protein (RBP) binding sites, which has been demonstrated in a small number of cells and for capturing dynamic RBP binding within short timeframes.
- Yu Xiao
- , Yan-Ming Chen
- & Chuan He
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Correspondence |
RepoRT: a comprehensive repository for small molecule retention times
- Fleming Kretschmer
- , Eva-Maria Harrieder
- & Michael Witting
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Article |
Mapping enzyme activity in living systems by real-time mid-infrared photothermal imaging of nitrile chameleons
Real-time mid-infrared photothermal imaging of nitrile chameleons enables simultaneous, multiplexed measurement of enzymatic activity in living systems and is poised to reveal the spatiotemporal regulation of enzymes in health and disease.
- Hongjian He
- , Jiaze Yin
- & Ji-Xin Cheng
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Article
| Open Access
RNA structure profiling at single-cell resolution reveals new determinants of cell identity
Single-cell structure probing of RNA transcripts enables simultaneous determination of transcript secondary structure and abundance in single cells, allowing new insights into RNA structural heterogeneity within and among cells.
- Jiaxu Wang
- , Yu Zhang
- & Yue Wan
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This Month |
Sizing a lab
Labs range in size, and no one size is likely to fit all. Here some researchers share their lab size experiences and preferences.
- Vivien Marx
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Brief Communication |
Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis
Cardinal v.3 is an open-source software for reproducible analysis of mass spectrometry imaging experiments, and includes data processing features such as mass recalibration, statistical analyses such as single-ion segmentation and rough annotation-based classification, and analyses of large-scale multitissue experiments.
- Kylie Ariel Bemis
- , Melanie Christine Föll
- & Olga Vitek
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Article
| Open Access
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA
RoseTTAFoldNA extends the RoseTTAFold2 platform to predict the structures of protein–DNA and protein–RNA complexes.
- Minkyung Baek
- , Ryan McHugh
- & Frank DiMaio
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Article |
Peptide sequencing based on host–guest interaction-assisted nanopore sensing
A phenylalanine-containing peptide probe can be used for discriminating all 20 amino acids via current blockage during translocation through an α-hemolysin (αHL) nanopore. The paper provides proof-of-concept peptide sequencing demonstrations.
- Yun Zhang
- , Yakun Yi
- & Hai-Chen Wu
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Article
| Open Access
OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis
OPUS-DSD is a neural network-based algorithm that reconstructs distinct conformations or continuous dynamics of the macromolecular structural landscape, starting from single-particle cryo-EM data.
- Zhenwei Luo
- , Fengyun Ni
- & Jianpeng Ma
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Article |
CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning
Few methods for three-dimensional structure modeling of nucleic acids from cryo-EM data exist. CryoREAD, a fully automated DNA/RNA atomic structure modeling method based on deep learning, was developed to fill this gap.
- Xiao Wang
- , Genki Terashi
- & Daisuke Kihara
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Article |
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells
A comprehensive redevelopment of the ribosome profiling workflow involves improved nuclease treatment and sequencing library preparation, enabling richer and more accurate translatome profiling with lower input and fewer technical hurdles.
- Lucas Ferguson
- , Heather E. Upton
- & Nicholas T. Ingolia
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Article
| Open Access
Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome
Single-cell Deep Visual Proteomics integrates imaging, cell segmentation, laser microdissection and multiplexed mass spectrometry for spatial single-cell proteomics measurements in complex tissues.
- Florian A. Rosenberger
- , Marvin Thielert
- & Matthias Mann
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Article |
Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore
A Ni2+-modified MspA nanopore construct can unambiguously discriminate the 20 proteogenic amino acids as well as several post-translational modifications.
- Kefan Wang
- , Shanyu Zhang
- & Shuo Huang
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Article
| Open Access
EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions
EzMechanism is a tool for automated prediction of the catalytic mechanisms of enzymes using their three-dimensional structures and chemical reactions as input.
- Antonio J. M. Ribeiro
- , Ioannis G. Riziotis
- & Janet M. Thornton
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This Month |
Happy labiversary
They started their lab mid-COVID. The new principal investigator adventure is a roller-coaster ride with some unexpected surprises.
- Vivien Marx
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Article |
Context-aware transcript quantification from long-read RNA-seq data with Bambu
Leveraging long-read RNA-seq data and machine learning, Bambu facilitates accurate transcript discovery and quantification.
- Ying Chen
- , Andre Sim
- & Jonathan Göke
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News & Views |
Identifying the structures of individual RNA isoforms inside cells
Nano-DMS-MaP focuses in on the structures of individual RNA isoforms, enabling direct examination of the structural diversity of different RNAs inside cells.
- Julia C. Kenyon
- & Johnson Mak
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Article |
Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells
The light-sensitive LOV domain was engineered into the TurboID enzyme, creating ‘LOV-Turbo’. LOV-Turbo enables optogenetic control over proximity labeling, increasing the spatiotemporal precision of this technique.
- Song-Yi Lee
- , Joleen S. Cheah
- & Alice Y. Ting
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Technology Feature |
Tuning in to epigenetic cross-talk
Chemical modifications to DNA, histones and RNA make changes happen. Scientists are exploring ways to track these modifications and how they interact.
- Vivien Marx
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Article |
Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer
Editor summary: A native-mass-spectrometry-based approach analyzes integral membrane protein–lipid complexes directly from near-physiological membrane conditions, providing information about protein oligomeric states, lipid identities, and membrane properties.
- Aniruddha Panda
- , Fabian Giska
- & Kallol Gupta
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Article
| Open Access
Nano-DMS-MaP allows isoform-specific RNA structure determination
Nano-DMS-MaP combines the power of DMS mutational profiling and long-read nanopore sequencing to resolve structural differences among RNA isoforms, revealing the structural landscape of HIV-1 transcripts in cells.
- Patrick Bohn
- , Anne-Sophie Gribling-Burrer
- & Redmond P. Smyth
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Research Briefing |
Accurate determination of molecular formulae using tandem mass spectrometry
We highlight the BUDDY software, which was developed to accurately determine the molecular formulae of unknown chemicals in mass spectrometry data. BUDDY is a bottom-up approach that shows superior annotation performance on reference spectra and experimental datasets. Incorporation of global peak annotation could enable BUDDY to refine formula annotations and reveal feature interrelationships.
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Article |
BUDDY: molecular formula discovery via bottom-up MS/MS interrogation
BUDDY is a bottom-up tandem MS (MS/MS) interrogation method for de novo molecular formula annotation with significance estimation.
- Shipei Xing
- , Sam Shen
- & Tao Huan
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Article
| Open Access
Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape
TEMPOmap combines pulse-chase metabolic labeling with multiplexed three-dimensional in situ sequencing to simultaneously profile the age and subcellular location of individual RNA molecules from thousands of genes to reveal RNA kinetic landscapes.
- Jingyi Ren
- , Haowen Zhou
- & Xiao Wang
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Research Briefing |
Extending the sensitivity, consistency and depth of single-cell proteomics
Simultaneous maximization of sensitivity, data completeness and throughput in mass-spectrometry proteomics often necessitates trade-offs. To mitigate these trade-offs, we introduce a prioritization algorithm that achieves high sensitivity and data completeness while maximizing throughput. With prioritized single-cell proteomics (pSCoPE), we consistently and accurately quantify proteins and their post-translational modifications in single macrophages and link them to endocytic activity.
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Brief Communication |
mScarlet3: a brilliant and fast-maturing red fluorescent protein
Two mScarlet variants with high brightness and fast maturation times have been evolved. These variants behave favorably as fusion tags and Förster resonance energy transfer acceptors.
- Theodorus W. J. Gadella Jr.
- , Laura van Weeren
- & Antoine Royant
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Analysis
| Open Access
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins
An international blind study confirms that smFRET measurements on dynamic proteins are highly reproducible across instruments, analysis procedures and timescales, further highlighting the promise of smFRET for dynamic structural biology.
- Ganesh Agam
- , Christian Gebhardt
- & Thorben Cordes
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Comment |
Tackling tumor complexity with single-cell proteomics
The development of mass spectrometry-based single-cell proteomics technologies opens unique opportunities to understand the functional crosstalk between cells that drive tumor development.
- Tamar Geiger
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Technology Feature |
Proteomics sets up single-cell and single-molecule solutions
New instruments are emerging in single-cell and single-molecule proteomics. This will offer labs a choice of technologies.
- Vivien Marx
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This Month |
Science meets art
It’s a creative, perhaps wild and sometimes challenging encounter. But some labs make a habit of inviting artists in.
- Vivien Marx
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Comment |
Making single-cell proteomics biologically relevant
Recent technological advances in mass spectrometry promise to add single-cell proteomics to the biologist’s toolbox. Here we discuss the current status and what is needed for this exciting technology to lead to biological insight — alone or as a complement to other omics technologies.
- Florian A. Rosenberger
- , Marvin Thielert
- & Matthias Mann
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Comment |
Mass spectrometry imaging: the rise of spatially resolved single-cell omics
Increasing evidence suggests that the spatial distribution of biomolecules within cells is a critical component in deciphering single-cell molecular heterogeneity. State-of-the-art single-cell MS imaging is uniquely capable of localizing biomolecules within cells, providing a dimension of information beyond what is currently available through in-depth omics investigations.
- Hua Zhang
- , Daniel G. Delafield
- & Lingjun Li
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Comment |
Sampling the proteome by emerging single-molecule and mass spectrometry methods
Mammalian cells have about 30,000 times as many protein molecules as mRNA molecules, which has major implications in the development of proteomics technologies. We discuss strategies that have been helpful for counting billions of protein molecules by liquid chromatography–tandem mass spectrometry and suggest that these strategies can benefit single-molecule methods, especially in mitigating the challenges posed by the wide dynamic range of the proteome.
- Michael J. MacCoss
- , Javier Antonio Alfaro
- & Nikolai Slavov
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Correspondence |
A standardized ontology for naming tRNA-derived RNAs based on molecular origin
- Andrew D. Holmes
- , Patricia P. Chan
- & Todd M. Lowe
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Review Article |
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry
This Review covers the state of the art in applying mass spectrometry- or next-generation sequencing-based techniques for single-cell proteomics analysis, offering suggestions for maximizing the advantages of both approaches.
- Hayley M. Bennett
- , William Stephenson
- & Spyros Darmanis
Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes
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