Analytical biochemistry articles within Nature Communications

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  • Article
    | Open Access

    CRISPR-Cas13a based methods currently use contiguous target RNA activation, which only enables single-target detection or editing. Here the authors propose a noncontiguous target RNA activation approach which can provide rapid, simultaneous and sensitive detection of two RNAs in a single readout, as well as parallel dual transgene knockdown.

    • Hongrui Zhao
    • , Yan Sheng
    •  & Jiaming Hu

  • Article
    | Open Access

    Perception and appreciation of food flavour depends on many factors, posing a challenge for effective prediction. Here, the authors combine extensive chemical and sensory analyses of 250 commercial Belgian beers to train machine learning models that enable flavour and consumer appreciation prediction.

    • Michiel Schreurs
    • , Supinya Piampongsant
    •  & Kevin J. Verstrepen

  • Article
    | Open Access

    Currently, only a few specialized labs can characterize O-glycans. The present study couples high-resolution ion mobility spectrometry with tandem mass spectrometry to efficiently identify complex O-glycan structures in clinical samples.

    • Leïla Bechtella
    • , Jin Chunsheng
    •  & Kevin Pagel

  • Article
    | Open Access

    O-acetylation is a common modification of sialic acids. Here, a library of synthetic O-acetylated sialosides made it possible to develop an ion mobility mass spectrometry (IM-MS) approach that can elucidate exact O-acetylation patterns and glycosidic linkage types of sialosides isolated from biological samples.

    • Gaёl M. Vos
    • , Kevin C. Hooijschuur
    •  & Geert-Jan Boons

  • Article
    | Open Access

    Fatty acids are fundamental biomolecular building blocks that are characterized by extraordinary structural diversity and present a formidable analytical challenge. Here the authors introduce a discovery workflow for de novo identification that adds more than 100 fatty acids to the human lipidome.

    • Jan Philipp Menzel
    • , Reuben S. E. Young
    •  & Stephen J. Blanksby

  • Article
    | Open Access

    Removing immunogenic uncapped mRNA from transcribed mRNA can be challenging, but is critical in mRNA research and clinical applications such as vaccines. Here, authors develop hydrophobic photocaged tag-modified cap analogs, which can be used to separate capped mRNA from uncapped mRNA, with subsequent tag removal using photo-irradiation.

    • Masahito Inagaki
    • , Naoko Abe
    •  & Hiroshi Abe

  • Article
    | Open Access

    Recombinant proteins in complex solutions are typically detected with tag-specific antibodies in Western blots. Here, the author describes an antibody-free alternative in which tagged proteins are detected directly in polyacrylamide gels via fluorophore-labelling of the tagged protein using a ligase.

    • Adrian C. D. Fuchs

  • Article
    | Open Access

    Ion mobility is used in mass spectrometers for structure analysis of biomolecules. Here, the authors show that ion mobility analysis in an ion trap under ultra-high fields enables isomer separation at resolutions over 10,000, wich they demonstrate for isomers of disaccharides, phospholipids, and peptides.

    • Xiaoyu Zhou
    • , Zhuofan Wang
    •  & Zheng Ouyang

  • Article
    | Open Access

    Biosensors using ligand-receptor binding tend to operate under equilibrium conditions, but this can make real-time monitoring challenging. Here the authors provide a theoretical foundation for biosensing where ligand concentrations can be continuously measured without needing to reach equilibrium.

    • Nicolò Maganzini
    • , Ian Thompson
    •  & Hyongsok Tom Soh

  • Article
    | Open Access

    A major challenge of enzyme-linked immunosorbent assays is discriminating true signal from non-specific binding. Here the authors present a Single-Molecule Colocalization Assay (SiMCA) which eliminates such effects, enabling reproducible detection of picomolar protein concentrations.

    • Amani A. Hariri
    • , Sharon S. Newman
    •  & H. Tom Soh

  • Article
    | Open Access

    Lipid nanoparticle delivery of mRNA vaccines has become of particular importance, however, mRNA stability is a major concern. Here, the authors report on a study of lipid impurity mRNA interactions using reverse phase ion pair HPLC to identify reactions which render the mRNA untranslatable, reducing vaccine efficiency.

    • Meredith Packer
    • , Dipendra Gyawali
    •  & Phil White

  • Article
    | Open Access

    Humans are exposed to many xenobiotic chemicals, but identification of low abundance xenobiotic exposures is limited by a lack of authentic standards for xenobiotic metabolites. Here the authors develop methods for enzymatic generation of diverse xenobiotic metabolites for use with high-resolution mass spectrometry for biology-based chemical identification.

    • Ken H. Liu
    • , Choon M. Lee
    •  & Dean P. Jones

  • Article
    | Open Access

    Existing methods for multimeric protein complex quantification in single cells suffer from limited selectivity and sensitivity. Here the authors report Single-cell protein Interaction Fractionation Through Electrophoresis and immunoassay Readout (SIFTER) and use this to probe the effects of cellular stress.

    • Julea Vlassakis
    • , Louise L. Hansen
    •  & Amy E. Herr

  • Article
    | Open Access

    Many current immunoassays require multiple washing, incubation and optimization steps. Here the authors present Ratiometric Plug-and-Play Immunodiagnostics (RAPPID), a generic assay platform that uses ratiometric bioluminescent detection to allow sandwich immunoassays to be performed directly in solution.

    • Yan Ni
    • , Bas J. H. M. Rosier
    •  & Maarten Merkx

  • Article
    | Open Access

    Predicting chromatographic retention times (RTs) has proven beneficial in proteomics but has not yet been achieved for crosslinked peptides. Here, the authors develop an RT prediction tool for crosslinked peptides and leverage predicted RTs to increase identifications in crosslinking mass spectrometry studies.

    • Sven H. Giese
    • , Ludwig R. Sinn
    •  & Juri Rappsilber

  • Comment
    | Open Access

    Proteins and peptides are amongst the most widely used research reagents but often their quality is inadequate and can result in poor data reproducibility. Here we propose a simple set of guidelines that, when correctly applied to protein reagents should provide more reliable experimental data.

    • Ario de Marco
    • , Nick Berrow
    •  & Bertrand Raynal

  • Article
    | Open Access

    RNA polymerase (Pol) I transcribes the ribosomal RNA precursor in eukaryotes. Here, the authors present three cryo-EM structure of S. pombe Pol I in different functional states among them a dimer structure and discuss conserved and organism-specific features of Pol I.

    • Florian B. Heiss
    • , Julia L. Daiß
    •  & Christoph Engel

  • Article
    | Open Access

    Mass spectrometry-based proteomics typically relies on highly sensitive nano-flow liquid chromatography (LC) but this can reduce robustness and reproducibility. Here, the authors show that micro-flow LC enables robust and reproducible high-throughput proteomics experiments at a very moderate loss of sensitivity.

    • Yangyang Bian
    • , Runsheng Zheng
    •  & Bernhard Kuster

  • Article
    | Open Access

    Imaging mass spectrometry is a powerful emerging tool for mapping the spatial distribution of biomolecules across tissue surfaces. Here the authors showcase an automated technology for deep proteome imaging that utilizes ultrasensitive microfluidics and a mass spectrometry workflow to analyze tissue voxels, generating quantitative cell-type-specific images.

    • Paul D. Piehowski
    • , Ying Zhu
    •  & Kristin E. Burnum-Johnson

  • Article
    | Open Access

    Clathrin light chains (CLCa and CLCb) are major constituents of clathrin-coated vesicles. Here authors find and structurally characterize the selective interaction between CLCa and the actin motor protein myosin VI which act together to generate the force that leads to invagination and fission at the apical surface.

    • Matteo Biancospino
    • , Gwen R. Buel
    •  & Simona Polo

  • Article
    | Open Access

    The use of antibodies to capture and profile exosomes limits the number of target proteins that can be detected. Here the authors develop a proximity-dependent barcoding assay that allows profiling of 38 surface proteins on individual exosomes from heterogeneous samples such as serum and seminal fluid.

    • Di Wu
    • , Junhong Yan
    •  & Masood Kamali-Moghaddam

  • Article
    | Open Access

    Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species, but these assays access only a subset of reaction possibilities. Here, the authors develop a band-collision gel electrophoresis (BCGE) approach that demonstrates a much wider variety of reaction types.

    • Dimitri A. Bikos
    •  & Thomas G. Mason

  • Article
    | Open Access

    Digital proximity ligation assay (dPLA) can measure proteins and mRNAs in single cells, but is not compatible with cell imaging and cannot quantify rare proteins due to a high dilution factor. Here the authors present an automated microfluidic device that combines live-cell imaging, chemical stimulation, and dPLA in a smaller reaction volume.

    • Jing Lin
    • , Christian Jordi
    •  & Savaş Tay

  • Article
    | Open Access

    Acyl carrier proteins (ACPs), a universal and highly conserved carrier of acyl intermediates during fatty acid and polyketide synthesis, are difficult to visualise. Here, the authors developed a facile, Raman spectroscopy-based method to detect ACP-substrate interactions.

    • Samuel C. Epstein
    • , Adam R. Huff
    •  & Louise K. Charkoudian

  • Article
    | Open Access

    Simultaneous quantification of DNA, RNA and protein at the single cell level has not yet been possible. Here the authors introduce a molecular labelling and detection strategy to quantify synthesis of these biomolecules and couple it to transient cell states through parallel quantification of state-dependent biomolecules.

    • Samuel C. Kimmey
    • , Luciene Borges
    •  & Sean C. Bendall

  • Article
    | Open Access

    The GTPase dynamin catalyzes membrane fission but activity of the dynamin-related ATPase EHD1 is unknown. Here, using in vitro reconstitution assays and molecular dynamics simulations, the authors report that EHD1 hydrolyzes ATP to remodel, causing fission of membrane tubes and that this is necessary for endocytic recycling.

    • Raunaq Deo
    • , Manish S. Kushwah
    •  & Thomas J. Pucadyil

  • Article
    | Open Access

    Ubiquitination and ubiquitin-like modifications of proteins regulate multiple cellular processes but identifying substrates of specific E2 and E3 enzymes remains challenging. Here, the authors conjugate E2 enzymes with enrichable ubiquitin derivatives to identify substrates of specific E2/E3 pairs by mass spectrometry.

    • Gábor Bakos
    • , Lu Yu
    •  & Jörg Mansfeld

  • Article
    | Open Access

    The specific glycosylation patterns of biological drugs often impact the efficacy and safety of the therapeutic product. Here the authors describe a native mass spectrometry approach that allows the resolution of highly complex glycosylation patterns on large proteins, which they apply to the therapeutic Fc-fusion protein Etanercept.

    • Therese Wohlschlager
    • , Kai Scheffler
    •  & Christian G. Huber

  • Article
    | Open Access

    The heat shock protein 90 (Hsp90) chaperone undergoes large conformational changes during its functional cycle. Here the authors combine in vivo, biochemical, biophysical and computational approaches and provide insights into the allosteric regulation of Hsp90 by identifying and characterizing a switch point in the Hsp90 middle domain.

    • Daniel Andreas Rutz
    • , Qi Luo
    •  & Johannes Buchner

  • Article
    | Open Access

    Spatial localization of genetic information is important for tissue heterogeneity but difficult to capture with current analytical techniques. Here the authors present “Pixelated RT-LAMP”, an approach that uses parallel on-chip reactions to provide the distribution of target sequences directly from tissue.

    • A. Ganguli
    • , A. Ornob
    •  & R. Bashir

  • Article
    | Open Access

    Levels of the enzyme myeloperoxidase in the blood are considered a biomarker for the severity of cardiovascular disease. Here the authors report a rapid and inexpensive method for measuring myeloperoxidase activity in human plasma by luminescence, after adsorption of the enzyme to a polymer surface.

    • Reece J. Goiffon
    • , Sara C. Martinez
    •  & David Piwnica-Worms

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