Mass spectrometry articles within Nature Communications

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  • Article
    | Open Access

    Proteogenomics enables the discovery of protein coding regions and disease-relevant mutations but their verification remains challenging. Here, the authors combine peptide discovery, curation and validation in an integrated proteogenomics workflow, robustly identifying unknown coding regions and mutations.

    • Yafeng Zhu
    • , Lukas M. Orre
    •  & Janne Lehtiö

  • Article
    | Open Access

    Mass cytometry is a powerful method of single cell analysis, but potential confounding effects of cell cycle and cell volume are not taken into account. Here the authors present a combined experimental and computational method to correct for these effects and reveal features of TNFα stimulation that are otherwise masked.

    • Maria Anna Rapsomaniki
    • , Xiao-Kang Lun
    •  & María Rodríguez Martínez

  • Article
    | Open Access

    Human tyrosyl-DNA phosphodiesterase 1 (Tdp1) repairs covalently trapped topoisomerase 1B-DNA complexes and other lesions, and is a target for anticancer drug development. Here the authors use an integrated structural approach to shed light onto the molecular basis of DNA end-processing by Tdp1.

    • Fiona J. Flett
    • , Emilija Ruksenaite
    •  & Julia M. Richardson

  • Article
    | Open Access

    Native mass spectrometry (MS) is a technique that preserves non-covalent interactions in the mass spectrometer. Here the authors use native MS to study integral membrane proteins, and find that lipids with different headgroups and tails can allosterically modulate protein-protein interactions in different fashions.

    • Xiao Cong
    • , Yang Liu
    •  & Arthur Laganowsky

  • Article
    | Open Access

    Ambient mass spectrometry-based approaches have found application in biology and medicine. Here the authors report a mass spectrometric imaging method (ambient nanoPALDI) for live hippocampal tissues, based on gold nanorodassisted femtosecond laser desorption and subsequent non-thermal plasma induced ionization.

    • Jae Young Kim
    • , Eun Seok Seo
    •  & Dae Won Moon

  • Article
    | Open Access

    Chitosanases are classified according to their specificity in cleaving bonds at GlcNAc residues but the current system may be too simplistic. Here, the authors use quantitative mass spectrometry to revisit chitosanase specificity and propose additional determinants for their classification.

    • Tobias Weikert
    • , Anna Niehues
    •  & Bruno M. Moerschbacher

  • Article
    | Open Access

    The human heart is composed of distinct regions and cell types, but relatively little is known about their specific protein composition. Here, the authors present a region- and cell type-specific proteomic map of the healthy human heart, revealing functional differences and potential cell type markers.

    • Sophia Doll
    • , Martina Dreßen
    •  & Matthias Mann

  • Article
    | Open Access

    Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.

    • Abdelaziz Al Ouahabi
    • , Jean-Arthur Amalian
    •  & Jean-François Lutz

  • Article
    | Open Access

    The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization. Here the authors employ hydrogen/deuterium exchange (HDX) mass spectrometry to study the conformational dynamics of VDRRXRα and give mechanistic insights into how VDRRXRα controls the transcriptional activity of specific genes.

    • Jie Zheng
    • , Mi Ra Chang
    •  & Patrick R. Griffin

  • Article
    | Open Access

    Synthetic nanochemistry currently lacks the molecular step-by-step routes afforded to organic chemistry by total synthesis. Here, the authors track the seeded growth of atom-precise gold nanoclusters using mass spectrometry, revealing that the clusters evolve through a series of intermediates in two-electron steps.

    • Qiaofeng Yao
    • , Xun Yuan
    •  & Jianping Xie

  • Article
    | Open Access

    The structures of inorganic clusters are commonly characterized by mass spectrometry (MS), but neutral sulfur clusters heavily fragment under MS conditions, preventing their exact mass determination. Here, the authors successfully perform MS on labile cyclic sulfur clusters by stabilizing them within ionic supramolecular capsules.

    • Sho Matsuno
    • , Masahiro Yamashina
    •  & Michito Yoshizawa

  • Article
    | Open Access

    Significant challenges exist for structural characterization of enzymes responsible for biomineralization. Here the authors show that native mass spectrometry and high resolution electron microscopy can define the subunit topology and copper binding of a manganese oxidizing complex, and describe early stage formation of its mineral products

    • Christine A. Romano
    • , Mowei Zhou
    •  & Bradley M. Tebo

  • Article
    | Open Access

    Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.

    • Ming-Qi Liu
    • , Wen-Feng Zeng
    •  & Peng-Yuan Yang

  • Article
    | Open Access

    Preparation of samples for diagnosis can affect the detection of biomarkers and metabolites. Here, the authors use a silver nanoparticle plasmonics approach for the detection of biomarkers in patients as well as investigate the distribution of drugs in serum and cerebral spinal fluid.

    • Lin Huang
    • , Jingjing Wan
    •  & Kun Qian

  • Article
    | Open Access

    The analysis of site-specific glycosylation of HIV Envelope glycoprotein (Env) is challenging as it contains 25–30 glycosylation sites with multiple glycan forms at each site. Here the authors present a generally applicable mass spectrometry-based method for site-specific analysis of protein glycosylation that they apply to the analysis of the HIV-1 Env.

    • Liwei Cao
    • , Jolene K. Diedrich
    •  & James C. Paulson

  • Article
    | Open Access

    Self-assembling proteins that form capsid-like structures act as molecular containers for diverse cargoes. Here, the authors solve the cryo-EM structures of lumazine synthase shells, and show that supercharged mutants form expanded assemblies, indicating that electrostatics can be exploited to engineer cage architecture.

    • Eita Sasaki
    • , Daniel Böhringer
    •  & Donald Hilvert

  • Article
    | Open Access

    Monitoring interfacial electron transfer in photocatalytic systems is fundamentally important but experimentally challenging. Here the authors use mass spectrometry to detect and monitor intermediates formed through photoelectron transfer and to image active crystalline facets of semiconductor photocatalysts.

    • Hongying Zhong
    • , Juan Zhang
    •  & Zhiwei Yuan

  • Review Article
    | Open Access

    The Human Proteome Project aims to catalogue the ∼20,000 proteins encoded by the human genome. In this review, Bakeret al. focus on the missing proteins, proteins that lack high stringency proteomic evidence, and launch MissingProteinPedia, a database aimed at accelerating the search for missing proteins.

    • Mark S. Baker
    • , Seong Beom Ahn
    •  & Shoba Ranganathan

  • Article
    | Open Access

    The atypical chemokine receptor 3 (ACKR3) is important for cell migration in development and cancer. Here the authors combine radiolytic footprinting, disulfide trapping, mutagenesis and molecular modelling to characterize the ligand interactions and ligand-induced conformational changes in ACKR3.

    • Martin Gustavsson
    • , Liwen Wang
    •  & Tracy M. Handel

  • Article
    | Open Access

    Ambient chemical transformations between nanoparticles are poorly explored in materials science. Here, the authors find that two atomically precise, isomorphic clusters of gold and silver can convert between each other in solution through a series of alloy clusters, preserving structure, topology, and metal-ligand stoichiometry.

    • K. R. Krishnadas
    • , Ananya Baksi
    •  & Thalappil Pradeep

  • Article
    | Open Access

    Many biopharmaceuticals exhibit mixed heterogeneity in their post-translational modifications (PTMs) that are essential for their function. Here the authors use a combination of mass spectrometry techniques to analyse human erythropoietin (EPO) and properdin to discover new PTMs on properdin and derive a biosimilarity score for various sources of EPO.

    • Yang Yang
    • , Fan Liu
    •  & Albert J. R. Heck

  • Article
    | Open Access

    Ribosome recycling orchestrated by ABCE1 connects translation termination and mRNA surveillance mechanisms with re-initiation. Using a cross-linking and mass spectrometry approach, Kiosze-Becker et al. provide new information on the large conformational rearrangements that occur during ribosome recycling.

    • Kristin Kiosze-Becker
    • , Alessandro Ori
    •  & Robert Tampé

  • Article
    | Open Access

    To advance our understanding of pathological features associated with Alzheimer’s disease (AD), chemical tools with distinct specificity towards AD targets would be valuable. Here the authors used a structure-mechanism-based design strategy to obtain small molecules as chemical regulators for distinct pathological factors linked to AD pathology.

    • Michael W. Beck
    • , Jeffrey S. Derrick
    •  & Mi Hee Lim

  • Article
    | Open Access

    Electron microscopy can reveal a material’s chemical structure down to the atomic level, but has so far been blind to isotopic differences. Here the authors are able to map isotope concentrations in graphene by measuring the probability of ejecting atoms, demonstrating a ‘mass spectrometer in the microscope’.

    • Toma Susi
    • , Christoph Hofer
    •  & Jani Kotakoski

  • Article
    | Open Access

    ADP-ribosylation is a reversible post-translational protein modification involved in many cellular processes. Here the authors describe a sensitive approach for the analysis of ADP-ribosylation sites under physiologic conditions and identify lysine residues as in vivotargets of ADP-ribosylation.

    • Rita Martello
    • , Mario Leutert
    •  & Michael L. Nielsen

  • Article
    | Open Access

    Protein phosphorylation mediates signalling and other important cellular processes, but the specific effect of cysteine phosphorylation is unclear. Here, the authors present a chemical strategy to selectively phosphorylate cysteine residues and a mass spectrometry approach to detect and characterize endogenous pCys sites.

    • Jordi Bertran-Vicente
    • , Martin Penkert
    •  & Christian P. R. Hackenberger

  • Article
    | Open Access

    How genetic diversity generates complex phenotypes along a continuum remains a fundamental question of biology. Here—applying the emerging SWATH proteomics technology—the authors describe a proteome wide association study (PWAS) of Drosophila wing size and identify functional protein clusters associated with this trait.

    • Hirokazu Okada
    • , H. Alexander Ebhardt
    •  & Ernst Hafen

  • Article
    | Open Access

    Unambiguous metabolite annotation is a critical, yet problematic step, in mass spectrometry based metabolomics. Here, Shahaf et al. present WEIZMASS, a platform consisting of a diverse spectral library of more than 3500 plant metabolites and software to aid their identification in biological samples.

    • Nir Shahaf
    • , Ilana Rogachev
    •  & Asaph Aharoni

  • Article
    | Open Access

    Deciphering patterns of histone modifications that modulate chromatin structure and function is important, but remains challenging. Here the authors describe a method to uncover patterns of site-specific histone acetylation by deconvolution of overlapping peptide isomer mass spectra.

    • Nebiyu Abshiru
    • , Olivier Caron-Lizotte
    •  & Pierre Thibault

  • Article
    | Open Access

    Detecting enantiomers in dilute mixtures of volatile organic compounds is a challenge. Here, the authors demonstrate a method to identify enantiomers and enantiomeric excess in a multi-component mixture containing two chiral species using laser mass spectrometry and photoelectron circular dichroism.

    • Mohammad M Rafiee Fanood
    • , N. Bhargava Ram
    •  & Maurice H. M. Janssen

  • Article
    | Open Access

    The protein factors that bind to regulatory regions in the genome have not been systematically mapped. Here the authors performed chromatin immunoprecipitations for histone modifications associated with promoters, enhancers or heterochromatin in mouse embryonic stem cells and assigned a genome location to many factors important for pluripotency.

    • Erik Engelen
    • , Johannes H. Brandsma
    •  & Raymond A. Poot

  • Article
    | Open Access

    Mass spectral analysis is used to map the composition of materials and surfaces in numerous fields. Here, the authors report a mass spectral technique based on extreme ultraviolet laser ablation that allows three-dimensional imaging of chemical composition in addition to giving highly sensitive nanoscale resolution.

    • Ilya Kuznetsov
    • , Jorge Filevich
    •  & Carmen S. Menoni

  • Article
    | Open Access

    Mass spectrometry (MS) involves ionization of analytes with spectra dependent upon the mass-to-charge ratio. Here, the authors demonstrate that MS based on nanoelectromechanical systems gives results that are independent of the charge state and allow the mass spectrum of neutral species to be obtained.

    • Eric Sage
    • , Ariel Brenac
    •  & Sébastien Hentz

  • Article |

    Perfluorinated organic molecules have shown many uses, including as imaging agents. Here, the authors report that fluorinated gold nanoparticles offer an effective means of mass spectrometry tissue imaging, in addition to facilitating X-ray analysis providing complementary information to mass spectral images.

    • Michael E. Kurczy
    • , Zheng-Jiang Zhu
    •  & Gary Siuzdak

  • Article
    | Open Access

    Deubiquitylases (DUBs) remove ubiquitin chains from proteins. Here the authors develop a mass spectrometry-based DUB activity screen using unmodified diubiquitin isomers to characterize substrate specificity for 42 human DUBs, and assess the potency and selectivity of 11 DUB inhibitors.

    • Maria Stella Ritorto
    • , Richard Ewan
    •  & Matthias Trost

  • Article |

    The complexity and dynamic range of mammalian proteomes has stymied comprehensive protein quantification for the past twenty years. Zhou et al. develop DEEP SEQ mass spectrometry and use it to quantify a murine stem cell proteome to a depth equivalent to RNA-seq-based ribosome profiling.

    • Feng Zhou
    • , Yu Lu
    •  & Jarrod A. Marto

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