Proteomic analysis articles within Nature Communications

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  • Article
    | Open Access

    The first week of life impacts health for all of life, but the mechanisms are little-understood. Here the authors extract multi-omic data from small volumes of blood to study the dynamic molecular changes during the first week of life, revealing a robust developmental trajectory common to different populations.

    • Amy H. Lee
    • , Casey P. Shannon
    •  & Tobias R. Kollmann

  • Article
    | Open Access

    Inferring direct protein−protein interactions (PPIs) and modules in PPI networks remains a challenge. Here, the authors introduce an algorithm to infer potential direct PPIs from quantitative proteomic AP-MS data by identifying enriched interactions of each bait relative to the other baits.

    • Mihaela E. Sardiu
    • , Joshua M. Gilmore
    •  & Michael P. Washburn

  • Article
    | Open Access

    Spatial proteomics allows studying cellular protein localisations at system-wide scale. Here, the authors show that combining the previously developed hyperLOPIT method with differential centrifugation yields protein localisation maps at suborganellar resolution while reducing analysis time and input material.

    • Aikaterini Geladaki
    • , Nina Kočevar Britovšek
    •  & Kathryn S. Lilley

  • Article
    | Open Access

    In the mdx mouse model of Duchenne muscular dystrophy, muscle contractions lead to force loss, which is attributed to myofibre damage. Here, the authors show that force loss is instead mediated by a redox circuit involving NOX2, PROX1, myoglobin and cytoplasmic actins, and suggest that it may be a protective mechanism to prevent excessive contraction-induced myofibre damage.

    • John T. Olthoff
    • , Angus Lindsay
    •  & James M. Ervasti

  • Article
    | Open Access

    Protein NEDDylation increases upon proteotoxic stress but the function of this response remains to be elucidated. Here, the authors show that NEDDylation contributes to the cellular defence against proteotoxicity by promoting nuclear protein aggregation and protecting the ubiquitin proteasome system.

    • Chantal M. Maghames
    • , Sofia Lobato-Gil
    •  & Dimitris P. Xirodimas

  • Article
    | Open Access

    Oral cancer has region-specific histopathological and molecular characteristics, complicating its classification by the standard tumor-node-metastasis system. Here, the authors combine discovery and targeted proteomics with IHC to identify region-specific and saliva biomarkers for oral cancer prognosis.

    • Carolina Moretto Carnielli
    • , Carolina Carneiro Soares Macedo
    •  & Adriana Franco Paes Leme

  • Article
    | Open Access

    Eukaryotic elongation factor 1 alpha (eEF1A) is subject to extensive post-translational methylation but not all responsible enzymes are known. Here, the authors identify METTL13 as an eEF1A methyltransferase with dual specificity, which is involved in the codon-specific modulation of mRNA translation.

    • Magnus E. Jakobsson
    • , Jędrzej M. Małecki
    •  & Pål Ø. Falnes

  • Article
    | Open Access

    Carbon dioxide can interact with proteins to form carbamate post-translational modifications. Here, the authors developed a strategy to identify carbamate post-translational modifications by trapping carbon dioxide and subsequently identifying the carbamylated proteins.

    • Victoria L. Linthwaite
    • , Joanna M. Janus
    •  & Martin J. Cann

  • Article
    | Open Access

    Detecting proteins and post-translational modifications is important for drug screens, but the number of proteins measurable simultaneously is limited. Here the authors use antibodies tagged with DNA barcodes and high-throughput sequencing to detect up to 70 (phospho-)proteins in stem cells.

    • Jessie A. G. van Buggenum
    • , Jan P. Gerlach
    •  & Klaas W. Mulder

  • Article
    | Open Access

    An accurate quantitation of different proteoforms remains challenging due to incomplete protein sequence coverage in mass spectrometry datasets. Here the authors describe a method to facilitate the discovery of proteoforms that may otherwise not be considered due to incomplete protein coverage or ambiguities in mapping peptides back to proteins.

    • Casimir Bamberger
    • , Salvador Martínez-Bartolomé
    •  & John R. Yates III

  • Article
    | Open Access

    Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.

    • David S. Hewings
    • , Johanna Heideker
    •  & Ingrid E. Wertz

  • Article
    | Open Access

    SUMO and ubiquitin are key signal transducers in several cellular processes including the DNA-damage response. Here the authors describe a method for selective enrichment of ubiquitin substrates for E3 ligases from complex cellular proteomes and identify the SUMO conjugation machinery as direct RNF4 substrates.

    • Ramesh Kumar
    • , Román González-Prieto
    •  & Alfred C. O. Vertegaal

  • Article
    | Open Access

    Subcellular localization of RNAs and proteins is important for polarized cells such as neurons. Here the authors differentiate mouse embryonic stem cells into neurons, and analyze the local transcriptome, proteome, and translated transcriptome in their cell bodies and neurites, providing a unique resource for future studies on neuronal polarity.

    • Alessandra Zappulo
    • , David van den Bruck
    •  & Marina Chekulaeva

  • 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

    SWATH-mass spectrometry consists of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics on the scale of thousands of proteins. Here, using data generated by eleven groups worldwide, the authors show that SWATH-MS is capable of generating highly reproducible data across different laboratories.

    • Ben C. Collins
    • , Christie L. Hunter
    •  & Ruedi Aebersold

  • Article
    | Open Access

    Protein-protein interactions (PPIs) play a major role in defining biological functions. Here, the authors present PPiSeq, a method to quantitatively score dynamic PPIs in yeast combining fragment complementation assays, genomic double-barcoding, and an analytical framework to precisely call fitness from barcode lineage trajectories.

    • Ulrich Schlecht
    • , Zhimin Liu
    •  & Sasha F. Levy

  • Article
    | Open Access

    Protein glycosylation is an essential post-translational modification which analysis is complicated by the diversity of glycan composition and heterogeneity at individual attachment sites. Here the authors describe a method to selectively enrich N-linked glycopeptides to facilitate the detection of micro-heterogeneity in N-glycosylation.

    • Minyong Chen
    • , Xiaofeng Shi
    •  & James C. Samuelson

  • Article
    | Open Access

    Ubiquitylation and SUMOylation are two important related post-translational modifications. Here the authors present an approach for the simultaneous identification and quantification of protein-wide SUMO and ubiquitin sites from a single sample, uncovering widespread crosstalk between the two modifications.

    • Frédéric Lamoliatte
    • , Francis P. McManus
    •  & Pierre Thibault

  • Article
    | Open Access

    Dissecting cellular signalling requires the analysis of large numbers of proteins. Here the authors describe DigiWest, a high-throughput protein detection method that combines the concept of western and widely-used bead array systems that allows rapid quantification of hundreds of specific proteins.

    • Fridolin Treindl
    • , Benjamin Ruprecht
    •  & Markus F. Templin

  • Article
    | Open Access

    Fbw7 is a ubiquitin-ligase, which targets several oncoproteins for proteolysis, and is therefore important for the control and prevention of tumorigenesis. In this study, Arabi and colleagues carry out a proteomic screen of the targets of Fbw7, and identify Nuclear Factor of κ-B2 as a substrate.

    • Azadeh Arabi
    • , Karim Ullah
    •  & Olle Sangfelt

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