Proteomic analysis

  • Article
    | Open Access

    Proximity biotinylation is a powerful tool to profile interactomes, but it requires genetic engineering of the target protein. Here, the authors develop a proximity biotinylation enzyme that can be directed to the target using antibodies, enabling interactome profiling of endogenous proteins or PTMs.

    • Irene Santos-Barriopedro
    • , Guido van Mierlo
    •  & Michiel Vermeulen
  • Article
    | Open Access

    Mapping neuronal proteomes with genetic, subcellular, and temporal specificity is a challenging task. This study uncovers proteome dynamics in two classes of striatal spiny projection neurons in the mouse brain using a genetically targeted APEX2-based proximity labeling approach.

    • V. Dumrongprechachan
    • , R. B. Salisbury
    •  & Y. Kozorovitskiy
  • Article
    | Open Access

    Applying complexome profiling, Evers et al. unravel the composition of mitochondrial oxidative phosphorylation complexes in P. falciparum asexual and sexual blood stages. Abundance of these complexes differs between both stages, supporting the hypothesis that a mitochondrial metabolic switch is central to gametocyte development and functioning.

    • Felix Evers
    • , Alfredo Cabrera-Orefice
    •  & Taco W. A. Kooij
  • Article
    | Open Access

    The proximity extension assay (PEA) is a popular tool to measure plasma protein levels. Here, the authors extend the proteome coverage of PEA by combining it with next-generation sequencing, enabling the analysis of nearly 1500 proteins from minute amounts of plasma.

    • Wen Zhong
    • , Fredrik Edfors
    •  & Mathias Uhlén
  • Article
    | Open Access

    The network of proteins secreted for interorgan communication is poorly understood. Here, the authors develop a method, based on protein labeling, to study cell-specific secretomes and interorgan protein trafficking, and demonstrate their approach in Drosophila and mouse models.

    • Ilia A. Droujinine
    • , Amanda S. Meyer
    •  & Norbert Perrimon
  • Article
    | Open Access

    Skeletal muscle conveys the beneficial effects of physical exercise but due to its heterogeneity, studying the effects of exercise on muscle fibres is challenging. Here, the authors carry out proteomic analysis of myofibres from freeze-dried muscle biopsies, show fibre-type specific changes in response to exercise, and show that the oxidative and glycolytic muscle fibers adapt differentially to exercise training.

    • A. S. Deshmukh
    • , D. E. Steenberg
    •  & J. F. P. Wojtaszewski
  • Article
    | Open Access

    Protein ubiquitylation is often studied by proteomics but how data independent acquisition (DIA) may advance these studies remains to be explored. Here, the authors show that DIA improves ubiquitylation site identification and quantification, enabling them to characterize the circadian ubiquitinome in human cells.

    • Fynn M. Hansen
    • , Maria C. Tanzer
    •  & Matthias Mann
  • Article
    | Open Access

    Large population testing is a key step to controlling the COVID-19 pandemic. Here, the authors develop a targeted mass spectrometry system for peptide-based SARS-CoV-2 detection, allowing analysis of over 500 swab samples per day and enabling virus detection even after prolonged sample storage at room temperature.

    • Karina Helena Morais Cardozo
    • , Adriana Lebkuchen
    •  & Valdemir Melechco Carvalho
  • Article
    | Open Access

    How COVID-19 pathology differs from other drivers of pneumonia is unclear. Here the authors analyze urine from patients with COVID-19 and identify an immunosuppressive protein expression pattern that is distinct from the pattern in healthy individuals or patients with non-COVID-19 pneumonia.

    • Wenmin Tian
    • , Nan Zhang
    •  & Catherine C. L. Wong
  • Perspective
    | Open Access

    The Human Proteome Project (HPP) was launched in 2010 to enhance accurate annotation of the genome-encoded proteome. Ten years later, the HPP releases its first blueprint of the human proteome, annotating 90% of all known proteins at high-stringency and discussing the implications of proteomics for precision medicine.

    • Subash Adhikari
    • , Edouard C. Nice
    •  & Mark S. Baker
  • Article
    | Open Access

    To investigate the molecular foundation of sporadic Alzheimer’s disease (AD), Beckmann et al. constructed multiscale causal networks on a large human AD multi-omics dataset, detecting AD-associated networks and their top predicted regulator, VGF, with extensive validation in the 5xFAD mouse model.

    • Noam D. Beckmann
    • , Wei-Jye Lin
    •  & Eric E. Schadt
  • Article
    | Open Access

    The heterogeneity of IDH1/2 wild-type glioblastoma limits its prognosis and therapy. Here, the authors show a binary stratification, based on quantitative proteomic analysis of samples from patients with glioblastoma, with different prognosis and therapeutic vulnerabilities.

    • Sejin Oh
    • , Jeonghun Yeom
    •  & Hyun Seok Kim
  • Article
    | Open Access

    The blood circulation time is important to the biomedical application of nanomaterials. Here, the authors explore the effect of protein corona formation on the blood residency of nanomaterials and show circulation times are governed by the dynamic remodelling of protein opsonins in vivo.

    • Srinivas Abbina
    • , Lily E. Takeuchi
    •  & Jayachandran N. Kizhakkedathu
  • Article
    | Open Access

    Extracellular vesicles (EVs) in plasma can affect pathogenesis of parasites, but details remain unclear. Here, Toda et al. characterize plasma-derived EVs from Plasmodium vivax patients and show that PvEVs are preferentially taken up by human spleen fibroblasts, facilitating parasite cytoadherence.

    • Haruka Toda
    • , Miriam Diaz-Varela
    •  & Hernando A. del Portillo
  • Article
    | Open Access

    Here, Hashimoto et al. apply mass spectrometry-based thermal proximity coaggregation to characterize the temporal dynamics of virus-host protein-protein interactions during human cytomegalovirus (HCMV) infection, uncovering proviral functions including the internalization of the HCMV receptor integrin beta 1 with CD63.

    • Yutaka Hashimoto
    • , Xinlei Sheng
    •  & Ileana M. Cristea
  • 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

    Data-independent acquisition (DIA) is an emerging technology in proteomics but it typically relies on spectral libraries built by data-dependent acquisition (DDA). Here, the authors use deep learning to generate in silico spectral libraries directly from protein sequences that enable more comprehensive DIA experiments than DDA-based libraries.

    • Yi Yang
    • , Xiaohui Liu
    •  & Liang Qiao
  • Article
    | Open Access

    Analysis of the cell surface proteome (surfaceome) is essential for cell classification but is technically challenging. Here the authors miniaturize and automate the Cell Surface Capture method to increase sensitivity, reproducibility and throughput, and use it to create population-specific surfaceome maps of developing mouse B cells.

    • Marc van Oostrum
    • , Maik Müller
    •  & Bernd Wollscheid
  • Article
    | Open Access

    Comprehensive mapping of binary protein-protein interactions requires to combine several complementary assays. Here, the authors show that complete coverage could be reached with a minimal number of assays as long as they explore various experimental conditions.

    • Soon Gang Choi
    • , Julien Olivet
    •  & Yves Jacob
  • 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

    Multi-omic profiling is a powerful approach to dissecting molecular mechanisms in disease. Here the authors generate whole proteome, phosphoproteome and transcriptome profiles from two mouse models of high-grade glioma driven by different oncogenes, and validate identified master regulators with a CRISPR screen.

    • Hong Wang
    • , Alexander K. Diaz
    •  & Junmin Peng
  • Article
    | Open Access

    Squamous cell lung cancer has dismal prognosis due to the dearth of effective treatments. Here, the authors perform an integrated proteogenomic analysis of the disease, revealing three proteomics-based subtypes and suggesting potential therapeutic opportunities.

    • Paul A. Stewart
    • , Eric A. Welsh
    •  & Eric B. Haura
  • Article
    | Open Access

    Understanding of the genetic factors and molecular mechanisms underlying neurodevelopmental disorders remains incomplete. In this study, authors show that microdeletions in the gene ANKS1B lead to loss of the neuronal synapse-enriched protein AIDA-1 and to a novel neurodevelopmental syndrome

    • Abigail U. Carbonell
    • , Chang Hoon Cho
    •  & Bryen A. Jordan
  • Article
    | Open Access

    The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.

    • Zhen-Lin Chen
    • , Jia-Ming Meng
    •  & Si-Min He
  • 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 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