Mass spectrometry

  • Article
    | Open Access

    Protein turnover underpins biology but is challenging to measure in vivo across the entire proteome. Here, the authors provide a comprehensive resource of protein turnover in mouse tissues and develop a visualization platform to analyze these data.

    • Zach Rolfs
    • , Brian L. Frey
    •  & Nathan V. Welham
  • Article
    | Open Access

    The testing of engineered enzymes represents a bottleneck. Here the authors report a screening method combining microfluidics and mass spectrometry, to map the catalysis of a mutated enzyme, characterise the range of products generated and recover the sequences of variants with desired activities.

    • Linfeng Xu
    • , Kai-Chun Chang
    •  & Adam R. Abate
  • 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

    Several proteomic approaches allow the analysis of covalent protein SUMOylation, but it remains challenging to systematically study the consequences of a substrate being modified. Here, the authors combine proximity biotinylation and protein-fragment complementation to identify SUMO-dependent protein interactors.

    • Orhi Barroso-Gomila
    • , Fredrik Trulsson
    •  & James D. Sutherland
  • Article
    | Open Access

    The human 2-oxoglutarate (2OG) oxygenases FIH and AspH are relevant drug targets. Here, the authors show that synthetic and naturally occurring 2OG derivatives can selectively modulate FIH and AspH activities, suggesting that these compounds may serve as a basis to develop 2OG oxygenase-targeting probes and drugs.

    • Yu Nakashima
    • , Lennart Brewitz
    •  & Christopher J. Schofield
  • Article
    | Open Access

    Oxidized phosphatidylcholines (oxPCs) are a structurally diverse class of lipids associated with various diseases. Here, the authors use mass spectrometry to construct a spectral library of 465 oxPCs and subsequently profile oxPCs formed during acetaminophen-induced acute liver failure in mice.

    • Yuta Matsuoka
    • , Masatomo Takahashi
    •  & Ken-ichi Yamada
  • Article
    | Open Access

    The role of the post-translational modifications in tissue regeneration is still not clearly understood. Here, the authors show that many nuclear proteins change S-nitrosylation state in the regenerating zebrafish tailfin, highlighting the importance of Kdm1a S-nitrosylation in the repair process.

    • Gianfranco Matrone
    • , Sung Yun Jung
    •  & John P. Cooke
  • Article
    | Open Access

    Single-cell proteomics is an emerging technology but protein coverage, throughput and quantitation accuracy are often still insufficient. Here, the authors develop a nested nanowell chip that improves protein recovery, throughput and robustness of isobaric labeling-based quantitative single-cell proteomics.

    • Jongmin Woo
    • , Sarah M. Williams
    •  & Ying Zhu
  • Article
    | Open Access

    To prevent unregulated complement activation, extracellular chaperones capture soluble precursors to the membrane attack complex (sMAC). Here, structural analysis of sMAC reveals how clusterin recognizes heterogeneous sMAC complexes and inhibits polymerization of complement protein C9.

    • Anaïs Menny
    • , Marie V. Lukassen
    •  & Doryen Bubeck
  • Article
    | Open Access

    ADP-ribosylation is regulated by HPF1 and ARH3, but the cellular target spectrum of these enzymes is not fully understood. Here, the authors use quantitative proteomics to define the HPF1- and ARH3-dependent ADP-ribosylome, providing evidence that mono-ADP-ribosylation of serine predominates in cells.

    • Ivo A. Hendriks
    • , Sara C. Buch-Larsen
    •  & Michael L. Nielsen
  • Article
    | Open Access

    Humans are exposed to millions of chemicals but mass spectrometry (MS)-based targeted biomonitoring assays are usually limited to a few hundred known hazards. Here, the authors develop a workflow for MS-based untargeted exposome profiling of known and unidentified environmental chemicals.

    • Xin Hu
    • , Douglas I. Walker
    •  & Dean P. Jones
  • Article
    | Open Access

    The Spike protein of SARS-CoV-2 has a C-terminal cytoplasmic tail. Here the authors show that this tail binds trafficking machinery via sequences that appear optimised to ensure that Spike accumulates at the site of viral budding in the Golgi but that some can also traffic to the cell surface to induce syncytia formation.

    • Jérôme Cattin-Ortolá
    • , Lawrence G. Welch
    •  & Sean Munro
  • 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

    Mass spectrometry-based metabolomics is a powerful method for profiling large clinical cohorts but batch variations can obscure biologically meaningful differences. Here, the authors develop a computational workflow that removes unwanted data variation while preserving biologically relevant information.

    • Taiyun Kim
    • , Owen Tang
    •  & Jean Yee Hwa Yang
  • Article
    | Open Access

    Analogues of α-ketoglutarate are used in many cellular studies but assumptions are made about cellular uptake. Here, the authors show that esterified analogues rapidly hydrolyse in aqueous medium resulting in an analogue which can be quickly taken up by many cell lines, contrary to prevailing assumptions.

    • Seth J. Parker
    • , Joel Encarnación-Rosado
    •  & Alec C. Kimmelman
  • Article
    | Open Access

    Label-free quantitative proteomics by data dependent acquisition offers high protein identification rates but is often limited by missing values. Here, the authors develop a quantification workflow that substantially reduces missing values while maintaining high identification rates and quantification accuracy.

    • Mathias Kalxdorf
    • , Torsten Müller
    •  & Jeroen Krijgsveld
  • Article
    | Open Access

    Lipins need to bind cell membranes before they can function as phosphatidic acid phosphatases. Here, the authors elucidate the structural basis of lipin membrane-association and identify a lipin domain with a novel protein fold that is critical for membrane binding and full functionality of lipins.

    • Weijing Gu
    • , Shujuan Gao
    •  & Michael V. Airola
  • Article
    | Open Access

    Finding durable, high-density media for data storage is necessary to support the ever-expanding generation of digital data. Here, the authors use peptide sequences to store digital data and retrieve them using tandem mass spectrometry, proving that peptides can be used as a storage medium.

    • Cheuk Chi A. Ng
    • , Wai Man Tam
    •  & Zhong-Ping Yao
  • Article
    | Open Access

    Many proteins exist in various proteoforms but detecting these variants by bottom-up proteomics remains difficult. Here, the authors present a computational approach based on peptide correlation analysis to identify and characterize proteoforms from bottom-up proteomics data.

    • Isabell Bludau
    • , Max Frank
    •  & Ruedi Aebersold
  • Article
    | Open Access

    Fat synthesis is necessary for normal physiology, but its dysregulation contributes to the pathology of many diseases. Here, the authors report a high-resolution mass spectrometry approach that quantifies fat synthesis flux in humans and mice following a brief and low dose of deuterated water.

    • Xiaorong Fu
    • , Stanisław Deja
    •  & Shawn C. Burgess
  • Article
    | Open Access

    A large number of mass spectra from different samples have been collected, and to identify small molecules from these spectra, database searches are needed, which is challenging. Here, the authors report molDiscovery, a mass spectral database search method that uses an algorithm to generate mass spectrometry fragmentations and learns a probabilistic model to match small molecules with their mass spectra.

    • Liu Cao
    • , Mustafa Guler
    •  & Hosein Mohimani
  • Article
    | Open Access

    Formalin-fixed, paraffin-embedded (FFPE) specimens are an attractive resource for retrospective clinical proteomics studies. Here, the authors benchmark and optimize proteomics workflows for FFPE sample analysis and provide guidelines on which methods to use for different samples and applications.

    • Corinna Friedrich
    • , Simon Schallenberg
    •  & Philipp Mertins
  • Article
    | Open Access

    Several scenarios exist to explain the origins of the organic matter found in carbonaceous chondrites. Here, the authors show laboratory experiments confirming that a significant portion of the soluble organic matter can originate from organic ices inherited from the dense molecular cloud.

    • G. Danger
    • , V. Vinogradoff
    •  & P. Schmitt-Kopplin
  • Article
    | Open Access

    Here the authors use RT-qPCR and mass spectrometry to analyze longitudinal blood samples from intensive care unit (ICU) COVID-19 patients and controls. They find that viral RNA and pentraxin-3 predict 28-day ICU mortality and that galectin-3-binding protein is an interaction partner of SARS-CoV-2 spike glycoprotein with antiviral properties.

    • Clemens Gutmann
    • , Kaloyan Takov
    •  & Manuel Mayr
  • Article
    | Open Access

    The identification of HLA peptides by mass spectrometry is non-trivial. Here, the authors extended and used the wealth of data from the ProteomeTools project to improve the prediction of non-tryptic peptides using deep learning, and show their approach enables a variety of immunological discoveries.

    • Mathias Wilhelm
    • , Daniel P. Zolg
    •  & Bernhard Kuster
  • Article
    | Open Access

    Single-cell proteomics can provide insights into the molecular basis for cellular heterogeneity. Here, the authors develop a multiplexed single-cell proteomics and computational workflow, and show that their strategy captures the cellular hierarchies in an Acute Myeloid Leukemia culture model.

    • Erwin M. Schoof
    • , Benjamin Furtwängler
    •  & Bo T. Porse
  • Article
    | Open Access

    MALDI-mass spectrometry imaging (MSI) can reveal the distribution of proteins in tissues but tools for protein identification and annotation are sparse. Here, the authors develop an open-source bioinformatic workflow for false discovery rate-controlled protein annotation and spatial mapping from MALDI-MSI data.

    • G. Guo
    • , M. Papanicolaou
    •  & A. C. Grey
  • 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
  • Article
    | Open Access

    Mayaro virus (MAYV) is an emerging arbovirus in Central and South America that is transmitted by mosquitoes and causes arthritogenic disease. Here, the authors present the 4.4 Å resolution cryo-EM structure of MAYV and describe specific features of the virus, which could be exploited for the design of MAYV-specific diagnostics and therapeutics.

    • Helder V. Ribeiro-Filho
    • , Lais D. Coimbra
    •  & Rafael Elias Marques
  • Article
    | Open Access

    The search for life in the universe is difficult due to issues with defining signatures of living systems. Here, the authors present an approach based on the molecular assembly number and tandem mass spectrometry that allows identification of molecules produced by biological systems, and use it to identify biosignatures from a range of samples, including ones from outer space.

    • Stuart M. Marshall
    • , Cole Mathis
    •  & Leroy Cronin
  • Article
    | Open Access

    Analyzing the lipidomes of single cells remains a challenge. Here, the authors present a strategy to identify class, fatty acyl-chain, C=C locations and sn-positions of lipids in single cells, and use their method to identify individual gefitinib-resistant cells in a wild-type lung cancer cell population.

    • Zishuai Li
    • , Simin Cheng
    •  & Zheng Ouyang
  • Article
    | Open Access

    Phosphoproteomics can provide systematic insights into disease-associated cell signaling changes. Here, the authors present a sensitive workflow integrating library-based and direct data-independent acquisition approaches, and a hybrid spectral library resource for in-depth phosphoproteomic profiling.

    • Reta Birhanu Kitata
    • , Wai-Kok Choong
    •  & Yu-Ju Chen
  • Article
    | Open Access

    NOTCH1 is a driver of T-cell acute lymphoblastic leukemia that can be inhibited by γ-secretase inhibitors (GSIs), but their clinical efficacy is limited. Here, the authors compare the phosphoproteomes of GSI resistant and sensitive models, and identify potential kinase targets to overcome GSI resistance.

    • Giulia Franciosa
    • , Jos G. A. Smits
    •  & Jesper V. Olsen
  • Article
    | Open Access

    The tumor suppressor FBW7 is a substrate adaptor for the E3 ubiquitin ligase complex SKP1-CUL1-F-box (SCF) and itself a target for ubiquitylation. Here, the authors show that TRIP12 mediates branched K11-linked ubiquitylation of FBW7, to regulate its stability and thus abundance of a subset of SCFFBW7 substrates.

    • Omar M. Khan
    • , Jorge Almagro
    •  & Axel Behrens
  • Article
    | Open Access

    Aminoglycoside antibiotics target the ribosome and induce misreading, yet which translation errors induce bacterial cell death is unclear. Here authors use quantitative mass spectrometry and show that bactericidal aminoglycosides induce clusters of errors in full-length proteins in vivo with as many as four amino acid substitutions in a row.

    • Ingo Wohlgemuth
    • , Raffaella Garofalo
    •  & Marina V. Rodnina
  • Article
    | Open Access

    Adeno-associated viruses (AAVs) have emerged as promising gene therapy vectors.The AAV capsid consists of 60 subunits made up from three distinct viral proteins (VPs). Here authors record high-resolution native mass spectra of intact AAV capsids to assess the VP stoichiometries in a panel of serotypes and reveals an extremely heterogeneous population of capsids of variable composition.

    • Tobias P. Wörner
    • , Antonette Bennett
    •  & Albert J. R. Heck
  • Article
    | Open Access

    The global identification of enzyme substrates is still challenging. Here, the authors develop a method based on proteome-wide thermal shift assays to discover enzyme substrates directly from cell lysates, identifying known and novel oxidoreductase, kinase and poly-(ADP-ribose) polymerase substrates.

    • Amir Ata Saei
    • , Christian M. Beusch
    •  & Roman A. Zubarev
  • Article
    | Open Access

    Proteomics has been advanced by algorithms that can predict different peptide features, but predicting peptide collisional cross sections (CCS) has remained challenging. Here, the authors measure over one million CCS values of tryptic peptides and develop a deep learning model for peptide CCS prediction.

    • Florian Meier
    • , Niklas D. Köhler
    •  & Matthias Mann
  • Article
    | Open Access

    Spy is an ATP independent chaperone that can act as both a holdase and a foldase towards topologically simple substrates. Assessing the interaction of Spy and apoflavodoxin, a complex client, the authors show that Spy’s activity is substrate specific. Spy binds partially unfolded states of apoflavodoxin tightly, which limits the possibility of folding and converts Spy to a pure holdase.

    • Rishav Mitra
    • , Varun V. Gadkari
    •  & James C. A. Bardwell
  • Article
    | Open Access

    Small molecules stabilising a distorted TNF trimer can inhibit TNF signaling, but the underlying mechanism is unclear. Here, the authors characterize the inhibitor-bound TNF-receptor complex structurally and biochemically, showing that the inhibitors alter TNF-receptor binding stoichiometry and cluster formation.

    • David McMillan
    • , Carlos Martinez-Fleites
    •  & James O’Connell