Nature Search

Neutrophil extracellular traps in the central nervous system hinder bacterial clearance during pneumococcal meningitis

Neutrophils play critical roles in the host response to bacteria, including the production neutrophil extracellular traps (NET). Here the authors show that NET formation in the context of pneumococcal meningitis impairs bacterial clearance and targeting NET formation in this context could be a potential therapeutic option.

Tirthankar Mohanty
Jane Fisher
Adam Linder
ResearchOpen Access10 Apr 2019
Nature Communications

Volume: 10, P: 1-13
Dissecting the properties of circulating IgG against streptococcal pathogens through a combined systems antigenomics-serology workflow

In the study, Toledo and colleagues show an experimental and computational workflow to profile human antibodies against disease-causing bacteria (Group A Streptococcus) directly in clinical samples.

Alejandro Gomez Toledo
Sounak Chowdhury
Johan Malmström
ResearchOpen Access24 Feb 2025
Nature Communications

Volume: 16, P: 1-16
Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics

Sepsis can lead to multiple organ failure that could potentially be reflected by change in plasma protein abundance. Here the authors describe a proteomics strategy that allows the determination of plasma proteins tissue origin in a quantitative manner for use as biomarkers—illustrated in a mouse model of sepsis.

Erik Malmström
Ola Kilsgård
Johan Malmström
ResearchOpen Access06 Jan 2016
Nature Communications

Volume: 7, P: 1-10
Rapid determination of quaternary protein structures in complex biological samples

Protein structure determination in complex biological samples is still challenging. Here, the authors develop a computational modeling-guided cross-linking mass spectrometry method, obtaining a high-resolution model of a 1.8 MDa protein assembly from cross-links detected in a mixture of human plasma and bacteria.

Simon Hauri
Hamed Khakzad
Lars Malmström
ResearchOpen Access14 Jan 2019
Nature Communications

Volume: 10, P: 1-10
Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis

Deep neural networks hold significant promise in capturing the complexity of biological systems. However, they suffer from a lack of interpretability. Here, authors present a generalizable method for developing, interpreting, and visualizing biologically informed neural networks for proteomics data.

Erik Hartman
Aaron M. Scott
Johan Malmström
ResearchOpen Access02 Sept 2023
Nature Communications

Volume: 14, P: 1-13
A pharmacoproteomic landscape of organotypic intervention responses in Gram-negative sepsis

Sepsis can cause organ damage through disparate immunological and metabolic processes. Here the authors demonstrate a proteomics-based scoring strategy for quantifying quantitative and organotypic changes in relationship to dosing, timing, and potential synergistic intervention combinations during sepsis.

Tirthankar Mohanty
Christofer A. Q. Karlsson
Johan Malmström
ResearchOpen Access17 Jun 2023
Nature Communications

Volume: 14, P: 1-17
Streptolysin O accelerates the conversion of plasminogen to plasmin

Group A Streptococcus exploits the human fibrinolytic system to promote infection. Here, the authors reveal that the bacterial toxin streptolysin O binds to plasminogen and accelerates its conversion to plasmin, thereby dismantling blood clots and facilitating the spread within the human host.

Di Tang
Hamed Khakzad
Johan Malmström
ResearchOpen Access25 Nov 2024
Nature Communications

Volume: 15, P: 1-15
Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Hannes L. Röst
George Rosenberger
Ruedi Aebersold
Amendments and Corrections24 Feb 2020
Nature Biotechnology

Volume: 38, P: 374
Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

Selected reaction monitoring mass spectrometry (SRM-MS) can quantify dynamic changes in protein expression with high sensitivity. Karlsson et al. define optimal detection parameters for 10,412 distinct group A Streptococcus pyogenespeptides, which facilitates proteome-wide SRM-MS studies in this bacterium.

Christofer Karlsson
Lars Malmström
Johan Malmström
ResearchOpen Access18 Dec 2012
Nature Communications

Volume: 3, P: 1-9
The hinge-engineered IgG1-IgG3 hybrid subclass IgGh₄₇ potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies

Here, the authors elongated the hinge structure of IgG1 monoclonal antibodies. The modified IgG1-IgG3 hybrid subclass showed enhanced Fc-mediated function compared to IgG1 in two distinct biological systems, Streptococcus pyogenes and SARS-CoV-2.

Arman Izadi
Yasaman Karami
Pontus Nordenfelt
ResearchOpen Access27 Apr 2024
Nature Communications

Volume: 15, P: 1-22
Peptide clustering enhances large-scale analyses and reveals proteolytic signatures in mass spectrometry data

Studies of protein degradation through peptidomic analyses are complicated by the vast potential peptidomic landscapes. Here, the authors present a method that cluster peptides, simplifying down-stream analyses and apply it identify pathogen-specific peptide patterns in infected wounds.

Erik Hartman
Fredrik Forsberg
Artur Schmidtchen
ResearchOpen Access20 Aug 2024
Nature Communications

Volume: 15, P: 1-15
Mass spectrometry peptidomics data from infected and uninfected porcine wounds

Fredrik Forsberg
Sven Kjellström
Erik Hartman
ResearchOpen Access02 Sept 2025
Scientific Data

Volume: 12, P: 1-6
Pathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections

Group A streptococcus causes a wide range of human diseases and significantly contributes to morbidity and mortality worldwide. Here, Toledo et al show how streptococcus alters the structure and function of endogenous and therapeutic antibodies during infection and how this is affected by the host microenvironment.

Alejandro Gomez Toledo
Eleni Bratanis
Johan Malmström
ResearchOpen Access23 Oct 2023
Nature Communications

Volume: 14, P: 1-16
A quantitative Streptococcus pyogenes–human protein–protein interaction map reveals localization of opsonizing antibodies

Characterizing host-pathogen protein interactions can help elucidate the molecular basis of bacterial infections. Here, the authors use an integrative proteomics approach to generate a quantitative map of protein interactions between Streptococcus pyogenes and human saliva and plasma.

Lotta Happonen
Simon Hauri
Johan Malmström
ResearchOpen Access21 Jun 2019
Nature Communications

Volume: 10, P: 1-15
Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cells

Hefzi et al. engineer cells to nearly eliminate lactate production and increase mitochondrial use of pyruvate by deleting both lactate dehydrogenases and pyruvate dehydrogenase kinases with the goal of circumventing pH and osmolarity issues that arise in bioreactor-based production of biopharmaceuticals.

Hooman Hefzi
Iván Martínez-Monge
Nathan E. Lewis
Research14 Jan 2025
Nature Metabolism

Volume: 7, P: 212-227
Visual proteomics of the human pathogen Leptospira interrogans

Protein complexes can be detected, counted and localized within the bacterium Leptospira interrogans by combining quantitative mass spectrometry–based proteomics analysis with cryo-electron tomography, with the aid of an improved template-matching method.

Martin Beck
Johan A Malmström
Ruedi Aebersold
Research18 Oct 2009
Nature Methods

Volume: 6, P: 817-823
Immunostimulatory AdCD40L gene therapy combined with low-dose cyclophosphamide in metastatic melanoma patients

Angelica Loskog
Aglaia Maleka
Gustav Ullenhag
ResearchOpen Access31 Mar 2016
British Journal of Cancer

Volume: 114, P: 872-880
Quantifying extracellular matrix turnover in human lung scaffold cultures

Oskar Rosmark
Emma Åhrman
Johan Malmström
ResearchOpen Access03 Apr 2018
Scientific Reports

Volume: 8, P: 1-13
A high-quality catalog of the Drosophila melanogaster proteome

Erich Brunner
Christian H Ahrens
Ruedi Aebersold
Research01 May 2007
Nature Biotechnology

Volume: 25, P: 576-583
Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics

A generalized precursor scoring method increases protein identification rates and overall quantitative accuracy in data independent acquisition mass spectrometry proteomics and can generalize to new data.

Aaron M. Scott
Christofer Karlsson
Lars Malmström
ResearchOpen Access10 Jun 2023
Communications Biology

Volume: 6, P: 1-13
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

Absolute protein concentration measurements of a considerable fraction of the proteome have, until now, only been derived from genetically altered Saccharomyces cerevisiae cells, using a technique that is not directly portable from yeast to other species. A mass-spectrometry-based method is now used to determine the absolute protein abundance for a significant fraction of the proteome of the human pathogen Leptospira interrogans.

Johan Malmström
Martin Beck
Ruedi Aebersold
Research15 Jul 2009
Nature

Volume: 460, P: 762-765
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Hannes L Röst
George Rosenberger
Ruedi Aebersold
Correspondence10 Mar 2014
Nature Biotechnology

Volume: 32, P: 219-223
Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry

Sara Rolandsson Enes
Emma Åhrman
Gunilla Westergren-Thorsson
ResearchOpen Access24 Aug 2017
Scientific Reports

Volume: 7, P: 1-12
Proteogenomics decodes the evolution of human ipsilateral breast cancer

A proteogenomic analysis of matching primary breast cancer and ipsilateral breast tumor recurrence (IBTR) samples provides insight into the development of IBTR and may be useful in identifying biomarkers for IBTR formation.

Tommaso De Marchi
Paul Theodor Pyl
Emma Niméus
ResearchOpen Access02 Feb 2023
Communications Biology

Volume: 6, P: 1-14
Specific interaction between genotype, smoking and autoimmunity to citrullinated α-enolase in the etiology of rheumatoid arthritis

Karin Lundberg and colleagues explore gene-gene and gene-environment interactions in susceptibility to rheumatoid arthritis, reporting an association of HLA-DRB1, PTPN22 and smoking stratified by the autoantigen CEP-1.

Hiba Mahdi
Benjamin A Fisher
Karin Lundberg
Research08 Nov 2009
Nature Genetics

Volume: 41, P: 1319-1324
Proteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling

Tommaso De Marchi
Chun-Fui Lai
Emma Niméus
ResearchOpen Access22 Mar 2024
Scientific Reports

Volume: 14, P: 1-16
Alveolar epithelial cells are competent producers of interstitial extracellular matrix with disease relevant plasticity in a human in vitro 3D model

Oskar Rosmark
Måns Kadefors
Gunilla Westergren-Thorsson
ResearchOpen Access31 May 2023
Scientific Reports

Volume: 13, P: 1-17
Time dependent effects of adjuvant tamoxifen therapy on cerebrovascular disease: results from a randomised trial

J Rosell
B Nordenskjöld
J Carstensen
ResearchOpen Access22 Feb 2011
British Journal of Cancer

Volume: 104, P: 899-902

Search

Neutrophil extracellular traps in the central nervous system hinder bacterial clearance during pneumococcal meningitis

Dissecting the properties of circulating IgG against streptococcal pathogens through a combined systems antigenomics-serology workflow

Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics

Rapid determination of quaternary protein structures in complex biological samples

Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis

A pharmacoproteomic landscape of organotypic intervention responses in Gram-negative sepsis

Streptolysin O accelerates the conversion of plasminogen to plasmin

Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

The hinge-engineered IgG1-IgG3 hybrid subclass IgGh₄₇ potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies

Peptide clustering enhances large-scale analyses and reveals proteolytic signatures in mass spectrometry data

Mass spectrometry peptidomics data from infected and uninfected porcine wounds

Pathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections

A quantitative Streptococcus pyogenes–human protein–protein interaction map reveals localization of opsonizing antibodies

Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cells

Visual proteomics of the human pathogen Leptospira interrogans

Immunostimulatory AdCD40L gene therapy combined with low-dose cyclophosphamide in metastatic melanoma patients

Quantifying extracellular matrix turnover in human lung scaffold cultures

A high-quality catalog of the Drosophila melanogaster proteome

Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry

Proteogenomics decodes the evolution of human ipsilateral breast cancer

Specific interaction between genotype, smoking and autoimmunity to citrullinated α-enolase in the etiology of rheumatoid arthritis

Proteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling

Alveolar epithelial cells are competent producers of interstitial extracellular matrix with disease relevant plasticity in a human in vitro 3D model

Time dependent effects of adjuvant tamoxifen therapy on cerebrovascular disease: results from a randomised trial

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