Complexome Profiling: Assembly and Remodeling of Protein Complexes

Selective cross‐linking of coinciding protein assemblies by in‐gel cross‐linking mass spectrometry

(2021) Johannes F Hevler et al.   EMBO JOURNAL

Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)

(2021) Matthias Riediger et al.   PLANT CELL

SILAC-based complexome profiling dissects the structural organization of the human respiratory supercomplexes in SCAFIKO cells

(2021) Erika Fernández-Vizarra et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Loss of COX4I1 Leads to Combined Respiratory Chain Deficiency and Impaired Mitochondrial Protein Synthesis

(2021) Kristýna Čunátová et al.   Cells

Multiplexed complexome profiling using tandem mass tags

(2021) Sergio Guerrero-Castillo et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing

(2021) Akio Masuda et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Impaired complex I repair causes recessive Leber’s hereditary optic neuropathy

(2021) Sarah L. Stenton et al.   JOURNAL OF CLINICAL INVESTIGATION

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

(2021) Milan Gerovac et al.   Frontiers in Molecular Biosciences

Quantitative density gradient analysis by mass spectrometry (qDGMS) and complexome profiling analysis (ComPrAn) R package for the study of macromolecular complexes

(2021) Petra Páleníková et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

CEDAR, an online resource for the reporting and exploration of complexome profiling data

(2021) Joeri van Strien et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Complexome profiling reveals novel insights into the composition and assembly of the mitochondrial ATP synthase of Arabidopsis thaliana

(2021) Helene Röhricht et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Protein interaction patterns in Arabidopsis thaliana leaf mitochondria change in dependence to light

(2021) Nils Rugen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

ComplexFinder: A software package for the analysis of native protein complex fractionation experiments

(2021) Hendrik Nolte et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Duplexing complexome profiling with SILAC to study human respiratory chain assembly defects

(2021) Petra Páleníková et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Recent progress in mass spectrometry-based strategies for elucidating protein–protein interactions

(2021) Teck Yew Low et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Probing membrane protein–lipid interactions

(2021) Mark T. Agasid et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Pulse-chase SILAC–based analyses reveal selective oversynthesis and rapid turnover of mitochondrial protein components of respiratory complexes

(2020) Daniel F. Bogenhagen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

(2020) Jens Hör et al.   EMBO JOURNAL

Proteomic and interactomic insights into the molecular basis of cell functional diversity

(2020) Isabell Bludau et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A salvage pathway maintains highly functional respiratory complex I

(2020) Karolina Szczepanowska et al.   Nature Communications

TMEM70 functions in the assembly of complexes I and V

(2020) Laura Sánchez-Caballero et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Multiple pathways coordinate assembly of human mitochondrial complex IV and stabilization of respiratory supercomplexes

(2020) Teresa Lobo‐Jarne et al.   EMBO JOURNAL

Bi‐allelic pathogenic variants in NDUFC2 cause early‐onset Leigh syndrome and stalled biogenesis of complex I

(2020) Ahmad Alahmad et al.   EMBO Molecular Medicine

Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli

(2020) Jens Hör et al.   NUCLEIC ACIDS RESEARCH

From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks

(2020) Ilaria Iacobucci et al.   Journal of Proteomics

COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome

(2019) Joeri Van Strien et al.   BIOINFORMATICS

Complex‐centric proteome profiling by SEC‐SWATH‐MS

(2019) Moritz Heusel et al.   Molecular Systems Biology

Complexome profiling reveals association of PPR proteins with ribosomes in the mitochondria of plants

(2019) Nils Rugen et al.   MOLECULAR & CELLULAR PROTEOMICS

Pick a Tag and Explore the Functions of Your Pet Protein

(2019) Giel Vandemoortele et al.   TRENDS IN BIOTECHNOLOGY

Complexome analysis of the nitrite-dependent methanotroph Methylomirabilis lanthanidiphila

(2019) Wouter Versantvoort et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The role of protein complexes in human genetic disease

(2019) L. Therese Bergendahl et al.   PROTEIN SCIENCE

METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis

(2019) Lindsey Van Haute et al.   NUCLEIC ACIDS RESEARCH

Protein Complex Identification and quantitative complexome by CN-PAGE

(2019) Michal Gorka et al.   Scientific Reports

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

(2019) Catrin Swantje Müller et al.   Jove-Journal of Visualized Experiments

Pathogenic Bi-allelic Mutations in NDUFAF8 Cause Leigh Syndrome with an Isolated Complex I Deficiency

(2019) Charlotte L. Alston et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cross-linking/mass spectrometry to get a closer view on protein interaction networks

(2019) Claudio Iacobucci et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bi-allelic Mutations in the Mitochondrial Ribosomal Protein MRPS2 Cause Sensorineural Hearing Loss, Hypoglycemia, and Multiple OXPHOS Complex Deficiencies

(2018) Thatjana Gardeitchik et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Degradation of the mitochondrial complex I assembly factor TMEM126B under chronic hypoxia

(2018) Dominik C. Fuhrmann et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Absence of Complex I Implicates Rearrangement of the Respiratory Chain in European Mistletoe

(2018) Jennifer Senkler et al.   CURRENT BIOLOGY

Assembly of mammalian oxidative phosphorylation complexes I–V and supercomplexes

(2018) Alba Signes et al.   Essays in Biochemistry

Deactivation of mitochondrial complex I after hypoxia–ischemia in the immature brain

(2018) Anna Stepanova et al.   JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM

Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states

(2018) Ahmed-Noor A. Agip et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry Profiling

(2018) Katelyn E. Connelly et al.   PROTEOMICS

Building a complex complex: Assembly of mitochondrial respiratory chain complex I

(2018) Luke E. Formosa et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states

(2018) Ahmed-Noor A. Agip et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Biallelic Mutations in NDUFA6 Establish Its Role in Early-Onset Isolated Mitochondrial Complex I Deficiency

(2018) Charlotte L. Alston et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Barth syndrome cells display widespread remodeling of mitochondrial complexes without affecting metabolic flux distribution

(2018) Iliana A. Chatzispyrou et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

The ribosome receptors Mrx15 and Mba1 jointly organize cotranslational insertion and protein biogenesis in mitochondria

(2018) Braulio Vargas Möller-Hergt et al.   MOLECULAR BIOLOGY OF THE CELL

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The assembly pathway of complex I in Arabidopsis thaliana

(2018) Joanna Ligas et al.   PLANT JOURNAL

The mitochondrial complexome of Arabidopsis thaliana

(2017) Jennifer Senkler et al.   PLANT JOURNAL

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MR-1S Interacts with PET100 and PET117 in Module-Based Assembly of Human Cytochrome c Oxidase

(2017) Sara Vidoni et al.   Cell Reports

Cytochrome c Oxidase Biogenesis and Metallochaperone Interactions: Steps in the Assembly Pathway of a Bacterial Complex

(2017) Sonja Schimo et al.   PLoS One

Mutations in Complex I Assembly Factor TMEM126B Result in Muscle Weakness and Isolated Complex I Deficiency

(2016) Laura Sánchez-Caballero et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Biallelic Mutations in TMEM126B Cause Severe Complex I Deficiency with a Variable Clinical Phenotype

(2016) Charlotte L. Alston et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Global profiling of protein complexes: current approaches and their perspective in biomedical research

(2016) Elena L. Rudashevskaya et al.   Expert Review of Proteomics

The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein

(2016) Kim-Kristin Prior et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteomic profiling of the mitochondrial ribosome identifies Atp25 as a composite mitochondrial precursor protein

(2016) Michael W. Woellhaf et al.   MOLECULAR BIOLOGY OF THE CELL

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein

(2016) Alexandre Smirnov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of membrane-protein complexes of the marine sulfate reducerDesulfobacula toluolicaTol2 by 1D blue native-PAGE complexome profiling and 2D blue native-/SDS-PAGE

(2016) Lars Wöhlbrand et al.   PROTEOMICS

Cryo-slicing Blue Native-Mass Spectrometry (csBN-MS), a Novel Technology for High Resolution Complexome Profiling

(2015) Catrin S. Müller et al.   MOLECULAR & CELLULAR PROTEOMICS

Characterization of Small Protein Aggregates and Oligomers Using Size Exclusion Chromatography with Online Detection by Native Electrospray Ionization Mass Spectrometry

(2014) Khaja Muneeruddin et al.   ANALYTICAL CHEMISTRY

NOVA: a software to analyze complexome profiling data

(2014) H. Giese et al.   BIOINFORMATICS

Complexome Profiling Identifies TMEM126B as a Component of the Mitochondrial Complex I Assembly Complex

(2012) Heinrich Heide et al.   Cell Metabolism

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

(2012) L. Arike et al.   Journal of Proteomics

Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography

(2012) Alexander Leitner et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Large pore gels to separate mega protein complexes larger than 10 MDa by blue native electrophoresis: Isolation of putative respiratory strings or patches

(2010) Valentina Strecker et al.   PROTEOMICS

LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes

(2009) Hans J. C. T. Wessels et al.   PROTEOMICS

SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function

(2008) Marcus Krüger et al.   CELL

High confidence determination of specific protein–protein interactions using quantitative mass spectrometry

(2008) Michiel Vermeulen et al.   CURRENT OPINION IN BIOTECHNOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Global analysis of cellular protein translation by pulsed SILAC

(2008) Björn Schwanhäusser et al.   PROTEOMICS