Mass spectrometry–based proteomics in cell biology

The global analysis of protein composition, modifications, and dynamics are important goals in cell biology. Mass spectrometry (MS)–based proteomics has matured into an attractive technology for this purpose. Particularly, high resolution MS methods have been extremely successful for quantitative analysis of cellular and organellar proteomes. Rapid advances in all areas of the proteomic workflow, including sample preparation, MS, and computational analysis, should make the technology more easily available to a broad community and turn it into a staple methodology for cell biologists.

• Publication year

  2010

• Venue

  Journal of Cell Biology

• Publication date

  2010-08-23

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1083/jcb.201004052PMID 20733050PMCID 2928005
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux

  2010cited by this paper
• Quantitative proteomics reveals subset-specific viral recognition in dendritic cells.

  2010cited by this paper
• A guided tour of the Trans‐Proteomic Pipeline

  2010cited by this paper
• Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

  2010cited by this paper
• Super-SILAC mix for quantitative proteomics of human tumor tissue

  2010cited by this paper
• Regulation of Cellular Metabolism by Protein Lysine Acetylation

  2010cited by this paper
• Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics.

  2009cited by this paper
• Proteome differences between brown and white fat mitochondria reveal specialized metabolic functions.

  2009cited by this paper
• Quantitative proteomics in biological research

  2009cited by this paper
• A sensitive mass spectrometric method for hypothesis-driven detection of peptide post-translational modifications: multiple reaction monitoring-initiated detection and sequencing (MIDAS)

  2009cited by this paper
• Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics.

  2009cited by this paper
• Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

  2009cited by this paper
• A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

  2009cited by this paper
• Mapping organelle proteins and protein complexes in Drosophila melanogaster.

  2009cited by this paper
• A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage

  2009cited by this paper
• Universal sample preparation method for proteome analysis

  2009cited by this paper
• Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

  2009cited by this paper
• Identification of SUMO target proteins by quantitative proteomics.

  2009cited by this paper
• Universal sample preparation method for proteome analysis

  2009cited by this paper
• Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells

  2009cited by this paper
• Quantitative interaction proteomics using mass spectrometry

  2009influential reference
• Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

  2009cited by this paper
• Bioinformatics analysis of mass spectrometry‐based proteomics data sets

  2009cited by this paper
• A Complex-based Reconstruction of the Saccharomyces cerevisiae Interactome *S⃞

  2009cited by this paper
• Quantitative phosphoproteomics by mass spectrometry: Past, present, and future

  2008cited by this paper
• A quantitative analysis software tool for mass spectrometry–based proteomics

  2008cited by this paper
• A Versatile Nanotrap for Biochemical and Functional Studies with Fluorescent Fusion Proteins*S

  2008cited by this paper
• Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

  2008cited by this paper
• Quantitative phosphoproteomic analysis of signaling network dynamics.

  2008cited by this paper
• MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

  2008cited by this paper
• Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

  2008cited by this paper
• SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function.

  2008cited by this paper
• Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae*S

  2007cited by this paper
• Top‐down MS, a powerful complement to the high capabilities of proteolysis proteomics

  2007cited by this paper
• Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation

  2007cited by this paper
• The biological impact of mass-spectrometry-based proteomics

  2007cited by this paper
• Mapping protein post-translational modifications with mass spectrometry

  2007cited by this paper
• Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks

  2007cited by this paper
• Analysis of protein complexes using mass spectrometry

  2007cited by this paper
• Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors

  2007cited by this paper
• A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS

  2006cited by this paper
• Mass Spectrometry and Protein Analysis

  2006cited by this paper
• Proteome survey reveals modularity of the yeast cell machinery

  2006cited by this paper
• Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

  2006cited by this paper
• Rapid protein identification using direct infusion nanoelectrospray ionization mass spectrometry

  2006cited by this paper
• Orbitrap Mass Analyzer – Overview and Applications in Proteomics

  2006cited by this paper
• Substrate and functional diversity of lysine acetylation revealed by a proteomics survey.

  2006cited by this paper
• Interpreting the protein language using proteomics

  2006cited by this paper
• Orbitrap Mass Analyzer - Overview and Applications

  2006cited by this paper
• Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

  2006cited by this paper
• Mass spectrometry–based proteomics turns quantitative

  2005cited by this paper
• Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics*S

  2005cited by this paper
• A Combined Approach for the Localization and Tandem Affinity Purification of Protein Complexes from Metazoans

  2005cited by this paper
• Hybrid quadrupole/time-of-flight mass spectrometers for analysis of biomolecules.

  2005cited by this paper
• Nucleolar proteome dynamics

  2005cited by this paper
• Strategies for measuring dynamics: the temporal component of proteomics.

  2005cited by this paper
• Proteomics of organelles and large cellular structures

  2005cited by this paper
• Fluorescent Proteins as Proteomic Probes*S

  2005cited by this paper
• Fragmentation pathways of protonated peptides.

  2005cited by this paper
• Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein*S

  2005cited by this paper
• Localization of Organelle Proteins by Isotope Tagging (LOPIT)*S

  2004cited by this paper
• Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book

  2004cited by this paper
• TANDEM: matching proteins with tandem mass spectra.

  2004cited by this paper
• Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S

  2004cited by this paper
• A model for random sampling and estimation of relative protein abundance in shotgun proteomics.

  2004cited by this paper
• Global analysis of protein localization in budding yeast

  2003cited by this paper
• Interfacing the orbitrap mass analyzer to an electrospray ion source.

  2003cited by this paper
• The study of macromolecular complexes by quantitative proteomics

  2003cited by this paper
• Nuclear Membrane Proteins with Potential Disease Links Found by Subtractive Proteomics

  2003cited by this paper
• A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

  2003cited by this paper
• Stable-isotope dimethyl labeling for quantitative proteomics.

  2003cited by this paper
• Proteomic characterization of the human centrosome by protein correlation profiling

  2003cited by this paper
• Global analysis of protein expression in yeast

  2003cited by this paper
• Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics*

  2002cited by this paper
• Large-scale analysis of the yeast proteome by multidimensional protein identification technology

  2001cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• The Yeast Nuclear Pore Complex

  2000cited by this paper
• The Yeast Nuclear Pore Complex: Composition, Architecture, and Transport Mechanism

  2000cited by this paper
• Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis

  2000cited by this paper
• A generic protein purification method for protein complex characterization and proteome exploration

  1999cited by this paper
• Direct analysis of protein complexes using mass spectrometry

  1999cited by this paper
• Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex.

  1999cited by this paper
• Binding of RHOA G17V to p300 enhances its HAT activity: a new mechanism of epigenetic deregulation in TFH lymphoma

  1999cited by this paper
• Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry.

  1997cited by this paper
• Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.

  1996cited by this paper
• An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

  1994cited by this paper
• Electrospray ionization for mass spectrometry of large biomolecules.

  1989cited by this paper
• Biological Research

  year unknowncited by this paper

• Characterization of substrate distribution and functional implication of lysine acylations in Staphylococcus aureus.

  2025cites this paper
• Comprehensive Prediction of Protein Localization and Signal Peptides Using MULocDeep.

  2025cites this paper
• Visualisations to guide enriched proteome analyses

  2025cites this paper
• Proteomic and ubiquitinome analysis reveal that microgravity affects glucose metabolism of mouse hearts by remodeling non-degradative ubiquitination

  2024cites this paper
• Proteomic analysis of granulomas from cattle and pigs naturally infected with Mycobacterium tuberculosis complex by MALDI imaging

  2024cites this paper
• Mapping the human brain proteome: opportunities, challenges, and clinical potential

  2024cites this paper
• Substrate and functional characterization of the lysine acetyltransferase MsKat and deacetylase MsCobB in Mycobacterium smegmatis.

  2024cites this paper
• A bovine model of hypoxia-induced pulmonary hypertension reveals a gradient of immune and matrisome response with a complement signature found in circulation.

  2024cites this paper
• Data mining antibody sequences for database searching in bottom-up proteomics

  2024cites this paper
• Single-cell spatial proteomics.

  2024cites this paper
• Resolving the Amino Acid Sequence of Aβ1‐42 at the Single‐Residue Level Using Subnanopores in Ultrathin Films

  2024cites this paper
• Direct Determination of the Structure of Single Biopolymer Molecules Using Nanopore Sequencing

  2024cites this paper
• Proteomic approaches to study ubiquitinomics.

  2023cites this paper
• Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology

  2023cites this paper
• Bioorthogonal Peptide Enrichment from Complex Samples Using a Rink‐Amide‐Based Catch‐and‐Release Strategy

  2023cites this paper
• Yeast Svf1 binds ceramides and contributes to sphingolipid metabolism at the ER cis-Golgi interface

  2023cites this paper
• Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome

  2023cites this paper
• Mass spectrometry-based proteomics for advancing solid organ transplantation research

  2023cites this paper
• Needler: An Algorithm to Develop a Comprehensive Targeted MS Method Capable of Monitoring the Human Proteome

  2022cites this paper
• Protein Subcellular Localization Prediction Model Based on Graph Convolutional Network

  2022cites this paper
• Proteomic Comparison of Three Wild-Type Pseudorabies Virus Strains and the Attenuated Bartha Strain Reveals Reduced Incorporation of Several Tegument Proteins in Bartha Virions

  2022cites this paper
• SeqMapPDB: A Standalone Pipeline to Identify Representative Structures of Protein Sequences and Mapping Residue Indices in Real-Time at Proteome Scale

  2022cites this paper
• Investigating the effects of glyphosate on the bumblebee proteome and microbiota.

  2022cites this paper
• Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant–Pathogen Interactions

  2022cites this paper
• Bioinformatic Analysis of the Perilymph Proteome to Generate a Human Protein Atlas

  2022cites this paper
• Mass spectrometry-based proteomics in neurodegenerative lysosomal storage disorders.

  2022cites this paper
• Application of quantitative proteomics to investigate fruit ripening and eating quality.

  2022cites this paper
• Simple But Efficacious Enrichment of Integral Membrane Proteins and Their Interactions for In-Depth Membrane Proteomics

  2022cites this paper
• Protein Extraction and Sample Preparation Methods for Shotgun Proteomics with Central Nervous System Cells and Brain Tissue.

  2022cites this paper
• On-Cell Catalytic Detection of Epithelial-to-Mesenchymal Transition by a Clusterzyme Bioprobe.

  2022cites this paper
• Functional Micropeptides Encoded by Long Non-Coding RNAs: A Comprehensive Review

  2022cites this paper
• Proteomics for Target Identification in Psychiatric and Neurodegenerative Disorders.

  2021cites this paper
• Mass spectrometry based proteomics for developmental neurobiology in the amphibian Xenopus laevis.

  2021cites this paper
• Proteome analysis using machine learning approaches and its applications to diseases.

  2021cites this paper
• Human Embryos, Induced Pluripotent Stem Cells, and Organoids: Models to Assess the Effects of Environmental Plastic Pollution

  2021cites this paper
• Mass Spectrometry Based Proteomics for Neurodevelopmental Biology in the Amphibian Xenopus laevis

  2021cites this paper
• Phosphoproteomic Analysis of G Protein-Coupled

  2021cites this paper
• Phosphoproteomic Analysis of G Protein-Coupled

  2021cites this paper
• Research Progress of Space Microbial Experimental Technologiesormalsize

  2021cites this paper
• Protein Composition and Biogenesis of the Pancreatic Zymogen Granules

  2021cites this paper
• Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue.

  2021cites this paper
• Mapping the SARS-CoV-2–Host Protein–Protein Interactome by Affinity Purification Mass Spectrometry and Proximity-Dependent Biotin Labeling: A Rational and Straightforward Route to Discover Host-Directed Anti-SARS-CoV-2 Therapeutics

  2021influential citation
• Solid-state and polymer nanopores for protein sensing: A review.

  2021cites this paper
• The New Omics Era into Systems Approaches: What Is the Importance of Separation Techniques?

  2021cites this paper
• MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation

  2020cites this paper
• Protocol for the Bottom-Up Proteomic Analysis of Mouse Spleen

  2020cites this paper
• Proteomic Approaches to Investigate Regulated Trafficking and Signaling of G Protein–Coupled Receptors

  2020cites this paper
• Advances of omics analysis technology in precise diagnosis and treatment of tumor: from single level analysis to multi-omics integrative approaches

  2020cites this paper
• Proteome-scale studies of protein stability

  2020cites this paper
• Immunoaffinity-Based Mass Spectrometry ― a Method for the Analysis of Combinatorial Pesticide Effects on Liver Proteins in HepaRG Cells

  2020cites this paper
• Ensemble deep learning in bioinformatics

  2020cites this paper
• Proteomic analysis of 2-chloroethanol extracts of rice (Oryza sativa L.) seeds

  2020cites this paper
• Application of Solid-State Nanopore in Protein Detection

  2020cites this paper
• The antioxidant function of Sco proteins depends on a critical surface-exposed residue.

  2020cites this paper
• Single-cell proteomics in complex tissues using microprobe capillary electrophoresis mass spectrometry.

  2019cites this paper
• Hepatitis C Virus Entry: Protein Interactions and Fusion Determinants Governing Productive Hepatocyte Invasion.

  2019cites this paper
• A BONCAT-iTRAQ method enables temporally resolved quantitative profiling of newly synthesised proteins in Leishmania mexicana parasites during starvation

  2019cites this paper
• Discovery and Interrogation of Functional Protein Modifications by Hotspot Thermal Profiling

  2019cites this paper
• Proteomics in the World of Induced Pluripotent Stem Cells

  2019cites this paper
• Accelerating Lipidomic Method Development through in silico Simulation.

  2019cites this paper
• Interferon-stimulated gene 15 modulates cell migration by interacting with Rac1 and contributes to lymph node metastasis of oral squamous cell carcinoma cells

  2019cites this paper
• Decoding the PTM-switchboard of Notch

  2019cites this paper
• Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics

  2019cites this paper
• Proteomics: Tools of the Trade.

  2019cites this paper
• Label-free quantification of protein expression in the rainbow trout (Oncorhynchus mykiss) in response to short-term exposure to heat stress.

  2019cites this paper
• High Throughput Discovery of Functional Protein Modifications by Hotspot Thermal Profiling

  2019cites this paper
• Molecular investigation of pathogenic bacteria in the presence of phenolic acids

  2019cites this paper
• Xiao-Xu-Ming decoction extract regulates differentially expressed proteins in the hippocampus after chronic cerebral hypoperfusion

  2019cites this paper
• Protein identification strategies in MALDI imaging mass spectrometry: a brief review.

  2019cites this paper
• Mass Spectrometry-Based Analysis of TRPP2 Phosphorylation.

  2019cites this paper
• A systems biology investigation into age-related changes in the maintenance of collagen and extracellular matrix in human skin

  2019cites this paper
• Mass Spectrometry for Proteomics and Recent Developments in ESI, MALDI and other Ionization Methodologies

  2019cites this paper
• Proteomic profiling of the oncogenic septin 9 reveals isoform-specific interactions in breast cancer cells

  2019cites this paper
• An integrated workflow for global, glyco-, and phospho-proteomic analysis of tumor tissues.

  2019cites this paper
• Experimental Platforms for Extracting Biological Data: Mass Spectrometry, Microarray, Next Generation Sequencing

  2019cites this paper
• α-Amidated Peptides: Approaches for Analysis.

  2019cites this paper
• 16 Analysis of Organelle Dynamics by Quantitative Mass Spectrometry Based Proteomics

  2018cites this paper
• Elucidating the role of JAK/STAT signalling in polycythaemia vera and essential thrombocythaemia using proteomics

  2018cites this paper
• A multi-omics approach to microbial nitrogen and sulfur cycling in the oxygen starved ocean

  2018cites this paper
• Quantitative proteome analyses of phosphorylated proteins and alternative splice variants in human cell lines and urine

  2018cites this paper
• CELL CYCLE AND PROTEIN COMPLEX DYNAMICS IN DISCOVERING SIGNALING PATHWAYS IN YEAST (DINÁMICAS DEL CICLO CELULAR Y COMPLEJOS DE PROTEÍNAS EN EL

  2018cites this paper
• From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology

  2018cites this paper
• Elucidation of Histone Modifications and Nucleosomal Structure Using Novel Mass Spectrometry Approaches

  2018cites this paper
• Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale.

  2018cites this paper
• A new instrument with high mass and high ion mobility resolution

  2018cites this paper
• Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease

  2018cites this paper
• Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol.

  2018cites this paper
• Digging deeper into the human proteome: A novel nanoflow LCMS setup using micro pillar array columns (μPAC™)

  2018cites this paper
• Differential Proteome Analysis of Chikungunya Virus and Dengue Virus Coinfection in Aedes Mosquitoes.

  2018cites this paper
• Biosurveillance of forest insects: part I—integration and application of genomic tools to the surveillance of non-native forest insects

  2018cites this paper
• Drug Resistance in Leishmania Parasites

  2018cites this paper
• The Role of Proteomics in the Study of Drug Resistance

  2018cites this paper
• Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2.

  2018cites this paper
• Quantitative proteomic study of mitoxantrone-resistant NCI-H460 cell-xenograft tumors.

  2018cites this paper
• A LC-MS/MS-Based Approach to Studying the Saccharomyces cerevisiae Cca1 Protein

  2018cites this paper
• Identification of biomarkers using-omics approach for the early detection of chronic kidney disease and its complications

  2018cites this paper
• Comparison of gel-aided sample preparation (GASP) and two in-solution digestion workflows for proteomic analysis using Saccharomyces cerevisiae lysate

  2018cites this paper
• Paving the way to single-molecule protein sequencing

  2018cites this paper
• Plasma CAMK2A predicts chemotherapy resistance in metastatic triple negative breast cancer.

  2018cites this paper
• Comparison of Proteomic Quantification Approaches for Hepatic Drug Transporters: Multiplexed Global Quantitation Correlates with Targeted Proteomic Quantitation

  2018cites this paper