☆ 4.6 Review

Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology

CELLS (2023)

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Summary: Data-independent acquisition mass spectrometry (DIA-MS) is a highly reproducible proteome profiling method that generates permanent digital maps for retrospective analysis. Recent advancements have improved the sensitivity and coverage of DIA-MS. This review discusses the evolution of DIA-MS techniques, recent applications, and challenges.

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Bo Sun et al.

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The dawn of the functional genomics era in muscle physiology

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High sensitivity top-down proteomics captures single muscle cell heterogeneity in large proteoforms

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Mass spectrometry-based proteomics approaches to interrogate skeletal muscle adaptations to exercise

Daniel T. Cervone et al.

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Proteomic features of skeletal muscle adaptation to resistance exercise training as a function of age

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CELLS (2023)

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Overview and considerations in bottom-up proteomics

Rachel M. Miller et al.

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ACS OMEGA (2023)

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Uncovering biology by single-cell proteomics

M. Shahid Mansuri et al.

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COMMUNICATIONS BIOLOGY (2023)

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Review Biochemical Research Methods

Biochemical and proteomic insights into sarcoplasmic reticulum Ca2+-ATPase complexes in skeletal muscles

Paul Dowling et al.

Summary: This article outlines the proteomic profiling of membrane proteins and large protein assemblies in skeletal muscles, including a critical overview of separation techniques and mass spectrometric approaches. The proteomic detection and characterization of the Ca2+-ATPase of the sarcoplasmic reticulum is discussed as an illustrative example. The biological role of this large protein complex in normal muscle functioning is evaluated from a proteomics perspective.

EXPERT REVIEW OF PROTEOMICS (2023)

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Article Chemistry, Applied

Insight on the meat quality and carbonylation profile of breast muscle of broilers in response to chronic heat stress: A proteomic research

Yingsen Liu et al.

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FOOD CHEMISTRY (2023)

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Proteomic analysis by mass spectrometry of postmortem muscle protein degradation for PMI estimation: A pilot study

Alessio Battistini et al.

Summary: In this study, skeletal muscle tissue from pigs was degraded at different temperatures to identify proteins useful for postmortem interval estimation. PDLIM7, TPM1, and ATP2A2 were validated as potential markers for PMI assessment. The use of mass spectrometry analysis increased the number of identified protein species, expanding the panel for PMI evaluation.

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Article Biochemical Research Methods

Technological development of multidimensional liquid chromatography-mass spectrometry in proteome research

Hailong Yu et al.

Summary: Liquid chromatography-mass spectrometry (LC-MS) is the preferred method for high-throughput proteomic research. The development of proteomics has been hampered by the limited peak capacity of conventional single-dimensional LC. To overcome this challenge, multidimensional liquid chromatography (MDLC) with high peak capacity has been developed by combining different separation modes orthogonally. This paper reviews the advances of MDLC-MS-based methodologies and technologies in proteomics studies, including novel application scenarios, proteomic targets, automation, miniaturization, and the improvement of classic methods in recent years. The attempts of new MDLC-MS models and the outlook of MDLC-MS-based proteomics methods are also mentioned.

JOURNAL OF CHROMATOGRAPHY A (2023)

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Review Biochemistry & Molecular Biology

Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution

Wenbo Guo et al.

Summary: Spatial omics technologies provide valuable insights into cells and tissues within a complex context, enhancing our understanding of complex biological systems. Laser capture microdissection (LCM) is an advanced method that quickly collects regions of interest (ROIs) from heterogeneous tissues, and is widely used for studying the cellular and molecular mechanisms of diseases.

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Article Biochemistry & Molecular Biology

Optimized Proteome Reduction for Integrative Top-Down Proteomics

Breyer Woodland et al.

Summary: Integrative top-down proteomics is an effective approach for analyzing proteomes, and it requires a rigorous review of methodology to ensure accurate quantitative analysis. In this study, an optimized protocol using DTT, TBP, and HED as reduction agents was developed to improve protein resolution in 2DE. Compared to other reduction protocols, this optimized protocol showed improved spot counts, total signal, and spot circularity, indicating its potential for enhancing routine top-down proteomic analyses.

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Article Biochemical Research Methods

A Complete Workflow for High Throughput Human Single Skeletal Muscle Fiber Proteomics

Amanda Momenzadeh et al.

Summary: Skeletal muscle is composed of various fiber types that are differentially affected by aging and diseases. Analyzing changes in the proteome of specific fiber types is essential. A new single-cell proteomics method enables fast and efficient quantification of single muscle fiber proteomes, allowing for future studies across hundreds of individuals.

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MS-Based Proteomics of Body Fluids: The End of the Beginning

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Article Biochemical Research Methods

Estimating the time of human decomposition based on skeletal muscle biopsy samples utilizing an untargeted LC-MS/MS-based proteomics approach

Lana Brockbals et al.

Summary: The aim of this study was to investigate the human decomposition process up to 3 months after death and propose novel time-dependent biomarkers for the estimation of decomposition time. An untargeted liquid chromatography tandem mass spectrometry-based bottom-up proteomics workflow was utilized to analyze skeletal muscle, and multiple peptide ratios were successfully proposed as a first step towards generalized, objective biochemical estimation of decomposition time.

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Article Agriculture, Dairy & Animal Science

Thigh muscle metabolic response is linked to feed efficiency and meat characteristics in slow-growing chicken

Pramin Kaewsatuan et al.

Summary: The Korat chicken is a Thai chicken breed with slow growth and relatively poor feed efficiency but high-quality meat. This study aims to understand the genetic basis for feed efficiency and meat characteristics of this breed by evaluating various traits and using proteomic analysis.

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Review Biochemistry & Molecular Biology

Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy

Paul Dowling et al.

Summary: The progressive degeneration of skeletal musculature in Duchenne muscular dystrophy is accompanied by myofibrosis, fat substitution, and inflammation. Animal models have contributed to the understanding of the pathogenesis, discovery of new biomarkers, and testing of therapeutic strategies. Mass spectrometry-based proteomics can be used to study changes in key components of dystrophic fibers, and new biomarkers can be tested for diagnostic and therapeutic purposes.

BIOMOLECULES (2023)

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Article Biology

Purification of functional mouse skeletal muscle mitochondria using percoll density gradient centrifugation

Rea Victoria P. Anunciado-Koza et al.

Summary: By using the Percoll density gradient method, we successfully isolated purified mitochondria from mouse skeletal muscle, obtaining high-quality and minimally contaminated samples. The bioenergetic function and purity of the mitochondria were assessed using Seahorse Extracellular Flux (XF) Analyses and mass spectrometry. This methodology allows for the rapid preparation of high-quality mitochondria for downstream analyses such as mitochondrial bioenergetics and proteomics.

BMC RESEARCH NOTES (2023)

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Article Mathematical & Computational Biology

Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics

Taojunfeng Su et al.

Summary: Alternative splicing plays a crucial role in regulating gene expression and protein diversity in eukaryotic cells. Traditional short-read RNA sequencing has been widely used for studying alternative splicing, but the emergence of long-read RNA sequencing and top-down mass spectrometry offers new opportunities to identify alternative splicing events and protein isoforms with higher accuracy. This review summarizes the recent improvements in short-read RNA sequencing and computational methods for alternative splicing analysis, as well as the approaches used in top-down proteomics to identify protein isoforms. However, future efforts are needed to further enhance the effectiveness, integration, and proteome coverage of alternative splicing events.

ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE (2023)

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Article Biochemistry & Molecular Biology

Mass spectrometers as cryoEM grid preparation instruments

Michael S. Westphall et al.

Summary: Single-particle cryoEM has become a mature technique for structure determination in structural biology. However, the traditional plunge-freezing method used for preparing cryoEM grids still has limitations. The use of native mass spectrometry to create cryoEM samples offers a potential solution by avoiding sample damage and orientation issues. Although there are uncertainties and challenges, the combination of cryoEM and mass spectrometry shows great promise.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2023)

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Review Spectroscopy

Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms

Trisha Tucholski et al.

Summary: In this article, the application of Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in the study of proteoforms is reviewed. The unique features of FT-ICR MS in measuring proteoform mass with ultrahigh resolution and accuracy, obtaining comprehensive proteoform sequence coverage, and identifying modifications are highlighted. The importance of quantifying and characterizing proteoforms in biological systems such as the heart and skeletal muscle is emphasized, along with the use of FT-ICR MS in monoclonal antibody and proteomics studies. It is predicted that FT-ICR MS will continue to advance the study of complex proteoforms and play a key role in clinical diagnostics.

MASS SPECTROMETRY REVIEWS (2022)

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Review Chemistry, Multidisciplinary

Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions-A Method for All Seasons

Lolita Piersimoni et al.

Summary: Mass spectrometry (MS) is a key technology in structural biology, and chemical cross-linking combined with mass spectrometry (XL-MS) plays an important role in studying protein structures and protein-protein interactions. This review outlines the contributions of XL-MS, including cross-linking reagents, software tools, workflows, and significant examples, in characterizing proteins and their interactions in vitro and in vivo. Computational modeling and integration with other structural biology techniques have greatly enhanced the capabilities of XL-MS.

CHEMICAL REVIEWS (2022)

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Review Biochemical Research Methods

Subcellular Transcriptomics and Proteomics: A Comparative Methods Review

Josie A. Christopher et al.

Summary: The internal environment of cells is crowded with molecules, requiring spatial organization through subcellular compartmentalization. These compartments provide specific conditions for molecules to carry out their biological functions, and molecules traffic between these compartments. Aberrant localization of proteins or RNA species is associated with various pathological conditions. Differential expression studies often overlook the importance of subcellular information, and subcellular transcriptomics and proteomics data do not always overlap, highlighting their complementary nature.

MOLECULAR & CELLULAR PROTEOMICS (2022)

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Article Biochemistry & Molecular Biology

New horizons in the stormy sea of multimodal single-cell data integration

Christopher A. Jackson et al.

Summary: While measurements of RNA expression have dominated the field of single-cell analyses, new techniques now allow collection of different data types, including molecules, structural connections, and intermolecular interactions. Integrating these multimodal single-cell datasets is a bioinformatics challenge and requires careful experimental design. The ultimate goal is to learn new causal and mechanistic biology, ranging from mapping cellular heterogeneity to assembling system-wide causal networks.

MOLECULAR CELL (2022)

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Article Biochemistry & Molecular Biology

The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms

Michael A. R. Hollas et al.

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Review Biochemistry & Molecular Biology

Leveraging crosslinking mass spectrometry in structural and cell biology

Andrea Graziadei et al.

Summary: Crosslinking mass spectrometry is a versatile tool that provides structural insights into protein conformation and protein-protein interactions. It has been used for protein structure validation and integrative modeling, and complements the resolution revolution in electron microscopy. Its flexibility and high-throughput nature make it valuable in protein research.

STRUCTURE (2022)

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Review Chemistry, Multidisciplinary

Studying protein structure and function by native separation-mass spectrometry

Guusje van Schaick et al.

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NATURE REVIEWS CHEMISTRY (2022)

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Review Chemistry, Multidisciplinary

High-Resolution Native Mass Spectrometry

Sem Tamara et al.

Summary: Native mass spectrometry is a method for analyzing and characterizing macromolecules while preserving their native structural features. It has experienced significant growth in the past decade, especially in enhancing sensitivity and resolving power, and has a wide range of applications.

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Review Biochemical Research Methods

An overview of technologies for MS-based proteomics-centric multi-omics

Andrew T. Rajczewski et al.

Summary: Proteomics, using mass spectrometry, is a valuable tool in biomedical and basic biological research to identify proteins in a system of interest. When integrated with other 'omics' data, such as transcriptomics, genomics, and metabolomics, it provides a more comprehensive understanding of biological systems and their responses to stimuli. This integration, known as multi-omics, requires complete and accurate proteomics data and can be challenging for inexperienced researchers.

EXPERT REVIEW OF PROTEOMICS (2022)

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Article Biochemical Research Methods

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Richard D. LeDuc et al.

Summary: It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence. The ProForma 2.0 notation aims to unify the representation of proteoforms and peptidoforms, supporting different proteomics approaches and allowing the encoding of highly modified proteins and peptides using a human- and machine-readable string.

JOURNAL OF PROTEOME RESEARCH (2022)

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Article Biochemical Research Methods

Mapping the Proteoform Landscape of Five Human Tissues

Bryon S. Drown et al.

Summary: To understand the human body's functions, it is necessary to study the relationship between protein structure and function on a large scale. Proteins' chemical structure is regulated at multiple levels, resulting in various products with different functions within cells. The term "proteoform" encompasses the complexity of chemical composition. Mapping the proteoform landscape in human tissues requires sensitive and comprehensive analytical techniques. In this study, a top-down proteomics approach combining capillary zone electrophoresis and nanoflow reversed-phase liquid chromatography was used to identify and characterize proteoforms from different organs. The combination of these techniques provided enhanced coverage of post-translational modifications and proteoforms. Among the identified proteoforms, a significant percentage had not been reported before. The differential regulation of proteoforms in different organs provides insights into their function and regulation in human health and disease.

JOURNAL OF PROTEOME RESEARCH (2022)

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Article Biochemical Research Methods

Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics

Benjamin Furtwangler et al.

Summary: Improving global proteome characterization in single-cell proteomics is crucial, and this study demonstrates the effectiveness of real-time search and a new acquisition strategy in enhancing quantitative accuracy and proteome coverage.

MOLECULAR & CELLULAR PROTEOMICS (2022)

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Review Biochemistry & Molecular Biology

Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research

Anca-Narcisa Neagu et al.

Summary: Mass spectrometry enables the analysis of proteins and peptides, including identification of mass, amino acid sequence, and post-translational modifications. In biomedical research, mass spectrometry can be used to identify relevant biomarkers for diagnostic and therapeutic purposes.

MOLECULES (2022)

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Review Biotechnology & Applied Microbiology

The emerging role of mass spectrometry-based proteomics in drug discovery

Felix Meissner et al.

Summary: This Review discusses the potential of proteomics and chemoproteomics approaches in drug discovery, specifically in target identification, validation, and identification of safety hazards. The advancements in biochemical methods and mass spectrometry-based proteomics have allowed for a better understanding of disease mechanisms and the development of targeted drugs.

NATURE REVIEWS DRUG DISCOVERY (2022)

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Review Biotechnology & Applied Microbiology

Single-cell mass spectrometry

Mohammad Tajik et al.

Summary: Recent advances in mass spectrometry (MS) have allowed for the measurement of multiple molecules in single cells. This is crucial for understanding the molecular heterogeneity and function of individual cells. In this review, we discuss different methods of single-cell MS, including high-throughput, targeted, mass cytometry-based approaches, and antibody-free methods, for detailed profiling of the proteome and metabolome of single cells. We also explore the advantages and disadvantages of these methods and the challenges and opportunities for further improvements in single-cell MS. These methods have found applications in biomedical research, such as revealing tumor heterogeneity and conducting high-content drug screening.

TRENDS IN BIOTECHNOLOGY (2022)

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Article Biology

High-intensity interval training remodels the proteome and acetylome of human skeletal muscle

Morten Hostrup et al.

Summary: Exercise is effective in preventing and treating metabolic diseases. High-intensity interval training (HIIT) can induce changes in the proteome and acetylome of human skeletal muscle, leading to metabolic adaptations. Furthermore, HIIT increases the acetylation of mitochondrial proteins.

ELIFE (2022)

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Article Multidisciplinary Sciences

Proteomics and phosphoproteomics datasets of a muscle-specific STIM1 loss-of-function mouse model

Scott P. Lyons et al.

Summary: This article focuses on the role of STIM1 in skeletal muscle and its impact on mitochondrial ultrastructure. Large-scale proteomics and phosphoproteomics experiments were conducted to analyze the changes in specific proteins and phosphorylation sites in STIM1-deficient mice. The findings provide important insights into calcium ion regulation and related diseases.

DATA IN BRIEF (2022)

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Review Biochemistry & Molecular Biology

Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics

Katerina Danko et al.

Summary: The gel-free bottom-up shotgun proteomics is a crucial method for advanced proteome research. Strategies have been developed to mitigate the negative impact of detergents on LC-MS analysis.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Article Biochemical Research Methods

Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

Juraj Lenco et al.

Summary: This article discusses the importance of understanding the fundamental processes of chromatography and the properties of peptides in order to fully utilize the capabilities of advanced MS instruments in peptide separation using LC-MS. It provides an overview of critical aspects of peptide separation and discusses the key parameters of LC-MS methods.

JOURNAL OF PROTEOME RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Structural mass spectrometry of membrane proteins

Angelique Sanchez Dafun et al.

Summary: The development of mass spectrometry (MS) in analyzing proteins and protein complexes has greatly advanced since the invention of electrospray ionization (ESI) in the mid 80s. It has evolved to analyze increasingly heterogeneous and complex samples, with recent applications focusing on membrane proteins. These MS-based methods provide a wealth of information on membrane protein structure, covering sequencing, stoichiometry, ligand binding, conformations, dynamics and distance restraints for modeling.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2022)

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Review Biochemical Research Methods

Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications

Jessica Brandi et al.

Summary: This review provides an overview of the most common post-translational modifications (PTMs) of proteins and discusses enrichment methods for MS-based proteomics analysis. Both traditional affinity strategies and chemical enrichment strategies are detailed, and the challenges and future trends in the field are discussed.

JOURNAL OF CHROMATOGRAPHY A (2022)

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Review Biochemistry & Molecular Biology

Unbiased spatial proteomics with single-cell resolution in tissues

Andreas Mund et al.

Summary: Mass spectrometry-based proteomics is a powerful technology for quantifying proteins in cells or tissues. Single-cell transcriptomes are influenced by stochastic noise due to low transcript numbers, whereas single-cell proteomes appear to be more complete. With the combination of imaging and spatial transcriptomics, the spatial organization of cells in tissues can be studied alongside ultra-sensitive proteomics.

MOLECULAR CELL (2022)

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Article Biochemical Research Methods

High-throughput proteomic sample preparation using pressure cycling technology

Xue Cai et al.

Summary: This article describes a detailed protocol for pressure cycling technology-assisted sample preparation for proteomic analysis of biopsy tissues. The method allows efficient and reproducible protein extraction and proteolysis digestion, enabling mass spectrometry-based proteomics analysis.

NATURE PROTOCOLS (2022)

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Review Biochemical Research Methods

Recent advances in isobaric labeling and applications in quantitative proteomics

Michael K. Sivanich et al.

Summary: This article provides an overview of the application of mass spectrometry (MS) in quantitative proteomics. Liquid chromatography-mass spectrometry (LC-MS) is a powerful technique for accurately quantifying proteins and peptides in complex biological samples. Isobaric tagging, a commonly used chemical isotopic labeling technique, allows for quantification based on MS2 peptide analysis. The article also discusses recent developments in isobaric tagging methods and improvements, as well as limitations and approaches to address them. The review highlights the diverse applications of isobaric tags in biomarker discovery, thermal proteome profiling, cross-linking structural investigations, single-cell analysis, top-down proteomics, and analysis of neuropeptides, glycans, metabolites, and lipids. Considerations and evaluations are provided for each application.

PROTEOMICS (2022)

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Review Biochemical Research Methods

Targeted proteomics on its way to discovery

Marta L. Mendes et al.

Summary: In the past, targeted and discovery proteomics focused on different areas of detection spectrum, with targeted proteomics concentrating on small target sets. However, recent advances in highly multiplexed analysis have expanded the coverage of targeted proteomics to include less complex proteomes such as the blood proteome, which has low protein detection counts due to dynamic range restrictions. These developments have significant implications for biomarker discovery and the potential use of targeted proteomics for diagnostics.

PROTEOMICS (2022)

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Article Chemistry, Analytical

Targeted N-Glycan Analysis with Parallel Reaction Monitoring Using a Quadrupole-Orbitrap Hybrid Mass Spectrometer

Byeong Gwan Cho et al.

Summary: Targeted mass spectrometric analysis, including techniques like selected reaction monitoring and multiple reaction monitoring, has been widely used in structural analysis of biomolecules. The recent innovation of parallel reaction monitoring (PRM) allows simultaneous detection of all product ions, simplifying the workflow and improving data quality. PRM offers advantages in reducing background interference and improving sensitivity, attributed to developments in sensitive mass analyzers like orbitrap and time of flight.

ANALYTICAL CHEMISTRY (2022)

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Article Biochemistry & Molecular Biology

Native mass spectrometry for the investigation of protein structural (dis) order

Carlo Santambrogio et al.

Summary: A central challenge in structural biology is to describe dynamic and heterogeneous systems, such as proteins in solution, especially intrinsically disordered proteins(IDPs). Mass spectrometry(MS) has become a central tool in this field, offering different approaches to study the structure of folded or disordered proteins. The methods can be categorized into labeling molecules in solution and characterizing labeling products by denaturing MS, or exploring different conformational components directly by non-denaturing(native) MS. These methods can also be applied to study noncovalent complexes and post-translational modifications.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2022)

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Article Biotechnology & Applied Microbiology

Transcription and proteome changes involved in re-innervation muscle following nerve crush in rats

Haotao Li et al.

Summary: In this study, multi-dimensional data integrating transcriptome and proteome profiles were used to investigate the mechanism of re-innervation in muscles. The results showed that differentially expressed genes and proteins were enriched in the PPARs signaling pathway and energy metabolism. The RN group demonstrated better tibial nerve function and recovery of muscle atrophy compared to the DN group. This study provides basic information regarding genes and proteins involved in re-innervation-induced muscle atrophy and identifies potential treatment targets.

BMC GENOMICS (2022)

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Review Microbiology

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in the diagnosis of microorganisms

Antonio J. J. Evangelista et al.

Summary: This study evaluated the importance of MALDI-TOF MS technique in microbiological diagnosis through a literature review. The results showed that MALDI-TOF MS can accurately identify different types of microorganisms, as well as assess their resistance to antimicrobials. Therefore, widespread application of this technique in clinical laboratories can improve the accuracy and efficiency of microbial diagnosis.

FUTURE MICROBIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Tissue- and cell-specific whole-transcriptome meta-analysis from brain and retina reveals differential expression of dystrophin complexes and new dystrophin spliced isoforms

Cesar Garcia-Cruz et al.

Summary: This study provides a first RNA-Seq-based reference showing tissue- and cell-specific differential expression of dystrophins, splice variants, and associated proteins in mouse brain and retina. The study discovers that a cell type may express multiple dystrophin complexes and identifies new splicing events. Additionally, the study reveals that transcripts with stop codons are translated into truncated proteins lacking their C-terminus.

HUMAN MOLECULAR GENETICS (2022)

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Article Biochemical Research Methods

1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC-MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins

Changming Chen et al.

Summary: This study introduces a method that combines SDS-PAGE, whole-gel slicing, and quantitative LC-MS/MS to analyze protein distributions in a proteome, providing proteoform-correlated information for in-depth proteomics. The research revealed that about 30% of proteins have multiple proteoforms in gels, with complex profiles categorized into six types based on distribution and deviations between abundance-peak apparent M(w)s and calculated M(w)s.

JOURNAL OF PROTEOME RESEARCH (2022)

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Review Biochemistry & Molecular Biology

Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research

Laura Darie-Ion et al.

Summary: Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is widely used in proteomics for the structural identification and characterization of proteins and peptides, including their modified forms. MALDI-MS and MALDI-MS/MS offer sensitive analysis of small and large molecules, enabling direct analysis of biological samples with minimal preparation. MALDI-MS/MS has greatly aided in understanding the molecular function and involvement in disease pathogenesis of peptides and proteins. This review highlights the applications of MALDI-MS and MALDI-MS/MS for analyzing biomedical relevant proteins and peptides, including the use of MALDI-MSI for spatial analysis of molecular weight proteins in tissues.

MOLECULES (2022)

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Article Multidisciplinary Sciences

The muscle proteome reflects changes in mitochondrial function, cellular stress and proteolysis after 14 days of unilateral lower limb immobilization in active young men

Thomas M. Doering et al.

Summary: This study, using data independent proteomics and GSEA, demonstrates that unilateral lower limb immobilization leads to mitochondrial dysfunction, cellular stress, and proteolysis. Through GSEA and network mapping, 27 hub proteins were identified as potential protein/gene candidates for further exploration.

PLOS ONE (2022)

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Review Biochemical Research Methods

Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis

Zehu Xie et al.

Summary: This review summarizes the recent advances in the application of novel functionalized materials for sample preparation in phosphoproteome and glycoproteome analysis. It discusses the design and preparation of functionalized materials based on different enrichment mechanisms and proposes research directions and potential challenges for proteomic PTMs research.

PROTEOMICS (2022)

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Article Food Science & Technology

A Combined Differential Proteome and Transcriptome Profiling of Fast- and Slow-Twitch Skeletal Muscle in Pigs

Wei Wei et al.

Summary: Skeletal muscle fiber types can affect pork quality parameters. This study identified key proteins regulating muscle fiber types in pigs using proteomics and transcriptome data, and explored potential regulatory mechanisms through functional enrichment and protein-protein interaction analysis.

FOODS (2022)

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Article Biochemistry & Molecular Biology

Thermal proteome profiling: Insights into protein modifications, associations, and functions

Cecile Le Sueur et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2022)

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Review Biochemistry & Molecular Biology

Potential Satellite Cell-Linked Biomarkers in Aging Skeletal Muscle Tissue: Proteomics and Proteogenomics to Monitor Sarcopenia

Diego Fernandez-Lazaro et al.

Summary: Sarcopenia (Sp) is the loss of skeletal muscle mass associated with aging. With advancing age, there is a decrease in the efficiency of the regenerative response of satellite cells (Sc) which are myogenic stem cells. Liquid biopsy detection of biomarkers could provide valuable insights into the molecular biology and heterogeneity of Sp. Certain proteogenomic biomarkers enhance Sc activity and proliferation, modulating and delaying Sp progression, while others contribute to early Sp development by impairing Sc function.

PROTEOMES (2022)

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Article Multidisciplinary Sciences

Signatures of muscle disuse in spaceflight and bed rest revealed by single muscle fiber proteomics

Marta Murgia et al.

Summary: Astronauts experience muscle loss, decreased strength, and insulin resistance in space, as well as during prolonged bed rest. By using proteomics, the study reveals molecular remodeling and changes in muscle proteins during bed rest and spaceflight, shedding light on the effects of microgravity and inactivity. Muscle focal adhesions and antioxidant response pathways are downregulated during unloading and restored upon reloading. Additionally, markers of neuromuscular damage are upregulated during unloading.

PNAS NEXUS (2022)

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Review Biochemistry & Molecular Biology

Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis

Nicole C. Beller et al.

Summary: The SILAC technique in proteomics uses stable isotope labeling in cell culture to differentiate and quantify unlabeled and labeled cells. The pulsed SILAC technique provides a new quantitative dimension for temporal analysis in proteomics. These innovative techniques have contributed to the development of various SILAC-based temporal and spatial labeling applications.

MOLECULAR OMICS (2022)

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Article Medical Laboratory Technology

Proteoforms and their expanding role in laboratory medicine

Lauren M. Forgrave et al.

Summary: The term proteoforms refers to the different structures of a protein product, including variations in amino acid sequence and post-translational modifications, and plays a crucial role in the complexity of biological organisms. The use of proteoforms as biomarkers in medicine has been long-established. Analytical techniques, such as mass spectrometry, have evolved to detect and quantify proteoforms, with various applications in clinical research and patient care.

PRACTICAL LABORATORY MEDICINE (2022)

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Article Biochemical Research Methods

Spatial Proteomic Approach to Characterize Skeletal Muscle Myofibers

Katherine M. Fomchenko et al.

Summary: In this study, a visual proteomic approach was used to analyze the protein expression in skeletal muscle myofibers, leading to the identification of a large number of potentially fiber-type-specific novel proteins.

JOURNAL OF PROTEOME RESEARCH (2021)

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Article Biochemical Research Methods

BAC-DROP: Rapid Digestion of Proteome Fractionated via Dissolvable Polyacrylamide Gel Electrophoresis and Its Application to Bottom-Up Proteomics Workflow

Ayako Takemori et al.

Summary: The study developed a rapid digestion workflow to overcome the limitations of GeLC-MS, allowing for quick separation and digestion of proteins in gels. The introduction of this workflow significantly shortened the sample preparation time and successfully quantified markers from human serum samples.

JOURNAL OF PROTEOME RESEARCH (2021)

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Article Biochemical Research Methods

Ethical Principles, Constraints, and Opportunities in Clinical Proteomics

Sebastian Porsdam Mann et al.

Summary: Recent advances in MS-based proteomics have greatly enhanced the quality and range of biological information available from human samples. Proteomics is becoming increasingly relevant in biomedical and clinical contexts, leading to a rise in ethical responsibilities regarding the impact on individual health, privacy, and well-being. Discussions on ethical issues in clinical proteomics is essential to ensure that healthcare practices and regulations are well-informed and anticipate potential opportunities and challenges as technology continues to advance.

MOLECULAR & CELLULAR PROTEOMICS (2021)

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Review Biochemical Research Methods

Proteomic profiling of carbonic anhydrase CA3 in skeletal muscle

Paul Dowling et al.

Summary: Carbonic anhydrase (CA) is a key enzyme in mediating the reversible hydration of carbon dioxide. Skeletal muscles contain high levels of cytosolic isoform CA3, which has antioxidative function and plays a crucial role in maintaining intracellular pH homeostasis. Recent proteomics analyses have confirmed CA3 as a valuable marker for both physiological and pathophysiological alterations in skeletal muscles, especially in slow-twitching type I fibers. Changes in CA3 levels in neuromuscular diseases, age-related muscle wasting, and dystrophinopathy establish this enzyme as a suitable biomarker for disease diagnosis and monitoring.

EXPERT REVIEW OF PROTEOMICS (2021)

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Review Biochemical Research Methods

Laser Capture Proteomics: spatial tissue molecular profiling from the bench to personalized medicine

Lance A. Liotta et al.

Summary: LCM is a powerful tool for isolating specific cells in tissue samples for molecular analysis. Recent advancements in LCM technology have enabled in-depth profiling of tissues at the single cell level, with the integration of proteomics, genomics, and transcriptomics data. The future of LCM is envisioned to involve digital and AI-guided imaging, automation, and telepathology to achieve comprehensive multi-omic profiling.

EXPERT REVIEW OF PROTEOMICS (2021)

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Article Biochemistry & Molecular Biology

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

Huaiyu Mi et al.

Summary: PANTHER is a resource for evolutionary and functional classification of protein-coding genes, with extensive improvements made in the past two years, including the refactoring of Protein Class ontology and addition of services for programmatic access. The resource provides comprehensive classification and annotation information for genes from different taxonomic groups and also allows users to add their own protein sequences for evolutionary context and fine-grained annotations.

NUCLEIC ACIDS RESEARCH (2021)

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Article Multidisciplinary Sciences

Deep muscle-proteomic analysis of freeze-dried human muscle biopsies reveals fiber type-specific adaptations to exercise training

A. S. Deshmukh et al.

Summary: The study developed a workflow for proteomics analysis of isolated muscle fibers from freeze-dried human muscle biopsies, identifying over 4000 proteins in slow- and fast-twitch muscle fibers. Exercise training altered expression of proteins involved in various metabolic pathways in a fiber type-specific manner, providing insights into molecular mechanisms underlying muscle function and health.

NATURE COMMUNICATIONS (2021)

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Article Biochemical Research Methods

An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community

Pallab Bhowmick et al.

Summary: Targeted proteomics with internal standards achieves precise protein quantification for longitudinal and cohort studies. Public repositories offer information on targeted proteomics assays, while MRMAssayDB provides an integrated resource with extensive annotations and visualization options. The database has expanded to include a large number of assays, proteins, pathways, Gene Ontology terms, and annotations, with new features for molecular structural annotation browsing.

JOURNAL OF PROTEOME RESEARCH (2021)

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Review Biochemical Research Methods

Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives

Arman Kulyyassov et al.

Summary: LC-MS/MS is the main analytical method for identification and quantification of peptides and proteins in biological samples, with MRM and PRM methods providing high specificity, accuracy, and reproducibility for data analysis. These methods are crucial for discovery and quantitative comparison of biomarkers in modern research.

PROTEOMICS (2021)

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Review Biochemistry & Molecular Biology

Crosslinking mass spectrometry: A link between structural biology and systems biology

Xiaoting Tang et al.

Summary: Protein structure is crucial for biological functions, and understanding it is fundamental in biological and biomedical research. Crosslinking mass spectrometry is an emerging technique that can capture transient information on protein interactions in their native environment. Combining XL-MS with traditional techniques has the potential to bridge the gap between structural biology and systems biology approaches.

PROTEIN SCIENCE (2021)

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Review Biochemical Research Methods

Microproteomic sample preparation

Michal Alexovic et al.

Summary: Proteomics applications in various fields such as life and health sciences, pathology, and pharmacology often require handling small cell and tissue samples, where microproteomics plays a crucial role in addressing specific considerations for processing these samples efficiently.

PROTEOMICS (2021)

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Review Biochemistry & Molecular Biology

Single-Cell Proteomics

Luke F. Vistain et al.

Summary: The inability to make broad, minimally biased measurements of a cell's proteome is a major bottleneck in understanding gene expression and cellular phenotype. Current methods for single-cell proteomic measurements typically focus on either absolute quantification of a small number of proteins or highly multiplexed protein measurements, with advancements in microfluidics and output encoding enabling major improvements. Emerging technologies like single-cell mass spectrometry may provide unbiased measurement of cellular proteomes.

TRENDS IN BIOCHEMICAL SCIENCES (2021)

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Article Cell Biology

Protein profile of fiber types in human skeletal muscle: a single-fiber proteomics study

Marta Murgia et al.

Summary: This study utilized single-fiber proteomics to identify 404 proteins with significant differences among different fiber types, including many specific markers for type 1 or 2X fibers. It also revealed other major patterns of protein distribution and highlighted the selective enrichment of certain proteins in specific fiber types, suggesting potential implications in muscle pathophysiology. Single-fiber proteomics, combined with emerging single-cell proteomics approaches, are crucial for exploring and quantifying muscle cell heterogeneity.

SKELETAL MUSCLE (2021)

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Review Multidisciplinary Sciences

The Human Proteoform Project: Defining the human proteome

Lloyd M. Smith et al.

Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.

SCIENCE ADVANCES (2021)

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Review Genetics & Heredity

Quantitative Proteomics Using Isobaric Labeling: A Practical Guide

Xiulan Chen et al.

Summary: Isobaric labeling technology has become a key tool for comparing protein expression in biological samples, although challenges remain in terms of quantitative accuracy and precision. The different types of isobaric mass tags and advantages and disadvantages of the labeling method are detailed, along with precautions needed at each step of the workflow for reliable quantification results. The broad applications of isobaric labeling technology in biological and clinical studies, with a focus on thermal proteome profiling and proteogenomics, are also discussed.

GENOMICS PROTEOMICS & BIOINFORMATICS (2021)

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Article Biochemical Research Methods

Novel Strategies to Address the Challenges in Top-Down Proteomics

Jake A. Melby et al.

Summary: Top-down proteomics is a powerful technology for comprehensively characterizing proteoforms and understanding protein functions, disease mechanisms, and biomarkers. However, challenges in protein solubility, data analysis, and proteome complexity remain. Recent technological developments include the development of new surfactants, nanoparticles for enriching proteoforms, and strategies for multi-dimensional chromatography separation of proteins.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2021)

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Review Biochemistry & Molecular Biology

Discovering the landscape of protein modifications

Keith E. Keenan et al.

Summary: Protein modifications play a significant role in cell biology across various organisms. Discoveries in the early 20th century challenged traditional definitions of amino acids, and the advent of mass-spectrometry-based proteomics in the latter part led to a rapid increase in known protein modifications, with over 500 identified today. New computational tools in data science, machine learning, and artificial intelligence are expected to further advance the discovery and understanding of protein modifications in the future.

MOLECULAR CELL (2021)

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Article Cell Biology

Progressive and Coordinated Mobilization of the Skeletal Muscle Niche throughout Tissue Repair Revealed by Single-Cell Proteomic Analysis

Matthew Borok et al.

Summary: The study utilized mass cytometry to track changes in different cell types during muscle regeneration, revealing rapid proteomic changes in various cell types following early activation. After injury induction, there is a drastic reduction in myogenic, vascular, and mesenchymal cell lineages, while immune cells invade the damaged tissue significantly.

CELLS (2021)

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Review Cell Biology

Advances in Aptamer-Based Biomarker Discovery

Jie Huang et al.

Summary: The discovery and identification of biomarkers are crucial for the advancement of medical diagnosis and therapeutics. Aptamers, as a potential technology for biomarker discovery, offer many advantages such as flexible design and easy synthesis, and have been successfully applied in CELL-SELEX and SOMAScan technologies.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2021)

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Article Biochemical Research Methods

Isotope-Coded Maleimide Affinity Tags for Proteomics Applications

Adam P. Wdowiak et al.

Summary: ICMATs are newly designed affinity tags for mass spectrometry analysis of thiol oxidation enzymes and muscle proteomes, showing improved selectivity and adduct formation rates compared to traditional ICATs.

BIOCONJUGATE CHEMISTRY (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction for the human proteome

Kathryn Tunyasuvunakool et al.

Summary: Using the AlphaFold method, the structural coverage of the proteome has been significantly expanded, covering 98.5% of human proteins with 58% of residues having confident predictions and 36% having very high confidence. Introducing new metrics to interpret the dataset and identify disordered regions, this study aims to provide high-quality predictions for generating biological hypotheses.

NATURE (2021)

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Review Physiology

The Role of the Skeletal Muscle Secretome in Mediating Endurance and Resistance Training Adaptations

Aurel B. B. Leuchtmann et al.

Summary: Exercise induces molecular and cellular adaptations in various organs beyond skeletal muscles. The release of signaling molecules from skeletal muscle plays a central role in systemic plasticity, with the long-term training adaptation secretome still not well understood. Targeting these factors could have implications for athletic performance and disease prevention.

FRONTIERS IN PHYSIOLOGY (2021)

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Review Biochemistry & Molecular Biology

Proteomes Are of Proteoforms: Embracing the Complexity

Katrina Carbonara et al.

Summary: Proteomes are more complex than genomes or transcriptomes, and their analysis requires considering a wide range of proteoforms. Various analytical methods are currently used to study proteomes, but further improvements and refinements are needed in order to gain a deeper understanding of proteomic complexity.

PROTEOMES (2021)

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Article Biochemistry & Molecular Biology

Advanced Fiber Type-Specific Protein Profiles Derived from Adult Murine Skeletal Muscle

Britta Eggers et al.

Summary: Research on skeletal muscle fiber types has revealed unique protein profiles with distinct metabolic properties and multifunctionality. Additionally, proteins associated with myopathy were found to be enriched in specific fiber types, providing valuable insights for disease studies.

PROTEOMES (2021)

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Article Cell Biology

Mass-spectrometry-based proteomics reveals mitochondrial supercomplexome plasticity

Alba Gonzalez-Franquesa et al.

Summary: The study examines mitochondrial supercomplexes in skeletal muscle using native electrophoresis and mass spectrometry, revealing non-stoichiometric changes in subunits and assembly proteins after exercise-induced mitochondrial biogenesis. These alterations impact mitochondrial respiration and highlight complexities in mitochondrial plasticity previously unseen.

CELL REPORTS (2021)

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Review Chemistry, Analytical

Spatial proteomics for understanding the tissue microenvironment

Yiheng Mao et al.

Summary: The tissue microenvironment is a complex ecosystem where cells interact and are influenced by the surroundings. Spatial proteomics is a key method to study protein abundance and distribution in diseased tissue microenvironments. Technological advancements and biomedical applications of spatial proteomics show great potential for future research and clinical use.

ANALYST (2021)

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Article Biochemical Research Methods

Trapped Ion Mobility Spectrometry and Parallel Accumulation-Serial Fragmentation in Proteomics

Florian Meier et al.

Summary: The recent development of TIMS coupled to TOF mass analysis, particularly the PASEF operation mode, offers advantages in sequencing speed and sensitivity. By synchronizing ion release with downstream precursor selection, PASEF can increase the number of peptide fragment ion spectra obtained while maintaining sensitivity. The correlation between ion mobility and mass, as well as the ability to predict collisional cross section values based on peptide sequences, make TIMS quadrupole TOF PASEF a powerful platform for proteomics and beyond.

MOLECULAR & CELLULAR PROTEOMICS (2021)

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Review Medicine, Research & Experimental

Skeletal muscle: A review of molecular structure and function, in health and disease

Kavitha Mukund et al.

WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE (2020)

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Article Biochemical Research Methods

LFQ-Analyst: An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant

Anup D. Shah et al.

JOURNAL OF PROTEOME RESEARCH (2020)

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Review Biochemical Research Methods

Proteomic profiling of fatty acid binding proteins in muscular dystrophy

Paul Dowling et al.

EXPERT REVIEW OF PROTEOMICS (2020)

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Article Biochemistry & Molecular Biology

Quantification of exercise-regulated ubiquitin signaling in human skeletal muscle identifies protein modification cross talk via NEDDylation

Benjamin L. Parker et al.

FASEB JOURNAL (2020)

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Article Biochemical Research Methods

The evolution of two-dimensional gel electrophoresis - from proteomics to emerging alternative applications

Pey Yee Lee et al.

JOURNAL OF CHROMATOGRAPHY A (2020)

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Article Biochemical Research Methods

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

Dorte B. Bekker-Jensen et al.

MOLECULAR & CELLULAR PROTEOMICS (2020)

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Review Multidisciplinary Sciences

Beyond mass spectrometry, the next step in proteomics

Winston Timp et al.

SCIENCE ADVANCES (2020)

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Article Multidisciplinary Sciences

Proteomic analyses of sheep (ovis aries) embryonic skeletal muscle

Xinyue Wang et al.

SCIENTIFIC REPORTS (2020)

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Review Endocrinology & Metabolism

Muscle-Organ Crosstalk: The Emerging Roles of Myokines

Mai Charlotte Krogh Severinsen et al.

ENDOCRINE REVIEWS (2020)

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Article Geriatrics & Gerontology

Comparative proteomic analyses of Duchenne muscular dystrophy and Becker muscular dystrophy muscles: changes contributing to preserve muscle function in Becker muscular dystrophy patients

Daniele Capitanio et al.

JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE (2020)

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Article Cell Biology

High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

Sebastian Kallabis et al.

SKELETAL MUSCLE (2020)

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Review Cell Biology

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

Isabell Bludau et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)

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Article Biochemistry & Molecular Biology

Adaptation of rat fast-twitch muscle to endurance activity is underpinned by changes to protein degradation as well as protein synthesis

Stuart J. Hesketh et al.

FASEB JOURNAL (2020)

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Review Endocrinology & Metabolism

Muscle, Bone, and Fat Crosstalk: the Biological Role of Myokines, Osteokines, and Adipokines

Ben Kirk et al.

CURRENT OSTEOPOROSIS REPORTS (2020)

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Article Biochemical Research Methods

Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data

Leah Schaffer et al.

JOURNAL OF PROTEOME RESEARCH (2020)

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Review Biochemical Research Methods

Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry

Elisabetta Boeri Erba et al.

JOURNAL OF PROTEOMICS (2020)

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Article Oncology

JNK signaling contributes to skeletal muscle wasting and protein turnover in pancreatic cancer cachexia

Scott E. Mulder et al.

CANCER LETTERS (2020)

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Article Biochemistry & Molecular Biology

A Quantitative Proteome Map of the Human Body

Lihua Jiang et al.

CELL (2020)

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Article Biochemical Research Methods

Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project

Gilbert S. Omenn et al.

JOURNAL OF PROTEOME RESEARCH (2020)

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Article Multidisciplinary Sciences

A high-stringency blueprint of the human proteome

Subash Adhikari et al.

NATURE COMMUNICATIONS (2020)

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Review Biochemical Research Methods

The application of proteomics in muscle exercise physiology

Stuart J. Hesketh et al.

Summary: Exercise offers protection from non-communicable diseases and extends healthspan by offsetting natural physiological declines that occur in older age. Muscle proteomics help in studying the protective effects of exercise. Dynamic proteome profiling methods offer new opportunities to study the mechanisms of muscle adaptation.

EXPERT REVIEW OF PROTEOMICS (2020)

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Editorial Material Biochemical Research Methods

The Human Proteome: 90% in the Light, 10% on the Dark Side

Christopher M. Overall

JOURNAL OF PROTEOME RESEARCH (2020)

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Article Biochemical Research Methods

Protocol for the Bottom-Up Proteomic Analysis of Mouse Spleen

Paul Dowling et al.

STAR PROTOCOLS (2020)

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Review Biochemistry & Molecular Biology

What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?

Katrin Marcus et al.

PROTEOMES (2020)

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Review Neurosciences

The impact of exercise and nutrition on the regulation of skeletal muscle mass

Chris McGlory et al.

JOURNAL OF PHYSIOLOGY-LONDON (2019)

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Article Biochemical Research Methods

Proteomic analysis of the sarcolemma-enriched fraction from dystrophic mdx-4cv skeletal muscle

Sandra Murphy et al.

JOURNAL OF PROTEOMICS (2019)

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Review Biochemical Research Methods

Proteomic profiling of giant skeletal muscle proteins

Sandra Murphy et al.

EXPERT REVIEW OF PROTEOMICS (2019)

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Article Cell Biology

Proteomic profiling of the mouse diaphragm and refined mass spectrometric analysis of the dystrophic phenotype

Sandra Murphy et al.

JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY (2019)

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Article Biochemical Research Methods

Suspension Trapping (S-Trap) Is Compatible with Typical Protein Extraction Buffers and Detergents for Bottom-Up Proteomics

Dalia Elinger et al.

JOURNAL OF PROTEOME RESEARCH (2019)

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Article Biochemistry & Molecular Biology

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

Dongxue Wang et al.

MOLECULAR SYSTEMS BIOLOGY (2019)

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Article Biochemical Research Methods

Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags while Significantly Reducing Instrument Time

Jonathan R. Krieger et al.

JOURNAL OF PROTEOME RESEARCH (2019)

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Article Biochemical Research Methods

Universal Solid-Phase Protein Preparation (USP3) for Bottom-up and Top-down Proteomics

Laura F. Dagley et al.

JOURNAL OF PROTEOME RESEARCH (2019)

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Article Biochemical Research Methods

Top or Middle? Up or Down? Toward a Standard Lexicon for Protein Top-Down and Allied Mass Spectrometry Approaches

Frederik Lermyte et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2019)

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Review Biochemical Research Methods

Identification and Quantification of Proteoforms by Mass Spectrometry

Leah Schaffer et al.

PROTEOMICS (2019)

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Article Biochemistry & Molecular Biology

Comparative Proteomics Analysis of Four Commonly Used Methods for Identification of Novel Plasma Membrane Proteins

Kubra Karaosmanoglu Yoneten et al.

JOURNAL OF MEMBRANE BIOLOGY (2019)

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Article Chemistry, Analytical

Filter Aided Sample Preparation - A tutorial

Jacek R. Wisniewski

ANALYTICA CHIMICA ACTA (2019)

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Review Spectroscopy

Proteome analysis of tissues by mass spectrometry

Irena Dapic et al.

MASS SPECTROMETRY REVIEWS (2019)

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Review Medical Laboratory Technology

Proteogenomics: From next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine

Mia Yang Ang et al.

CLINICA CHIMICA ACTA (2019)

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Review Physiology

Fiber typing human skeletal muscle with fluorescent immunohistochemistry

Kevin A. Murach et al.

JOURNAL OF APPLIED PHYSIOLOGY (2019)

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Review Biochemical Research Methods

Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery

Pey Yee Lee et al.

BIOANALYSIS (2019)

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Article Biology

Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria

Ceereena Ubaida-Mohien et al.

ELIFE (2019)

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Article Biochemical Research Methods

Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

Christopher S. Hughes et al.

NATURE PROTOCOLS (2019)

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Review Biochemical Research Methods

Connecting Proteomics to Next-Generation Sequencing: Proteogenomics and Its Current Applications in Biology

Teck Yew Low et al.

PROTEOMICS (2019)

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Review Biochemistry & Molecular Biology

Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level

Xianquan Zhan et al.

PROTEOMES (2019)

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Article Biochemical Research Methods

Proteomic profiling of large myofibrillar proteins from dried and long-term stored polyacrylamide gels

Sandra Murphy et al.

ANALYTICAL BIOCHEMISTRY (2018)

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Article Biochemistry & Molecular Biology

Next-generation antibodies for post-translational modifications

Takamitsu Hattori et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)

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Article Biochemical Research Methods

Comparative gel-based proteomic analysis of chemically crosslinked complexes in dystrophic skeletal muscle

Sandra Murphy et al.

ELECTROPHORESIS (2018)

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Article Biochemical Research Methods

Application of targeted mass spectrometry in bottom-up proteomics for systems biology research

Nathan P. Manes et al.

JOURNAL OF PROTEOMICS (2018)

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Article Biochemistry & Molecular Biology

How many human proteoforms are there?

Ruedi Aebersold et al.

NATURE CHEMICAL BIOLOGY (2018)

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Article Biochemical Research Methods

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

Florian Meier et al.

NATURE METHODS (2018)

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Review Cell Biology

A mini review: Proteomics approaches to understand disused vs. exercised human skeletal muscle

Yoshitake Cho et al.

PHYSIOLOGICAL GENOMICS (2018)

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Review Cell Biology

Diversification of the muscle proteome through alternative splicing

Kiran Nakka et al.

SKELETAL MUSCLE (2018)

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Review Biochemical Research Methods

Proteomics and frailty: a clinical overview

Elisa Danese et al.

EXPERT REVIEW OF PROTEOMICS (2018)

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Article Biochemical Research Methods

Single Muscle Fiber Proteomics Reveals Distinct Protein Changes in Slow and Fast Fibers during Muscle Atrophy

Franziska Lang et al.

JOURNAL OF PROTEOME RESEARCH (2018)

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Review Biochemistry & Molecular Biology

Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial

Christina Ludwig et al.

MOLECULAR SYSTEMS BIOLOGY (2018)

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Article Biochemical Research Methods

Updates of the In-Gel Digestion Method for Protein Analysis by Mass Spectrometry

Jennifer K. Goodman et al.

PROTEOMICS (2018)

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Review Cell Biology

Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease

Maria Gomez-Serrano et al.

OXIDATIVE MEDICINE AND CELLULAR LONGEVITY (2018)

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Article Chemistry, Analytical

Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families

Leah V. Schaffer et al.

ANALYTICAL CHEMISTRY (2018)

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Article Biochemistry & Molecular Biology

A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles

Sehyun Chae et al.

EXPERIMENTAL AND MOLECULAR MEDICINE (2018)

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Review Cell Biology

The Effects of Acute and Chronic Exercise on Skeletal Muscle Proteome

Bernardo A. Petriz et al.

JOURNAL OF CELLULAR PHYSIOLOGY (2017)

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Review Geriatrics & Gerontology

The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature

Marta Gonzalez-Freire et al.

JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE (2017)

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Review Biochemical Research Methods

Protein purification and analysis: next generation Western blotting techniques

Manish Mishra et al.

EXPERT REVIEW OF PROTEOMICS (2017)

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Review Biochemical Research Methods

Mapping the human skeletal muscle proteome: progress and potential

Daniele Capitanio et al.

EXPERT REVIEW OF PROTEOMICS (2017)

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Review Biochemical Research Methods

Integral membrane proteins: bottom-up, top-down and structural proteomics

Upendra K. Kar et al.

EXPERT REVIEW OF PROTEOMICS (2017)

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Article Biochemistry & Molecular Biology

Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise

Donny M. Camera et al.

FASEB JOURNAL (2017)

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Article Medicine, Research & Experimental

Mass spectrometric identification of dystrophin, the protein product of the Duchenne muscular dystrophy gene, in distinct muscle surface membranes

Sandra Murphy et al.

INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE (2017)

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Article Agriculture, Multidisciplinary

Proteome Analysis Using Isobaric Tags for Relative and Absolute Analysis Quantitation (iTRAQ) Reveals Alterations in Stress-Induced Dysfunctional Chicken Muscle

Tong Xing et al.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2017)

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Article Biochemical Research Methods

Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?

Francois Fenaille et al.

JOURNAL OF CHROMATOGRAPHY A (2017)

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Article Cell Biology

Proteomic profiling of the dystrophin complex and membrane fraction from dystrophic mdx muscle reveals decreases in the cytolinker desmoglein and increases in the extracellular matrix stabilizers biglycan and fibronectin

Sandra Murphy et al.

JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY (2017)

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Article Biochemical Research Methods

Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range

Malte Sielaff et al.

JOURNAL OF PROTEOME RESEARCH (2017)

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Article Biochemical Research Methods

Integral membrane proteins in proteomics. How to break open the black box?

O. Vit et al.

JOURNAL OF PROTEOMICS (2017)

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Article Cell Biology

Cellular and Molecular Anatomy of the Human Neuromuscular Junction

Ross A. Jones et al.

CELL REPORTS (2017)

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Article Cell Biology

Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging

Marta Murgia et al.

CELL REPORTS (2017)

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Article Geriatrics & Gerontology

Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: a pilot study

H. Alexander Ebhardt et al.

JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE (2017)

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Article Biochemical Research Methods

Coomassie staining provides routine (sub)femtomole in-gel detection of intact proteoforms: Expanding opportunities for genuine Top-down Proteomics

Nour Noaman et al.

ELECTROPHORESIS (2017)

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Article Cell Biology

Myosin content of individual human muscle fibers isolated by laser capture microdissection

Charles A. Stuart et al.

AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY (2016)

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Review Biochemical Research Methods

Proteomic profiling of muscle fibre type shifting in neuromuscular diseases

Paul Dowling et al.

EXPERT REVIEW OF PROTEOMICS (2016)

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Review Biochemical Research Methods

With or without you - Proteomics with or without major plasma/serum proteins

Elisabetta Gianazza et al.

JOURNAL OF PROTEOMICS (2016)

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Article Biochemical Research Methods

A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing

Remi Longuespee et al.

METHODS (2016)

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Review Multidisciplinary Sciences

Mass-spectrometric exploration of proteome structure and function

Ruedi Aebersold et al.

NATURE (2016)

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Article Biochemical Research Methods

Six alternative proteases for mass spectrometry-based proteomics beyond trypsin

Piero Giansanti et al.

NATURE PROTOCOLS (2016)

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Article Biochemical Research Methods

Quantitative proteome profiling of dystrophic dog skeletal muscle reveals a stabilized muscular architecture and protection against oxidative stress after systemic delivery of MuStem cells

Aurelie Lardenois et al.

PROTEOMICS (2016)

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Review Biochemistry & Molecular Biology

2D gel-based Proteomics: there's life in the old dog yet

Reiner Westermeier

ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY (2016)

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Article Neurosciences

New insights into the protein aggregation pathology in myotilinopathy by combined proteomic and immunolocalization analyses

A. Maerkens et al.

ACTA NEUROPATHOLOGICA COMMUNICATIONS (2016)

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Review Biochemistry & Molecular Biology

Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

Sandra Murphy et al.

PROTEOMES (2016)

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Article Cell Biology

Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates

Nolan J. Hoffman et al.

CELL METABOLISM (2015)

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Review Biochemistry & Molecular Biology

Proteomics beyond trypsin

Liana Tsiatsiani et al.

FEBS JOURNAL (2015)

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Review Chemistry, Analytical

Stable isotope labelling methods in mass spectrometry-based quantitative-proteomics

Osama Chahrour et al.

JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS (2015)

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Review Biochemical Research Methods

Less is More: Membrane Protein Digestion Beyond Urea-Trypsin Solution for Next-level Proteomics

Xi Zhang

MOLECULAR & CELLULAR PROTEOMICS (2015)

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Article Biochemical Research Methods

Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors

Atul S. Deshmukh et al.

MOLECULAR & CELLULAR PROTEOMICS (2015)

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Review Biochemical Research Methods

Current approaches and challenges in targeted absolute quantification of membrane proteins

Christian Troetschel et al.

PROTEOMICS (2015)

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Article Biochemical Research Methods

The interactions between mitochondria and sarcoplasmic reticulum and the proteome characterization of mitochondrion-associated membrane from rabbit skeletal muscle

Zhouying Liu et al.

PROTEOMICS (2015)

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Review Biochemical Research Methods

State of the art of 2D DIGE

Georgia Arentz et al.

PROTEOMICS CLINICAL APPLICATIONS (2015)

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Review Sport Sciences

Mitochondrial specialization revealed by single muscle fiber proteomics: focus on the Krebs cycle

S. Schiaffino et al.

SCANDINAVIAN JOURNAL OF MEDICINE & SCIENCE IN SPORTS (2015)

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Article Multidisciplinary Sciences

Tissue-based map of the human proteome

Mathias Uhlen et al.

SCIENCE (2015)

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Article Biotechnology & Applied Microbiology

Proteomics of muscle chronological ageing in post-menopausal women

Marine Gueugneau et al.

BMC GENOMICS (2014)

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Article Biochemical Research Methods

Horizontal comparative fluorescence two-dimensional gel electrophoresis for improved spot coordinate detection

Marina Hanneken et al.

ELECTROPHORESIS (2014)

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Review Genetics & Heredity

Genomics of alternative splicing: evolution, development and pathophysiology

Eric R. Gamazon et al.

HUMAN GENETICS (2014)

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Article Medicine, Research & Experimental

Proteomic and bioinformatic analysis of differentially expressed proteins in denervated skeletal muscle

Hualin Sun et al.

INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE (2014)

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Review Biochemical Research Methods

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

Navin Rauniyar et al.

JOURNAL OF PROTEOME RESEARCH (2014)

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Article Biochemical Research Methods

2DE: The Phoenix of Proteomics

Bruno M. Oliveira et al.

JOURNAL OF PROTEOMICS (2014)

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Article Biochemical Research Methods

Label-free Quantitative Protein Profiling of vastus lateralis Muscle During Human Aging

Laetitia Theron et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

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Article Multidisciplinary Sciences

A draft map of the human proteome

Min-Sik Kim et al.

NATURE (2014)

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Article Multidisciplinary Sciences

Mass-spectrometry-based draft of the human proteome

Mathias Wilhelm et al.

NATURE (2014)

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Article Biochemical Research Methods

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

Nils A. Kulak et al.

NATURE METHODS (2014)

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Article Biochemical Research Methods

Proteomic analysis of laser capture microscopy purified myotendinous junction regions from muscle sections

Tugba Can et al.

PROTEOME SCIENCE (2014)

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Article Biochemical Research Methods

Label-free profiling of skeletal muscle using high-definition mass spectrometry

Jatin G. Burniston et al.

PROTEOMICS (2014)

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Article Biochemical Research Methods

The first pilot project of the consortium for top-down proteomics: A status report

Xibei Dang et al.

PROTEOMICS (2014)

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Review Biochemistry & Molecular Biology

Looking at proteins from two dimensions: a review on five decades of 2D electrophoresis

Reiner Westermeier

ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY (2014)

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Review Genetics & Heredity

Physicochemical mechanisms of protein regulation by phosphorylation

Hafumi Nishi et al.

FRONTIERS IN GENETICS (2014)

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Review Medicine, Research & Experimental

Proteomic identification of biomarkers of skeletal muscle disorders

Kay Ohlendieck

BIOMARKERS IN MEDICINE (2013)

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Review Biochemistry & Molecular Biology

Proteomics methods for subcellular proteome analysis

Romain Drissi et al.

FEBS JOURNAL (2013)

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Review Biochemistry & Molecular Biology

Muscle type and fiber type specificity in muscle wasting

Stefano Ciciliot et al.

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2013)

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Article Cell Biology

O-GlcNAcylation of αB-crystallin regulates its stress-induced translocation and cytoprotection

Vigneshwaran Krishnamoorthy et al.

MOLECULAR AND CELLULAR BIOCHEMISTRY (2013)

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Letter Biochemical Research Methods

Proteoform: a single term describing protein complexity

Lloyd M. Smith et al.

NATURE METHODS (2013)

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Article Multidisciplinary Sciences

Isobaric Tagging-Based Quantification for Proteomic Analysis: A Comparative Study of Spared and Affected Muscles from mdx Mice at the Early Phase of Dystrophy

Cintia Yuri Matsumura et al.

PLOS ONE (2013)

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Article Biochemical Research Methods

Shotgun proteomic analysis of sarcoplasmic reticulum preparations from rabbit skeletal muscle

Zhouying Liu et al.

PROTEOMICS (2013)

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Article Biochemistry & Molecular Biology

Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity

Zulezwan A. Malik et al.

PROTEOMES (2013)

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Review Biochemical Research Methods

A blue dive: from 'blue fingers' to 'blue silver'. A comparative overview of staining methods for in-gel proteomics

Isabella Panfoli et al.

EXPERT REVIEW OF PROTEOMICS (2012)

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Article Medicine, Research & Experimental

Mass spectrometry-based proteomic analysis of middle-aged vs. aged vastus lateralis reveals increased levels of carbonic anhydrase isoform 3 in senescent human skeletal muscle

Lisa Staunton et al.

INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE (2012)

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Article Biochemical Research Methods

Comparative Study of Workflows Optimized for In-gel, In-solution, and On-filter Proteolysis in the Analysis of Plasma Membrane Proteins

Waeowalee Choksawangkarn et al.

JOURNAL OF PROTEOME RESEARCH (2012)

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Article Biochemical Research Methods

Large-Scale Quantitative Assessment of Different In-Solution Protein Digestion Protocols Reveals Superior Cleavage Efficiency of Tandem Lys-C/Trypsin Proteolysis over Trypsin Digestion

Timo Glatter et al.

JOURNAL OF PROTEOME RESEARCH (2012)

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Article Biochemical Research Methods

Differential proteome and transcriptome analysis of porcine skeletal muscle during development

Yongjie Xu et al.

JOURNAL OF PROTEOMICS (2012)

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Article Biochemical Research Methods

On Marathons and Sprints: An Integrated Quantitative Proteomics and Transcriptomics Analysis of Differences Between Slow and Fast Muscle Fibers

Hannes C. A. Drexler et al.

MOLECULAR & CELLULAR PROTEOMICS (2012)

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Article Biochemical Research Methods

Advances in human proteomics at high scale with the SOMAscan proteomics platform

Larry Gold et al.

NEW BIOTECHNOLOGY (2012)

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Article Biochemistry & Molecular Biology

Mass Spectrometric Characterization of the Sarcoplasmic Reticulum from Rabbit Skeletal Muscle by On-membrane Digestion

Lisa Staunton et al.

PROTEIN AND PEPTIDE LETTERS (2012)

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Review Biochemical Research Methods

Affinity purification of protein complexes for analysis by multidimensional protein identification technology

Charles A. S. Banks et al.

PROTEIN EXPRESSION AND PURIFICATION (2012)

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Article Orthopedics

Protein differences between human trapezius and vastus lateralis muscles determined with a proteomic approach

Jenny Hadrevi et al.

BMC MUSCULOSKELETAL DISORDERS (2011)

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Review Biochemical Research Methods

Diversity of human skeletal muscle in health and disease: Contribution of proteomics

Cecilia Gelfi et al.

JOURNAL OF PROTEOMICS (2011)

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Article Biochemical Research Methods

Two-dimensional gel electrophoresis in proteomics: A tutorial

Thierry Rabilloud et al.

JOURNAL OF PROTEOMICS (2011)

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Review Physiology

FIBER TYPES IN MAMMALIAN SKELETAL MUSCLES

Stefano Schiaffino et al.

PHYSIOLOGICAL REVIEWS (2011)

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Article Cell Biology

Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction

Suzanne E. Mate et al.

SKELETAL MUSCLE (2011)

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Review Cell Biology

Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques

Kay Ohlendieck

SKELETAL MUSCLE (2011)

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Review Physiology

Fibre types in skeletal muscle: a personal account

S. Schiaffino

ACTA PHYSIOLOGICA (2010)

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Article Biochemical Research Methods

Mass spectrometric identification of dystrophin isoform Dp427 by on-membrane digestion of sarcolemma from skeletal muscle

Caroline Lewis et al.

ANALYTICAL BIOCHEMISTRY (2010)

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Review Biochemistry & Molecular Biology

Proteomics of skeletal muscle glycolysis

Kay Ohlendieck

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2010)

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Biochemical markers of muscular damage

Paola Brancaccio et al.

CLINICAL CHEMISTRY AND LABORATORY MEDICINE (2010)

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Review Biochemical Research Methods

Mammalian mitochondrial proteomics: insights into mitochondrial functions and mitochondria-related diseases

Xiulan Chen et al.

EXPERT REVIEW OF PROTEOMICS (2010)

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Review Cell Biology

Mass spectrometry-based proteomics in cell biology

Tobias C. Walther et al.

JOURNAL OF CELL BIOLOGY (2010)

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Article Cell Biology

Myoferlin regulation by NFAT in muscle injury, regeneration and repair

Alexis R. Demonbreun et al.

JOURNAL OF CELL SCIENCE (2010)

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Review Biochemical Research Methods

Two-dimensional gel electrophoresis in proteomics: Past, present and future

Thierry Rabilloud et al.

JOURNAL OF PROTEOMICS (2010)

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Article Biochemical Research Methods

Long term bed rest with and without vibration exercise countermeasures: Effects on human muscle protein dysregulation

Manuela Moriggi et al.

PROTEOMICS (2010)

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Review Biochemical Research Methods

Subcellular fractionation methods and strategies for proteomics

Yie Hou Lee et al.

PROTEOMICS (2010)

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Article Engineering, Biomedical

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

John R. Yates et al.

Annual Review of Biomedical Engineering (2009)

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Article Biophysics

Plasticity of the Muscle Proteome to Exercise at Altitude

Martin Flueck

HIGH ALTITUDE MEDICINE & BIOLOGY (2009)

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Article Biochemical Research Methods

Peptide Separations by On-Line MudPIT Compared to Isoelectric Focusing in an Off-Gel Format: Application to a Membrane-Enriched Fraction from C2C12 Mouse Skeletal Muscle Cells

Sarah Elschenbroich et al.

JOURNAL OF PROTEOME RESEARCH (2009)

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Article Biochemical Research Methods

Characterization of Human Skeletal Muscle Biopsy Samples Using Shotgun Proteomics

Kenneth C. Parker et al.

JOURNAL OF PROTEOME RESEARCH (2009)

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Article Biochemical Research Methods

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

Jacek R. Wisniewski et al.

JOURNAL OF PROTEOME RESEARCH (2009)

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Article Biochemical Research Methods

Universal sample preparation method for proteome analysis

Jacek R. Wisniewski et al.

NATURE METHODS (2009)

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Article Biochemical Research Methods

Native-DIGE: A new look at the mitochondrial membrane proteome

Diksha Dani et al.

Biotechnology Journal (2008)

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Article Cell Biology

Lectin-based proteomic profiling of aged skeletal muscle: Decreased pyruvate kinase isozyme M1 exhibits drastically increased levels of N-glycosylation

Kathleen O'Connell et al.

EUROPEAN JOURNAL OF CELL BIOLOGY (2008)

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Article Biochemical Research Methods

Opposite pathobiochemical fate of pyruvate kinase and adenylate kinase in aged rat skeletal muscle as revealed by proteomic DIGE analysis

Philip Doran et al.

PROTEOMICS (2008)

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Article Biochemical Research Methods

A proteome map of murine heart and skeletal muscle

Katy Raddatz et al.

PROTEOMICS (2008)

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Article Biochemical Research Methods

Characterization of the human skeletal muscle proteome by one-dimensional gel electrophoresis and HPLC-ESI-MS/MS

Kurt Hojlund et al.

MOLECULAR & CELLULAR PROTEOMICS (2008)

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Article Biochemistry & Molecular Biology

Oxidation of Prx2 and phosphorylation of GRP58 by angiotensin II in human coronary smooth muscle cells identified by 2D-DIGE analysis

Yoshiko Tokutomi et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2007)

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Review Biochemical Research Methods

Analysis and validation of proteomic data generated by tandem mass spectrometry

Alexey I. Nesvizhskii et al.

NATURE METHODS (2007)

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Article Cell Biology

Aging skeletal muscle shows a drastic increase in the small heat shock proteins αB-crystallin/HspB35 and cvHsp/HspB7

Philip Doran et al.

EUROPEAN JOURNAL OF CELL BIOLOGY (2007)

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Article Biochemical Research Methods

Proteomic profiling of chronic low-frequency stimulated fast muscle

Pamela Donoghue et al.

PROTEOMICS (2007)

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Article Biochemical Research Methods

Subcellular proteomics of mice gastrocnemius and soleus muscles

Rui Vitorino et al.

ANALYTICAL BIOCHEMISTRY (2007)

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Review Biochemical Research Methods

Phosphoproteomics strategies for the functional analysis of signal transduction

Sandra Morandell et al.

PROTEOMICS (2006)

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Article Biochemical Research Methods

The human muscle proteome in aging

Cecilia Gelfi et al.

JOURNAL OF PROTEOME RESEARCH (2006)

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Review Multidisciplinary Sciences

Review - Mass spectrometry and protein analysis

B Domon et al.

SCIENCE (2006)

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Article Biochemical Research Methods

Blue native PAGE

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NATURE PROTOCOLS (2006)

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Article Biochemical Research Methods

Laser-capture microdissection

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NATURE PROTOCOLS (2006)

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Article Biochemical Research Methods

State-of-the-art two-dimensional gel electrophoresis: a key tool of proteomics research

Odile Carrette et al.

NATURE PROTOCOLS (2006)

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Article Endocrinology & Metabolism

Increase in S6K1 phosphorylation in human skeletal muscle following resistance exercise occurs mainly in type II muscle fibers

Rene Koopman et al.

AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM (2006)

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Article Biochemical Research Methods

2-D protein maps of rat gastrocnemius and soleus muscles: A tool for muscle plasticity assessment

C Gelfi et al.

PROTEOMICS (2006)

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Article Biochemical Research Methods

Concentrations of glycolytic enzymes and other cytosolic proteins in the diffusible fraction of a vertebrate muscle proteome

DW Maughan et al.

MOLECULAR & CELLULAR PROTEOMICS (2005)

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Article Biochemical Research Methods

Proteomic analysis of slow- and fast-twitch skeletal muscles

N Okumura et al.

PROTEOMICS (2005)

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Article Biochemical Research Methods

Comparison of protein expression in human deltoideus and vastus lateralis muscles using two-dimensional gel electrophoresis

D Capitanio et al.

PROTEOMICS (2005)

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Review Biochemical Research Methods

Current two-dimensional electrophoresis technology for proteomics

A Görg et al.

PROTEOMICS (2004)

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Article Biochemical Research Methods

Mapping of bovine skeletal muscle proteins using two-dimensional gel electrophoresis and mass spectrometry

J Bouley et al.

PROTEOMICS (2004)

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Review Biotechnology & Applied Microbiology

Proteomic analysis of post-translational modifications

M Mann et al.

NATURE BIOTECHNOLOGY (2003)

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Article Physiology

Drastic reduction of calsequestrin-like proteins and impaired calcium binding in dystrophic mdx muscle

K Culligan et al.

JOURNAL OF APPLIED PHYSIOLOGY (2002)

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