Toward an Optimized Workflow for Middle-Down Proteomics

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2016 update of the PRIDE database and its related tools

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Proteoform: a single term describing protein complexity

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Protein Analysis by Shotgun/Bottom-up Proteomics

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Interpretation of Shotgun Proteomic Data

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Mobile and localized protons: a framework for understanding peptide dissociation

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Deep proteome and transcriptome mapping of a human cancer cell line

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Mapping intact protein isoforms in discovery mode using top-down proteomics

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Shotgun identification of protein modifications from protein complexes and lens tissue

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Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry

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Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome

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Top Down proteomics: Facts and perspectives

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Decoding protein modifications using top-down mass spectrometry

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Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

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Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

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Six alternative proteases for mass spectrometry–based proteomics beyond trypsin

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Electron-capture dissociation tandem mass spectrometry

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Proteomics beyond trypsin

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The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer

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Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos

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Toward Full Peptide Sequence Coverage by Dual Fragmentation Combining Electron-Transfer and Higher-Energy Collision Dissociation Tandem Mass Spectrometry

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Improvements to the Percolator Algorithm for Peptide Identification from Shotgun Proteomics Data Sets

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[21] Cleavage at glutamic acid with staphylococcal protease

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[28] Cleavage at aspartic acid

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Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini

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Middle-Down Analysis of Monoclonal Antibodies with Electron Transfer Dissociation Orbitrap Fourier Transform Mass Spectrometry

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Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)

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Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis

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The importance of silica type for reverse-phase protein separations

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The top‐down, middle‐down, and bottom‐up mass spectrometry approaches for characterization of histone variants and their post‐translational modifications

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Chemical Cleavage at Aspartyl Residues for Protein Identification

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Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase

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A protease for 'middle-down' proteomics

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What does the future hold for top down mass spectrometry?

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Extended Range Proteomic Analysis (ERPA): A New and Sensitive LC−MS Platform for High Sequence Coverage of Complex Proteins with Extensive Post-translational ModificationsComprehensive Analysis of Beta-Casein and Epidermal Growth Factor Receptor (EGFR)

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Profiling of N-Acetylated Protein Termini Provides In-depth Insights into the N-terminal Nature of the Proteome

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Confetti: A Multiprotease Map of the HeLa Proteome for Comprehensive Proteomics

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Dynamic Profiling of the Post-translational Modifications and Interaction Partners of Epidermal Growth Factor Receptor Signaling after Stimulation by Epidermal Growth Factor Using Extended Range Proteomic Analysis (ERPA)

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Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains

Valkevich, E. M., Sanchez, N. A., Ge, Y., & Strieter, E. R. (2014) · Biochemistry · doi:10.1021/bi5006305 · Cited by 89 · see citing works

Middle‐down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post‐translational modifications in histones

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Strong cation exchange (SCX) based analytical methods for the targeted analysis of protein post-translational modifications

Mohammed, S., & Heck, A. J. R. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.09.005 · Cited by 87 · see citing works

193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology

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High-Throughput Middle-Down Analysis Using an Orbitrap

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Bottom-Up and Middle-Down Proteomics Have Comparable Accuracies in Defining Histone Post-Translational Modification Relative Abundance and Stoichiometry

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Tandem Mass Spectrometry with Ultrahigh Mass Accuracy Clarifies Peptide Identification by Database Retrieval

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Toward efficient analysis of <70 kDa proteins with 100% sequence coverage

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Proteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments

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Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation

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Advantages of Extended Bottom-Up Proteomics Using Sap9 for Analysis of Monoclonal Antibodies

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Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies

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In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis

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Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage

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Characterization of neurohistone variants and post-translational modifications by electron capture dissociation mass spectrometry

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Ultratrace liquid chromatography/mass spectrometry analysis of large peptides with post-translational modifications using narrow-bore poly(styrene-divinylbenzene) monolithic columns and extended range proteomic analysis

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Ion Mobility Separation of Variant Histone Tails Extending to the “Middle-Down” Range

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Proteomic Analyses Using Grifola frondosa Metalloendoprotease Lys-N

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H-Score, a Mass Accuracy Driven Rescoring Approach for Improved Peptide Identification in Modification Rich Samples

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ZIC-cHILIC as a fractionation method for sensitive and powerful shotgun proteomics

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Rapid Microwave-Assisted Chemical Cleavage - Mass Spectrometric Method for the Identification of Hemoglobin Variants in Blood

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Mass‐biased partitioning to enhance middle down proteomics analysis

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The growing role of precision and personalized medicine for cancer treatment

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A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

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Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems

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Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

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Decoding Post-Translational Modification Crosstalk With Proteomics

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Ion Activation Methods for Peptides and Proteins

Brodbelt, J. S. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04563 · Cited by 245 · see citing works

Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling

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The Role of Electron Transfer Dissociation in Modern Proteomics

Riley, N. M., & Coon, J. J. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04810 · Cited by 180 · see citing works

Enamel proteome shows that Gigantopithecus was an early diverging pongine

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The benefits of hybrid fragmentation methods for glycoproteomics

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Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry

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Proteomes Are of Proteoforms: Embracing the Complexity

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Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research

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Ion Activation Methods for Peptides and Proteins

Macias, L. A., Santos, I. C., & Brodbelt, J. S. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b04859 · Cited by 107 · see citing works

Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry

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Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides

Cassidy, L., Kaulich, P. T., Maaß, S., Bartel, J., Becher, D., & Tholey, A. (2021) · Proteomics · doi:10.1002/pmic.202100008 · Cited by 61 · see citing works

Reactivity of metal–oxo clusters towards biomolecules: from discrete polyoxometalates to metal–organic frameworks

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Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer

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Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers

Dunphy, K., Dowling, P., Bazou, D., & O’Gorman, P. (2021) · Cancers · doi:10.3390/cancers13081930 · Cited by 74 · see citing works

Snake Venomics: Fundamentals, Recent Updates, and a Look to the Next Decade

Tan, C. H. (2022) · Toxins · doi:10.3390/toxins14040247 · Cited by 64 · see citing works

Top-down proteomics for the analysis of proteolytic events - Methods, applications and perspectives

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Top-Down Characterization of Heavily Modified Histones Using 193 nm Ultraviolet Photodissociation Mass Spectrometry

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Critical considerations in N-glycoproteomics

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Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis.

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Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides

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Miniaturized LC in Molecular Omics

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Multidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame-encoded peptides in top-down proteomics

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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives

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Proteomics in Veterinary Medicine and Animal Science: Neglected Scientific Opportunities with Immediate Impact

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A Middle-Up Approach with Online Capillary Isoelectric Focusing/Mass Spectrometry for In-Depth Characterization of Cetuximab Charge Heterogeneity

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ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping

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Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

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Mass spectrometry profiling of low molecular weight proteins and peptides isolated by acetone precipitation

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Collision energies: Optimization strategies for bottom‐up proteomics

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Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle–Down Strategy

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De novo sequencing of proteins by mass spectrometry

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Middle-Down Multi-Attribute Analysis of Antibody-Drug Conjugates with Electron Transfer Dissociation

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Bioinformatics applied to biotechnology: A review towards bioenergy research

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Small proteins in bacteria – Big challenges in prediction and identification

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Molecular insights into cancer drug resistance from a proteomics perspective

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Proteoforms expand the world of microproteins and short open reading frame-encoded peptides

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Protein isoform-centric therapeutics: expanding targets and increasing specificity

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Proteomics and Peptidomics As a Tool to Compare the Proteins and Endogenous Peptides in Human, Cow, and Donkey Milk

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Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism

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The utility of proteases in proteomics, from sequence profiling to structure and function analysis

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Proteomics-Based Identification of Dysregulated Proteins and Biomarker Discovery in Invasive Ductal Carcinoma, the Most Common Breast Cancer Subtype

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Sample Preparation for Multi‐Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow

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Expanding the Scope of Polyoxometalates as Artificial Proteases towards Hydrolysis of Insoluble Proteins

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Selective Hydrolysis of Transferrin Promoted by Zr-Substituted Polyoxometalates

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Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases

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Rapid Analysis of Reduced Antibody Drug Conjugate by Online LC-MS/MS with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

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Digital Microfluidics for Sample Preparation in Low‐Input Proteomics

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Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis

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Post-translational modification control of viral DNA sensors and innate immune signaling

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PEPPI-MS: gel-based sample pre-fractionation for deep top-down and middle-down proteomics

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Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor

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A Multiple Protease Strategy to Optimise the Shotgun Proteomics of Mature Medicinal Cannabis Buds

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Self-Assembled Protein–Surfactant Nanoaggregates for Tunable Peptide Bond Hydrolysis by Polyoxometalate Nanoclusters

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Programmable 2D Metal‐Organic Framework Nanosheets for Enzyme‐Like Hydrolysis of Large Proteins

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Origins and clinical relevance of proteoforms in pediatric malignancies

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GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics

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High-Recovery Desalting Tip Columns for a Wide Variety of Peptides in Mass Spectrometry-Based Proteomics

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Partial enzymatic reactions: A missed opportunity in proteomics research

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Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down Proteomics

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Identification of Marker Peptides for the Whey Protein Quantification in Edam-Type Cheese

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Computational approaches to identify sites of phosphorylation

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Optimal Collision Energies and Bioinformatics Tools for Efficient Bottom-up Sequence Validation of Monoclonal Antibodies

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Next-Generation Sequencing for Venomics: Application of Multi-Enzymatic Limited Digestion for Inventorying the Snake Venom Arsenal

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Targeting proline in (phospho)proteomics

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Direct seminal fluid identification by protease‐free high‐resolution mass spectrometry

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α-Active Pyrylium Salt 2,4,5-Triphenylpyrylium for Improved Mass Spectrometry-Based Detection of Peptides

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Leveraging Complementary Ion Activation Methods with Proton Transfer Charge Reduction Reactions for Comprehensive Characterization of Monoclonal Antibody Heavy Chain Subunits

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Toxicity of Atmospheric Aerosols: Methodologies & Assays

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The Enzyme Effect: Broadening the Horizon of MS Optimization to Nontryptic Digestion in Proteomics

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Mapping Cellular Polarity Networks Using Mass Spectrometry-based Strategies

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Impact of Charge State on Characterization of Large Middle-Down Sized Peptides by Tandem Mass Spectrometry

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Increased EThcD Efficiency on the Hybrid Orbitrap Excedion Pro Mass Analyzer Extends the Depth in Identification and Sequence Coverage of HLA Class I Immunopeptidomes

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Advances in protein sequencing: Techniques, challenges and prospects

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Mass spectrometry-based proteomics in forensic investigations: a focused review of LC-MS applications

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Biochemical and proteomic insights into sarcoplasmic reticulum Ca 2+ -ATPase complexes in skeletal muscles

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The Shelf Life of Milk—A Novel Concept for the Identification of Marker Peptides Using Multivariate Analysis

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Defining atherosclerotic plaque biology by mass spectrometry-based omics approaches

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Progress in Top-Down LC-MS Analysis of Antibodies: Review

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Proteomic approaches for cancer epigenetics research

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Selected Reaction Monitoring Mass Spectrometry

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Separation of multiphosphorylated cyclopeptides and their positional isomers by hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS)

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Biological Applications for LC-MS-Based Proteomics

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Lysine Propionylation To Boost Sequence Coverage and Enable a “Silent SILAC” Strategy for Relative Protein Quantification

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Mass Spectrometry-Based Proteomics: Analyses Related to Drug-Resistance and Disease Biomarkers

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Computational Approaches in Proteomics

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The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines

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Harnessing the Dynamic Nature of a Zirconium‐Oxo Nanocluster for Reversible Protein Capture and Proteolysis

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MS‐Based Glycome Characterization of Biotherapeutics With N‐ and O‐Glycosylation

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Strategies for Acid and Amine Cross-linking and Labeling for Protein Structural Characterization Using Mass Spectrometry

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Simultaneous Quantification of Apolipoprotein C-III O-Glycoforms by Protein-MRM.

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An ESI Q-TOF study to understand the impact of arginine on CID MS/MS characteristics of polypeptides

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Decoding Ubiquitin Modifications by Mass Spectrometry

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Unravelling Post-translational Modification (PTM) Complexity: Advances in Quantitative Histone Proteoform Mass Spectrometry

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Photodissociation Mass Spectrometry of Peptides and Proteins

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Practical Considerations for Improving the Productivity of Mass Spectrometry-based Proteomics

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Middle-down proteomics: the pursuit for longer peptides

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Mass‐biased partitioning to enhance middle down proteomics analysis

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GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics

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