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

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Mass Spectrometry and Protein Analysis

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Evolution-assisted engineering of formate assimilation via the formyl phosphate route in Escherichia coli

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Comprehensive proteome analysis of fresh frozen and optimal cutting temperature (OCT) embedded primary non-small cell lung carcinoma by LC–MS/MS

inferred← citeshttps://doi.org/10.1016/j.ymeth.2015.04.032openalex-snapshot

Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry

inferred← citeshttps://doi.org/10.1016/j.ymeth.2015.06.005openalex-snapshot

Analysis of protein–RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry

inferred← citeshttps://doi.org/10.1016/s1872-2040(17)60998-8openalex-snapshot

Evaluation of Endoproteinase Lys-C/Trypsin Sequential Digestion Used in Proteomics Sample Preparation

inferred← citeshttps://doi.org/10.1021/ac402696bopenalex-snapshot

Dual Matrix-Based Immobilized Trypsin for Complementary Proteolytic Digestion and Fast Proteomics Analysis with Higher Protein Sequence Coverage

inferred← citeshttps://doi.org/10.1021/ac4027274openalex-snapshot

Quantitative Bottom-Up Proteomics Depends on Digestion Conditions

inferred← citeshttps://doi.org/10.1021/acs.analchem.0c03107openalex-snapshot

Development and Comparative Evaluation of Endolysosomal Proximity Labeling-Based Proteomic Methods in Human iPSC-Derived Neurons

inferred← citeshttps://doi.org/10.1021/acs.analchem.5b01215openalex-snapshot

Homogenous Phase Enrichment of Cysteine-Containing Peptides for Improved Proteome Coverage

inferred← citeshttps://doi.org/10.1021/acs.analchem.5b04123openalex-snapshot

Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

inferred← citeshttps://doi.org/10.1021/acs.analchem.6b00859openalex-snapshot

Quantitative Evaluation of Filter Aided Sample Preparation (FASP) and Multienzyme Digestion FASP Protocols

inferred← citeshttps://doi.org/10.1021/acs.analchem.6b04804openalex-snapshot

Large-Scale Filter-Aided Sample Preparation Method for the Analysis of the Ubiquitinome

inferred← citeshttps://doi.org/10.1021/acs.analchem.7b04410openalex-snapshot

Reversible Lysine Derivatization Enabling Improved Arg-C Digestion, a Highly Specific Arg-C Digestion Using Trypsin

inferred← citeshttps://doi.org/10.1021/acs.analchem.8b00661openalex-snapshot

Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis

inferred← citeshttps://doi.org/10.1021/acs.analchem.8b02448openalex-snapshot

Lys-C/Arg-C, a More Specific and Efficient Digestion Approach for Proteomics Studies

inferred← citeshttps://doi.org/10.1021/acs.analchem.9b03993openalex-snapshot

In-Line Sample Processing System with an Immobilized Trypsin-Packed Fused-Silica Capillary Tube for the Proteomic Analysis of a Small Number of Mammalian Cells

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00035openalex-snapshot

Optimization of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00578openalex-snapshot

Identification of Cytosolic Protein Targets of Catechol Estrogens in Breast Cancer Cells Using a Click Chemistry-Based Workflow

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00681openalex-snapshot

Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00890openalex-snapshot

Simple and Efficient Microsolid-Phase Extraction Tip-Based Sample Preparation Workflow to Enable Sensitive Proteomic Profiling of Limited Samples (200 to 10,000 Cells)

inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00265openalex-snapshot

In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods

inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00838openalex-snapshot

An Introduction to Mass Spectrometry-Based Proteomics

inferred← citeshttps://doi.org/10.1021/acs.jproteome.3c00135openalex-snapshot

ProtView: A Versatile Tool for In Silico Protease Evaluation and Selection in a Proteomic and Proteogenomic Context

inferred← citeshttps://doi.org/10.1021/acs.jproteome.4c00062openalex-snapshot

Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples

inferred← citeshttps://doi.org/10.1021/acs.jproteome.5b00236openalex-snapshot

Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence

inferred← citeshttps://doi.org/10.1021/acs.jproteome.5b00480openalex-snapshot

Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria

inferred← citeshttps://doi.org/10.1021/acs.jproteome.5b00654openalex-snapshot

Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells

inferred← citeshttps://doi.org/10.1021/acs.jproteome.5b00988openalex-snapshot

RePLiCal: A QconCAT Protein for Retention Time Standardization in Proteomics Studies

inferred← citeshttps://doi.org/10.1021/acs.jproteome.5c00572openalex-snapshot

Impact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics

inferred← citeshttps://doi.org/10.1021/acs.jproteome.5c00872openalex-snapshot

Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00048openalex-snapshot

Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00066openalex-snapshot

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00348openalex-snapshot

Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves

inferred← citeshttps://doi.org/10.1021/acs.jproteome.8b00216openalex-snapshot

Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2

inferred← citeshttps://doi.org/10.1021/acs.jproteome.8b00228openalex-snapshot

Quantitative Assessment of Urea In-Solution Lys-C/Trypsin Digestions Reveals Superior Performance at Room Temperature over Traditional Proteolysis at 37 °C

inferred← citeshttps://doi.org/10.1021/acs.jproteome.8b00620openalex-snapshot

Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Based Proteomics Method

inferred← citeshttps://doi.org/10.1021/acs.jproteome.9b00217openalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/acs.jproteome.9b00628openalex-snapshot

A Serial Sample Processing Strategy with Improved Performance for in-Depth Quantitative Analysis of Type III Secretion Events in Pseudomonas aeruginosa

inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.6b00033openalex-snapshot

Secreted Matrix Metalloproteinase-9 of Proliferating Smooth Muscle Cells as a Trigger for Drug Release from Stent Surface Polymers in Coronary Arteries

inferred← citeshttps://doi.org/10.1021/acs.nanolett.7b02886openalex-snapshot

Biomimetic Strategy To Reversibly Trigger Functionality of Catalytic Nanocompartments by the Insertion of pH-Responsive Biovalves

inferred← citeshttps://doi.org/10.1021/acs.orglett.4c03452openalex-snapshot

Fast and Selective Cysteine Conjugation Using para-Quinone Methides

inferred← citeshttps://doi.org/10.1021/acsmeasuresciau.3c00068openalex-snapshot

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

inferred← citeshttps://doi.org/10.1021/acsomega.4c11373openalex-snapshot

Refinement of Protein Extraction Protocols for Human Peripheral Nerve Tissue

inferred← citeshttps://doi.org/10.1021/acsomega.6c01140openalex-snapshot

Optimization of the Quantum-Si Platinum Single-Molecule Protein Sequencing Platform Toward Improved Complex-Matrix Protein Identification

inferred← citeshttps://doi.org/10.1021/acsomega.6c05628openalex-snapshot

Development of a Shapley Additive Explanations (SHAP)-Interpretable Model for Cardiovascular Risk Stratification in Type 2 Diabetes Mellitus: Implications of MDA-Modified Protein Adducts and Autoantibodies

inferred← citeshttps://doi.org/10.1021/acssynbio.2c00164openalex-snapshot

An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria

inferred← citeshttps://doi.org/10.1021/acssynbio.6b00282openalex-snapshot

Measurement of In Vivo Protein Binding Affinities in a Signaling Network with Mass Spectrometry

inferred← citeshttps://doi.org/10.1021/pr301012jopenalex-snapshot

The State of the Human Proteome in 2012 as Viewed through PeptideAtlas

inferred← citeshttps://doi.org/10.1021/pr3011414openalex-snapshot

Multiple Reaction Monitoring of Multiple Low-Abundance Transcription Factors in Whole Lung Cancer Cell Lysates

inferred← citeshttps://doi.org/10.1021/pr400611hopenalex-snapshot

Comprehensive Analysis of Protein Digestion Using Six Trypsins Reveals the Origin of Trypsin As a Significant Source of Variability in Proteomics

inferred← citeshttps://doi.org/10.1021/pr400743aopenalex-snapshot

Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging for Peptide and Protein Analyses: A Critical Review of On-Tissue Digestion

inferred← citeshttps://doi.org/10.1021/pr500294dopenalex-snapshot

Influence of the Digestion Technique, Protease, and Missed Cleavage Peptides in Protein Quantitation

inferred← citeshttps://doi.org/10.1021/pr500764eopenalex-snapshot

Protein Quantification Using a Cleavable Reporter Peptide

inferred← citeshttps://doi.org/10.1021/pr500834zopenalex-snapshot

DIGESTIF : A Universal Quality Standard for the Control of Bottom-Up Proteomics Experiments

inferred← citeshttps://doi.org/10.1021/pr500860copenalex-snapshot

Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites

inferred← citeshttps://doi.org/10.1021/pr500903bopenalex-snapshot

Evaluation of the Effect of Trypsin Digestion Buffers on Artificial Deamidation

inferred← citeshttps://doi.org/10.1021/pr5011179openalex-snapshot

Quantifying Protein Measurands by Peptide Measurements: Where Do Errors Arise?

inferred← citeshttps://doi.org/10.1038/cdd.2015.39openalex-snapshot

Synaptic dysfunction, memory deficits and hippocampal atrophy due to ablation of mitochondrial fission in adult forebrain neurons

inferred← citeshttps://doi.org/10.1038/nbt.2999openalex-snapshot

Global analysis of protein structural changes in complex proteomes

inferred← citeshttps://doi.org/10.1038/nbt.3418openalex-snapshot

The quantitative and condition-dependent Escherichia coli proteome

inferred← citeshttps://doi.org/10.1038/ncomms12467openalex-snapshot

Subcompartmentalization by cross-membranes during early growth of Streptomyces hyphae

inferred← citeshttps://doi.org/10.1038/nm.3807openalex-snapshot

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

inferred← citeshttps://doi.org/10.1038/nmicrobiol.2016.184openalex-snapshot

LadS is a calcium-responsive kinase that induces acute-to-chronic virulence switch in Pseudomonas aeruginosa

inferred← citeshttps://doi.org/10.1038/nprot.2013.120openalex-snapshot

Large-scale identification of ubiquitination sites by mass spectrometry

inferred← citeshttps://doi.org/10.1038/nprot.2014.052openalex-snapshot

Selective chemoprecipitation to enrich nitropeptides from complex proteomes for mass-spectrometric analysis

inferred← citeshttps://doi.org/10.1038/nprot.2015.062openalex-snapshot

Global, in situ, site-specific analysis of protein S-sulfenylation

inferred← citeshttps://doi.org/10.1038/nprot.2017.100openalex-snapshot

Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry

inferred← citeshttps://doi.org/10.1038/s41467-018-03511-6openalex-snapshot

Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes

inferred← citeshttps://doi.org/10.1038/s41467-019-13021-8openalex-snapshot

Quorum sensing modulates the formation of virulent Legionella persisters within infected cells

inferred← citeshttps://doi.org/10.1038/s41467-022-28141-xopenalex-snapshot

Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis

inferred← citeshttps://doi.org/10.1038/s41467-022-29960-8openalex-snapshot

Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages

inferred← citeshttps://doi.org/10.1038/s41467-023-44509-zopenalex-snapshot

The virulence regulator VirB from Shigella flexneri uses a CTP-dependent switch mechanism to activate gene expression

inferred← citeshttps://doi.org/10.1038/s41467-024-50444-4openalex-snapshot

A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis

inferred← citeshttps://doi.org/10.1038/s41467-024-51035-zopenalex-snapshot

DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3’-end of genes and involved in the recycling of cleavage factors

inferred← citeshttps://doi.org/10.1038/s41467-024-51702-1openalex-snapshot

Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community

inferred← citeshttps://doi.org/10.1038/s41467-024-53156-xopenalex-snapshot

Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies

showing the first 200 of 367

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