4.8 Article

The emerging landscape of single-molecule protein sequencing technologies

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biophysics

Single-aminoacid discrimination in proteins with homogeneous nanopore sensors and neural networks

David Rodriguez-Larrea

Summary: The study demonstrates the use of simple neural networks to identify protein mutants, with poor generalization ability. By utilizing a thermal annealing protocol and examining multiple mutants in repeated experiments, the generalizability of the neural network can be improved.

BIOSENSORS & BIOELECTRONICS (2021)

Article Chemistry, Multidisciplinary

High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)

Mike Filius et al.

Summary: The research team introduced a new method that allows for determining multiple distances between FRET pairs in a single object by resolving the FRET efficiency of multiple fluorophore pairs through transient binding of short DNA strands. This FRET X technology is expected to be a tool for high-resolution analysis of biomolecules and nanostructures.

NANO LETTERS (2021)

Review Biochemical Research Methods

Proteoform characterization based on top-down mass spectrometry

Jiancheng Zhong et al.

Summary: Proteins play a crucial role in living processes, and changes in their molecular structure are closely tied to disease pathology. Mass spectrometry enables the characterization of proteoforms, but faces various challenges that require the use of different methods and algorithms for optimization.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Chemistry, Multidisciplinary

Engineering an Enzyme for Direct Electrical Monitoring of Activity

Bintian Zhang et al.

ACS NANO (2020)

Article Biochemical Research Methods

Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry

Jared O. Kafader et al.

JOURNAL OF PROTEOME RESEARCH (2020)

Article Biotechnology & Applied Microbiology

Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore

Hadjer Ouldali et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes

Jared O. Kafader et al.

NATURE METHODS (2020)

Article Biochemistry & Molecular Biology

Solid-Phase Peptide Capture and Release for Bulk and Single-Molecule Proteomics

Cecil J. Howard et al.

ACS CHEMICAL BIOLOGY (2020)

Article Chemistry, Multidisciplinary

Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores

Gang Huang et al.

NANO LETTERS (2020)

Review Biotechnology & Applied Microbiology

Leveraging nature's biomolecular designs in next-generation protein sequencing reagent development

Jennifer Tullman et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2020)

Review Biochemical Research Methods

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

Claudio Iacobucci et al.

CURRENT OPINION IN BIOTECHNOLOGY (2020)

Article Chemistry, Multidisciplinary

Quantification of mRNA Expression Using Single-Molecule Nanopore Sensing

Yana Rozevsky et al.

ACS NANO (2020)

Article Chemistry, Multidisciplinary

Ultrasensitive Detection of Attomolar Protein Concentrations by Dropcast Single Molecule Assays

Connie Wu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Review Biochemical Research Methods

Single-cell Proteomics: Progress and Prospects

Ryan T. Kelly

MOLECULAR & CELLULAR PROTEOMICS (2020)

Article Multidisciplinary Sciences

Computational assessment of the feasibility of protonation-based protein sequencing

Giles Miclotte et al.

PLOS ONE (2020)

Article Multidisciplinary Sciences

On-chip protein separation with single-molecule resolution

Adam Zrehen et al.

SCIENTIFIC REPORTS (2020)

Article Engineering, Biomedical

Ultrasensitive high-resolution profiling of early seroconversion in patients with COVID-19

Maia Norman et al.

NATURE BIOMEDICAL ENGINEERING (2020)

Article Biology

Free-energy landscapes of membrane co-translocational protein unfolding

Christian Bech Rosen et al.

COMMUNICATIONS BIOLOGY (2020)

Article Multidisciplinary Sciences

A theoretical analysis of single molecule protein sequencing via weak binding spectra

Samuel G. Rodriques et al.

PLOS ONE (2019)

Article Chemistry, Multidisciplinary

Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model

James Wilson et al.

ACS SENSORS (2019)

Article Chemistry, Multidisciplinary

Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection

Joshua D. Spitzberg et al.

ADVANCED MATERIALS (2019)

Article Chemistry, Multidisciplinary

Bioinspired Thiophosphorodichloridate Reagents for Chemoselective Histidine Bioconjugation

Shang Jia et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Biochemical Research Methods

Proteomic navigation using proximity-labeling

Marc Gentzel et al.

METHODS (2019)

Article Biochemical Research Methods

Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification

Shilo Ohayon et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Chemistry, Multidisciplinary

A Physical Organic Approach to Tuning Reagents for Selective and Stable Methionine Bioconjugation

Alec H. Christian et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Nanoscience & Nanotechnology

Localized detection of ions and biomolecules with a force-controlled scanning nanopore microscope

Morteza Aramesh et al.

NATURE NANOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations

Giovanni Di Muccio et al.

SCIENTIFIC REPORTS (2019)

Article Chemistry, Multidisciplinary

Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore

Laura Restrepo-Perez et al.

ACS NANO (2019)

Editorial Material Biochemical Research Methods

A dream of single-cell proteomics

Vivien Marx

NATURE METHODS (2019)

Article Chemistry, Multidisciplinary

Label-Free Detection of Post-translational Modifications with a Nanopore

Laura Restrepo-Perez et al.

NANO LETTERS (2019)

Article Multidisciplinary Sciences

Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores

Chan Cao et al.

NATURE COMMUNICATIONS (2019)

Article Chemistry, Analytical

Measurement of Individual Ions Sharply Increases the Resolution of Orbitrap Mass Spectra of Proteins

Jared O. Kafader et al.

ANALYTICAL CHEMISTRY (2019)

Article Biotechnology & Applied Microbiology

Engineering ClpS for selective and enhanced N-terminal amino acid binding

Jennifer Tullman et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2019)

Article Chemistry, Physical

Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores

Daniel Verschueren et al.

SMALL METHODS (2019)

Review Chemistry, Multidisciplinary

The challenges of glycan recognition with natural and artificial receptors

Stefano Tommasone et al.

CHEMICAL SOCIETY REVIEWS (2019)

Article Chemistry, Multidisciplinary

Programmable autonomous synthesis of single-stranded DNA

Jocelyn Y. Kishi et al.

NATURE CHEMISTRY (2018)

Review Nanoscience & Nanotechnology

DNA nanotechnology

Nadrian C. Seeman et al.

NATURE REVIEWS MATERIALS (2018)

Article Chemistry, Multidisciplinary

Differential Enzyme Flexibility Probed Using Solid-State Nanopores

Rui Hu et al.

ACS NANO (2018)

Article Chemistry, Multidisciplinary

Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS

Ying Zhu et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Review Physiology

Mechanical Protein Unfolding and Degradation

Adrian O. Olivares et al.

ANNUAL REVIEW OF PHYSIOLOGY, VOL 80 (2018)

Article Biochemistry & Molecular Biology

Driving Forces of Translocation Through Bacterial Translocon SecYEG

Denis G. Knyazev et al.

JOURNAL OF MEMBRANE BIOLOGY (2018)

Article Chemistry, Multidisciplinary

A Solid-State Hard Microfluidic Nanopore Biosensor with Multilayer Fluidics and On-Chip Bioassay/Purification Chamber

Nitinun Varongchayakul et al.

ADVANCED FUNCTIONAL MATERIALS (2018)

Article Multidisciplinary Sciences

A protein functionalization platform based on selective reactions at methionine residues

Michael T. Taylor et al.

NATURE (2018)

Article Biotechnology & Applied Microbiology

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

Jagannath Swaminathan et al.

NATURE BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators

Sergio Dominguez-Medina et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

Direct electrical quantification of glucose and asparagine from bodily fluids using nanopores

Nicole Stephanie Galenkamp et al.

NATURE COMMUNICATIONS (2018)

Article Chemistry, Multidisciplinary

Light-Enhancing Plasmonic-Nanopore Biosensor for Superior Single-Molecule Detection

Ossama N. Assad et al.

ADVANCED MATERIALS (2017)

Review Spectroscopy

SINGLE-MOLECULE MASS SPECTROMETRY

David Z. Keifer et al.

MASS SPECTROMETRY REVIEWS (2017)

Article Nanoscience & Nanotechnology

Real-time shape approximation and fingerprinting of single proteins using a nanopore

Erik C. Yusko et al.

NATURE NANOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

Targeting the N terminus for site-selective protein modification

Christian B. Rosen et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Biochemical Research Methods

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics

Andy T. Kong et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Super-resolution microscopy with DNA-PAINT

Joerg Schnitzbauer et al.

NATURE PROTOCOLS (2017)

Article Instruments & Instrumentation

The nanopore mass spectrometer

Joseph Bush et al.

REVIEW OF SCIENTIFIC INSTRUMENTS (2017)

Article Multidisciplinary Sciences

Redox-based reagents for chemoselective methionine bioconjugation

Shixian Lin et al.

SCIENCE (2017)

Article Multidisciplinary Sciences

A DNA nanoscope via auto-cycling proximity recording

Thomas E. Schaus et al.

NATURE COMMUNICATIONS (2017)

Article Multidisciplinary Sciences

YidC and SecYEG form a heterotetrameric protein translocation channel

Ilie Sachelaru et al.

SCIENTIFIC REPORTS (2017)

Article Nanoscience & Nanotechnology

Observation of giant conductance fluctuations in a protein

Bintian Zhang et al.

NANO FUTURES (2017)

Article Chemistry, Multidisciplinary

Label-Free and Real-Time Detection of Protein Ubiquitination with a Biological Nanopore

Carsten Wloka et al.

ACS NANO (2017)

Article Chemistry, Multidisciplinary

Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes

Pradeep Waduge et al.

ACS NANO (2017)

Review Biochemistry & Molecular Biology

Protein Translocation into the Intermembrane Space and Matrix of Mitochondria: Mechanisms and Driving Forces

Sandra Backes et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2017)

Article Biochemical Research Methods

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

Kelly V. Ruggles et al.

MOLECULAR & CELLULAR PROTEOMICS (2016)

Article Chemistry, Analytical

Progress in Top-Down Proteomics and the Analysis of Proteoforms

Timothy K. Toby et al.

ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 9 (2016)

Article Biochemistry & Molecular Biology

Single-molecule fluorescence microscopy of native macromolecular complexes

Vasudha Aggarwal et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)

Review Biochemistry & Molecular Biology

Oxime conjugation in protein chemistry: from carbonyl incorporation to nucleophilic catalysis

Stijn M. Agten et al.

JOURNAL OF PEPTIDE SCIENCE (2016)

Article Biotechnology & Applied Microbiology

Three decades of nanopore sequencing

David Deamer et al.

NATURE BIOTECHNOLOGY (2016)

Article Biochemical Research Methods

Quantitative super-resolution imaging with qPAINT

Ralf Jungmann et al.

NATURE METHODS (2016)

Article Nanoscience & Nanotechnology

Optical imaging of individual biomolecules in densely packed clusters

Mingjie Dai et al.

NATURE NANOTECHNOLOGY (2016)

Article Chemistry, Multidisciplinary

Fast and selective labeling of N-terminal cysteines at neutral pH via thiazolidino boronate formation

Anupam Bandyopadhyay et al.

CHEMICAL SCIENCE (2016)

Article Mathematical & Computational Biology

The UniProtKB guide to the human proteome

Lionel Breuza et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)

Article Physics, Applied

Preserving the Sequence of a Biopolymer's Monomers as They Enter an Electrospray Mass Spectrometer

William Maulbetsch et al.

PHYSICAL REVIEW APPLIED (2016)

Article Chemistry, Multidisciplinary

Single-Molecule Analyte Recognition with ClyA Nanopores Equipped with Internal Protein Adaptors

Misha Soskine et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Biochemistry & Molecular Biology

One-step site-specific modification of native proteins with 2-pyridinecarboxyaldehydes

James I. MacDonald et al.

NATURE CHEMICAL BIOLOGY (2015)

Editorial Material Biochemical Research Methods

Successful test launch for nanopore sequencing

Nicholas J. Loman et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry

Fan Liu et al.

NATURE METHODS (2015)

Article Nanoscience & Nanotechnology

Inertial imaging with nanomechanical systems

M. Selim Hanay et al.

NATURE NANOTECHNOLOGY (2015)

Article Multidisciplinary Sciences

Neutral particle mass spectrometry with nanomechanical systems

Eric Sage et al.

NATURE COMMUNICATIONS (2015)

Article Biochemical Research Methods

A Theoretical Justification for Single Molecule Peptide Sequencing

Jagannath Swaminathan et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Single-molecule protein sequencing through fingerprinting: computational assessment

Yao Yao et al.

PHYSICAL BIOLOGY (2015)

Article Chemistry, Multidisciplinary

Discrimination among Protein Variants Using an Unfoldase-Coupled Nanopore

Jeff Nivala et al.

ACS NANO (2014)

Article Biophysics

High-Bandwidth Protein Analysis Using Solid-State Nanopores

Joseph Larkin et al.

BIOPHYSICAL JOURNAL (2014)

Review Chemistry, Multidisciplinary

Photodissociation mass spectrometry: new tools for characterization of biological molecules

Jennifer S. Brodbelt

CHEMICAL SOCIETY REVIEWS (2014)

Article Nanoscience & Nanotechnology

Detection of post-translational modifications in single peptides using electron tunnelling currents

Takahito Ohshiro et al.

NATURE NANOTECHNOLOGY (2014)

Article Nanoscience & Nanotechnology

Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

Yanan Zhao et al.

NATURE NANOTECHNOLOGY (2014)

Article Chemistry, Multidisciplinary

Fast Translocation of Proteins through Solid State Nanopores

Calin Plesa et al.

NANO LETTERS (2013)

Article Biotechnology & Applied Microbiology

Unfoldase-mediated protein translocation through an α-hemolysin nanopore

Jeff Nivala et al.

NATURE BIOTECHNOLOGY (2013)

Letter Biochemical Research Methods

Proteoform: a single term describing protein complexity

Lloyd M. Smith et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

Improving the Selectivity of the Phosphoric Acid β-Elimination on a Biotinylated Phosphopeptide

Lucrece Matheron et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2012)

Article Chemistry, Multidisciplinary

Optical Trapping of a Single Protein

Yuanjie Pang et al.

NANO LETTERS (2012)

Article Biochemical Research Methods

High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies

Rebecca J. Rose et al.

NATURE METHODS (2012)

Article Nanoscience & Nanotechnology

A nanomechanical mass sensor with yoctogram resolution

J. Chaste et al.

NATURE NANOTECHNOLOGY (2012)

Article Nanoscience & Nanotechnology

Single-protein nanomechanical mass spectrometry in real time

M. S. Hanay et al.

NATURE NANOTECHNOLOGY (2012)

Review Microbiology

The type II secretion system: biogenesis, molecular architecture and mechanism

Konstantin V. Korotkov et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Review Biochemical Research Methods

Affinity-purification coupled to mass spectrometry: Basic principles and strategies

Wade H. Dunham et al.

PROTEOMICS (2012)

Article Nanoscience & Nanotechnology

Controlling protein translocation through nanopores with bio-inspired fluid walls

Erik C. Yusko et al.

NATURE NANOTECHNOLOGY (2011)

Article Chemistry, Multidisciplinary

Tyrosine Bioconjugation through Aqueous Ene-Type Reactions: A Click-Like Reaction for Tyrosine

Hitoshi Ban et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Biotechnology & Applied Microbiology

Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations

David M. Rissin et al.

NATURE BIOTECHNOLOGY (2010)

Review Biochemistry & Molecular Biology

Metabolic glycoengineering: Sialic acid and beyond

Jian Du et al.

GLYCOBIOLOGY (2009)

Article Biochemical Research Methods

Dynamics of Ions of Intact Proteins in the Orbitrap Mass Analyzer

Alexander Makarov et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2009)

Article Nanoscience & Nanotechnology

Tunnelling readout of hydrogen-bonding-based recognition

Shuai Chang et al.

NATURE NANOTECHNOLOGY (2009)

Article Chemistry, Multidisciplinary

Specific N-terminal protein labelling: use of FMDV 3C(pro) protease and native chemical ligation

Gillian K. Busch et al.

CHEMICAL COMMUNICATIONS (2008)

Article Biochemical Research Methods

Efficiency of nano-electrospray ionization

A El-Faramawy et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2005)

Review Cell Biology

The ABC's (and XYZ's) of peptide sequencing

H Steen et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2004)

Article Biochemical Research Methods

Unimod: Protein modifications for mass spectrometry

DM Creasy et al.

PROTEOMICS (2004)

Article Physics, Applied

Ultrasensitive nanoelectromechanical mass detection

KL Ekinci et al.

APPLIED PHYSICS LETTERS (2004)