Beyond mass spectrometry, the next step in proteomics

Errors in long-read assemblies can critically affect protein prediction

(2019) Mick Watson et al.   NATURE BIOTECHNOLOGY

Detection of Single Proteins with a General Nanopore Sensor

(2019) Qiao Li et al.   ACS Sensors

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets

(2019) Arun Devabhaktuni et al.   NATURE BIOTECHNOLOGY

Measurements of the size and correlations between ions using an electrolytic point contact

(2019) Eveline Rigo et al.   Nature Communications

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

(2019) Shilo Ohayon et al.   PLoS Computational Biology

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

(2019) Sanne Boersma et al.   CELL

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Protein Translocation through a MoS2 Nanopore:A Molecular Dynamics Study

(2018) Huang Chen et al.   Journal of Physical Chemistry C

Single-File Protein Translocations through Graphene–MoS2 Heterostructure Nanopores

(2018) Binquan Luan et al.   Journal of Physical Chemistry Letters

Protein sequencing via nanopore based devices: a nanofluidics perspective

(2018) Mauro Chinappi et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms

(2018) Matthew The et al.   JOURNAL OF PROTEOME RESEARCH

Method for Dynamically Detecting Secretions from Single Cells Using a Nanopore

(2018) Eamonn Kennedy et al.   NANO LETTERS

Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes

(2018) Daniel V Verschueren et al.   NANOTECHNOLOGY

How many human proteoforms are there?

(2018) Ruedi Aebersold et al.   Nature Chemical Biology

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

(2018) Florian Meier et al.   NATURE METHODS

Maxwell-Hall access resistance in graphene nanopores

(2018) Subin Sahu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Single-molecule peptide fingerprinting

(2018) Jetty van Ginkel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Utility of Nanopore Technology for Protein and Peptide Sensing

(2018) Joseph W. F. Robertson et al.   PROTEOMICS

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore

(2018) Fabien Piguet et al.   Nature Communications

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

(2018) Ying Zhu et al.   Nature Communications

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

(2018) Guiping Wang et al.   Scientific Reports

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

(2018) Daniel Schulz et al.   Cell Systems

Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues

(2018) Kenneth D. Birnbaum   Annual Review of Genetics

Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop

(2018) Timothy Sterne-Weiler et al.   MOLECULAR CELL

Paving the way to single-molecule protein sequencing

(2018) Laura Restrepo-Pérez et al.   Nature Nanotechnology

A low-noise silicon nitride nanopore device on a polymer substrate

(2018) Wook Choi et al.   PLoS One

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

Proteomics goes parallel

(2018) Ben C Collins et al.   NATURE BIOTECHNOLOGY

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

(2018) Jagannath Swaminathan et al.   NATURE BIOTECHNOLOGY

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

(2017) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron

(2017) Chen Zhao et al.   RNA

Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores

(2017) Gang Huang et al.   Nature Communications

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-molecule protein identification by sub-nanopore sensors

(2017) Mikhail Kolmogorov et al.   PLoS Computational Biology

Graphene Nanopores for Protein Sequencing

(2016) James Wilson et al.   ADVANCED FUNCTIONAL MATERIALS

Progress in Top-Down Proteomics and the Analysis of Proteoforms

(2016) Timothy K. Toby et al.   Annual Review of Analytical Chemistry

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

Multiple Reaction Monitoring for Direct Quantitation of Intact Proteins Using a Triple Quadrupole Mass Spectrometer

(2016) Evelyn H. Wang et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

(2016) Johannes Griss et al.   NATURE METHODS

Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores

(2016) Nicholas A. W. Bell et al.   Nature Nanotechnology

Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore

(2016) Eamonn Kennedy et al.   Nature Nanotechnology

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

(2016) Erik C. Yusko et al.   Nature Nanotechnology

The neXtProt knowledgebase on human proteins: 2017 update

(2016) Pascale Gaudet et al.   NUCLEIC ACIDS RESEARCH

Mass measurement accuracy of the Orbitrap in intact proteome analysis

(2016) Fan Yu et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

A new view of transcriptome complexity and regulation through the lens of local splicing variations

(2016) Jorge Vaquero-Garcia et al.   eLife

The Size of the Human Proteome: The Width and Depth

(2016) Elena A. Ponomarenko et al.   International Journal of Analytical Chemistry

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Detection of Individual Proteins Bound along DNA Using Solid-State Nanopores

(2015) Calin Plesa et al.   NANO LETTERS

Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation

(2015) Miao Zhang et al.   NANOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Top-Down Proteomics: Turning Protein Mass Spec Upside-Down

(2015) Jeffrey M. Perkel   SCIENCE

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Discrimination among Protein Variants Using an Unfoldase-Coupled Nanopore

(2014) Jeff Nivala et al.   ACS Nano

Top Down proteomics: Facts and perspectives

(2014) Adam D. Catherman et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Mass spectrometry-based protein identification with accurate statistical significance assignment

(2014) Gelio Alves et al.   BIOINFORMATICS

High-Bandwidth Protein Analysis Using Solid-State Nanopores

(2014) Joseph Larkin et al.   BIOPHYSICAL JOURNAL

Communication: Charge, diffusion, and mobility of proteins through nanopores

(2014) M. Muthukumar   JOURNAL OF CHEMICAL PHYSICS

Improving Signal-to-Noise Performance for DNA Translocation in Solid-State Nanopores at MHz Bandwidths

(2014) Adrian Balan et al.   NANO LETTERS

Probing the size of proteins with glass nanopores

(2014) L. J. Steinbock et al.   Nanoscale

Single-molecule site-specific detection of protein phosphorylation with a nanopore

(2014) Christian B Rosen et al.   NATURE BIOTECHNOLOGY

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Low-Noise Solid-State Nanopore Platform Based on a Highly Insulating Substrate

(2014) Min-Hyun Lee et al.   Scientific Reports

Direct Visualization of Single-Molecule Translocations through Synthetic Nanopores Comparable in Size to a Molecule

(2013) Volker Kurz et al.   ACS Nano

Methodologies to decipher the cell secretome

(2013) Paromita Mukherjee et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

Node-pore sensing: a robust, high-dynamic range method for detecting biological species

(2013) Karthik R. Balakrishnan et al.   LAB ON A CHIP

Fast Translocation of Proteins through Solid State Nanopores

(2013) Calin Plesa et al.   NANO LETTERS

Integration of solid-state nanopores in a 0.5 μm CMOS foundry process

(2013) A Uddin et al.   NANOTECHNOLOGY

Unfoldase-mediated protein translocation through an α-hemolysin nanopore

(2013) Jeff Nivala et al.   NATURE BIOTECHNOLOGY

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

Multistep protein unfolding during nanopore translocation

(2013) David Rodriguez-Larrea et al.   Nature Nanotechnology

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The emergence of top-down proteomics in clinical research

(2013) John P Savaryn et al.   Genome Medicine

Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription

(2013) Igor D Vilfan et al.   JOURNAL OF NANOBIOTECHNOLOGY

Wild Type, Mutant Protein Unfolding and Phase Transition Detected by Single-Nanopore Recording

(2012) Céline Merstorf et al.   ACS Chemical Biology

Protein Transport through a Narrow Solid-State Nanopore at High Voltage: Experiments and Theory

(2012) Benjamin Cressiot et al.   ACS Nano

Using a nanopore for single molecule detection and single cell transfection

(2012) Edward M. Nelson et al.   ANALYST

Mass spectrometry-based proteomics: existing capabilities and future directions

(2012) Thomas E. Angel et al.   CHEMICAL SOCIETY REVIEWS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrated nanopore sensing platform with sub-microsecond temporal resolution

(2012) Jacob K Rosenstein et al.   NATURE METHODS

Stochastic sensing of proteins with receptor-modified solid-state nanopores

(2012) Ruoshan Wei et al.   Nature Nanotechnology

Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

(2012) Peter Smibert et al.   Cell Reports

Chemical, Thermal, and Electric Field Induced Unfolding of Single Protein Molecules Studied Using Nanopores

(2011) Kevin J. Freedman et al.   ANALYTICAL CHEMISTRY

Assigning spectrum-specific P-values to protein identifications by mass spectrometry

(2011) Victor Spirin et al.   BIOINFORMATICS

Comprehensive Analysis of Protein Modifications by Top-Down Mass Spectrometry

(2011) Han Zhang et al.   Circulation-Cardiovascular Genetics

Simultaneous and Extensive Site-specific N- and O-Glycosylation Analysis in Protein Mixtures

(2011) Charles C. Nwosu et al.   JOURNAL OF PROTEOME RESEARCH

Effects of particle's off-axis position, shape, orientation and entry position on resistance changes of micro Coulter counting devices

(2011) Zhenpeng Qin et al.   MEASUREMENT SCIENCE and TECHNOLOGY

Advances in resistive pulse sensors: Devices bridging the void between molecular and microscopic detection

(2011) Darby Kozak et al.   Nano Today

Nanopores in solid-state membranes engineered for single molecule detection

(2010) V Dimitrov et al.   NANOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy

(2009) Harold P. Erickson   BIOLOGICAL PROCEDURES ONLINE

Correlations between RNA and protein expression profiles in 23 human cell lines

(2009) Marcus Gry et al.   BMC GENOMICS

Determination of glycosylation sites and site-specific heterogeneity in glycoproteins

(2009) Hyun Joo An et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Automated de novo protein sequencing of monoclonal antibodies

(2008) Nuno Bandeira et al.   NATURE BIOTECHNOLOGY

Noise in solid-state nanopores

(2008) R. M. M. Smeets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor

(2007) Grigori Sigalov et al.   NANO LETTERS