Global detection of human variants and isoforms by deep proteome sequencing

Uncovering the impacts of alternative splicing on the proteome with current omics techniques

(2022) Marina Reixachs‐Solé et al.   Wiley Interdisciplinary Reviews-RNA

Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes

(2022) Alicia L. Richards et al.   JOURNAL OF PROTEOME RESEARCH

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

(2022) Simon A. Hardwick et al.   NATURE BIOTECHNOLOGY

Prediction of peptide mass spectral libraries with machine learning

(2022) Jürgen Cox   NATURE BIOTECHNOLOGY

Identifying individuals using proteomics: are we there yet?

(2022) Ivo Fierro-Monti et al.   Frontiers in Molecular Biosciences

Ethical Principles, Constraints and Opportunities in Clinical Proteomics

(2021) Sebastian Porsdam Mann et al.   MOLECULAR & CELLULAR PROTEOMICS

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

(2021) Anoushka Joglekar et al.   Nature Communications

The Human Proteoform Project: Defining the human proteome

(2021) Lloyd M. Smith et al.   Science Advances

Proteomics Using Protease Alternatives to Trypsin Benefits from Sequential Digestion with Trypsin

(2020) Therese Dau et al.   ANALYTICAL CHEMISTRY

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

(2020) Gilbert S. Omenn et al.   JOURNAL OF PROTEOME RESEARCH

A high-stringency blueprint of the human proteome

(2020) Subash Adhikari et al.   Nature Communications

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Dongxue Wang et al.   Molecular Systems Biology

Interactive Peptide Spectral Annotator: A Versatile Web-Based Tool for Proteomic Applications

(2019) Dain R. Brademan et al.   MOLECULAR & CELLULAR PROTEOMICS

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

(2019) Shivani Tiwary et al.   NATURE METHODS

Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data

(2019) Rachel M. Miller et al.   JOURNAL OF PROTEOME RESEARCH

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

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

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

Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity

(2017) Xiaojing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

The Relationship between Alternative Splicing and Proteomic Complexity

(2017) Benjamin J. Blencowe   TRENDS IN BIOCHEMICAL SCIENCES

Alternative Splicing May Not Be the Key to Proteome Complexity

(2017) Michael L. Tress et al.   TRENDS IN BIOCHEMICAL SCIENCES

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

(2017) Dorte B. Bekker-Jensen et al.   Cell Systems

Progress in Top-Down Proteomics and the Analysis of Proteoforms

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

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Six alternative proteases for mass spectrometry–based proteomics beyond trypsin

(2016) Piero Giansanti et al.   Nature Protocols

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

One-hour proteome analysis in yeast

(2015) Alicia L Richards et al.   Nature Protocols

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas

(2015) Piero Giansanti et al.   Cell Reports

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Expanding Proteome Coverage with Orthogonal-specificity α-Lytic Proteases

(2014) Jesse G. Meyer et al.   MOLECULAR & CELLULAR PROTEOMICS

Confetti: A Multiprotease Map of theHeLaProteome for Comprehensive Proteomics

(2014) Xiaofeng Guo et al.   MOLECULAR & CELLULAR PROTEOMICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences

(2013) Gloria M. Sheynkman et al.   JOURNAL OF PROTEOME RESEARCH

Distinct Splice Variants and Pathway Enrichment in the Cell-Line Models of Aggressive Human Breast Cancer Subtypes

(2013) Rajasree Menon et al.   JOURNAL OF PROTEOME RESEARCH

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

The challenge of the proteome dynamic range and its implications for in-depth proteomics

(2013) Roman A. Zubarev   PROTEOMICS

Global Proteome Analysis of the NCI-60 Cell Line Panel

(2013) Amin Moghaddas Gholami et al.   Cell Reports

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Shotgun Protein Sequencing with Meta-contig Assembly

(2012) Adrian Guthals et al.   MOLECULAR & CELLULAR PROTEOMICS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

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

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

Advances in shotgun proteomics and the analysis of membrane proteomes

(2010) Joshua M. Gilmore et al.   Journal of Proteomics

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach

(2009) Sharon Gauci et al.   ANALYTICAL CHEMISTRY

Complete Alternative Splicing Events Are Bubbles in Splicing Graphs

(2009) Michael Sammeth   JOURNAL OF COMPUTATIONAL BIOLOGY

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Evaluation of the Low-Specificity Protease Elastase for Large-Scale Phosphoproteome Analysis

(2008) Bin Wang et al.   ANALYTICAL CHEMISTRY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS