Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly

Highly Robust de Novo Full-Length Protein Sequencing

(2022) Zhi-Biao Mai et al.   ANALYTICAL CHEMISTRY

Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling

(2022) Douwe Schulte et al.   ANALYTICAL CHEMISTRY

A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies

(2022) Sebastiaan C. de Graaf et al.   mAbs

Accurate discrimination of leucine and isoleucine residues by combining continuous digestion with multiple MS3 spectra integration in protein sequence

(2022) Weijie Zhang et al.   TALANTA

Quality control of protein reagents for the improvement of research data reproducibility

(2021) Ario de Marco et al.   Nature Communications

Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme

(2021) Weiwei Peng et al.   JOURNAL OF PROTEOME RESEARCH

Progress and challenges in mass spectrometry-based analysis of antibody repertoires

(2021) Igor Snapkov et al.   TRENDS IN BIOTECHNOLOGY

Complementary Methods for de Novo Monoclonal Antibody Sequencing to Achieve Complete Sequence Coverage

(2020) Jianhui Cheng et al.   JOURNAL OF PROTEOME RESEARCH

Flying Blind, or Just Flying Under the Radar? The Underappreciated Power of de novo Methods of Mass Spectrometric Peptide Identification

(2020) Isabelle O'Bryon et al.   PROTEIN SCIENCE

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

(2019) Hao Yang et al.   BIOINFORMATICS

2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample

(2019) Lindsay Pino et al.   JOURNAL OF PROTEOME RESEARCH

Assessing protein sequence database suitability using de novo sequencing

(2019) Richard Johnson et al.   MOLECULAR & CELLULAR PROTEOMICS

Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework

(2019) Korrawe Karunratanakul et al.   MOLECULAR & CELLULAR PROTEOMICS

Discrimination of isoleucine and leucine by dimethylation-assisted MS3

(2018) Sheila Maibom-Thomsen et al.   ANALYTICAL CHEMISTRY

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

(2018) Harald Barsnes et al.   JOURNAL OF PROTEOME RESEARCH

A Potential Golden Age to Come - Current Tools, Recent Use Cases, and Future Avenues for de novo Sequencing in Proteomics

(2018) Thilo Muth et al.   PROTEOMICS

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing

(2018) Samuel E. Miller et al.   JOURNAL OF PROTEOME RESEARCH

Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework

(2018) Lev I. Levitsky et al.   JOURNAL OF PROTEOME RESEARCH

Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry

(2018) Ngoc Hieu Tran et al.   NATURE METHODS

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics

(2017) Bernhard Blank-Landeshammer et al.   JOURNAL OF PROTEOME RESEARCH

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

(2017) K. Ilker Sen et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Database-independent Protein Sequencing (DiPS) Enables Full-lengthde NovoProtein and Antibody Sequence Determination

(2017) Alon Savidor et al.   MOLECULAR & CELLULAR PROTEOMICS

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining phage display with de novo protein sequencing for reverse engineering of monoclonal antibodies

(2016) Keith W. Rickert et al.   mAbs

Complete De Novo Assembly of Monoclonal Antibody Sequences

(2016) Ngoc Hieu Tran et al.   Scientific Reports

Novor: Real-Time Peptide de Novo Sequencing Software

(2015) Bin Ma   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Reproducibility: Standardize antibodies used in research

(2015) Andrew Bradbury et al.   NATURE

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

Expanding Proteome Coverage with Orthogonal-specificity α-Lytic Proteases

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

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Fast and Accurate Database Searches with MS-GF+Percolator

(2013) Viktor Granholm et al.   JOURNAL OF PROTEOME RESEARCH

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

(2013) Thilo Muth et al.   JOURNAL OF PROTEOME RESEARCH

Lessons inde novopeptide sequencing by tandem mass spectrometry

(2013) Katalin F. Medzihradszky et al.   MASS SPECTROMETRY REVIEWS

Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

(2013) Teck Yew Low et al.   Cell Reports

The Structural Basis of Antibody-Antigen Recognition

(2013) Inbal Sela-Culang et al.   Frontiers in Immunology

Shotgun Protein Sequencing with Meta-contig Assembly

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

File Formats Commonly Used in Mass Spectrometry Proteomics

(2012) Eric W. Deutsch   MOLECULAR & CELLULAR PROTEOMICS

Protease bias in absolute protein quantitation

(2012) Mao Peng et al.   NATURE METHODS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Shotgun proteomics: concept, key points and data mining

(2010) Sabine Matallana-Surget et al.   Expert Review of Proteomics

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

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

Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy

(2009) Xiaowen Liu et al.   BIOINFORMATICS