A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

Xolik: finding cross-linked peptides with maximum paired scores in linear time

(2018) Jiaan Dai et al.   BIOINFORMATICS

Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus

(2018) Lei Lu et al.   JOURNAL OF PROTEOME RESEARCH

Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping

(2018) Kunhong Xiao et al.   Nature Protocols

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

(2018) Hao Chi et al.   NATURE BIOTECHNOLOGY

Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity

(2017) Fengchao Yu et al.   JOURNAL OF PROTEOME RESEARCH

Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications

(2017) Hao Yang et al.   JOURNAL OF PROTEOME RESEARCH

65TH ASMS Conference on Mass Spectrometry and Allied Topics

(2017) Judith Sjoberg   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification

(2017) Ming-Qi Liu et al.   Nature Communications

Xilmass: A New Approach toward the Identification of Cross-Linked Peptides

(2016) Şule Yılmaz et al.   ANALYTICAL CHEMISTRY

pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification

(2016) Rui-Xiang Sun et al.   ANALYTICAL CHEMISTRY

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

(2016) Yue-He Ding et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Structure of the voltage-gated calcium channel Cav1.1 at 3.6 Å resolution

(2016) Jianping Wu et al.   NATURE

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

(2016) Alexander Leitner et al.   TRENDS IN BIOCHEMICAL SCIENCES

Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states

(2016) Dan Tan et al.   eLife

Tandem Mass Spectrum Identification via Cascaded Search

(2015) Attila Kertesz-Farkas et al.   JOURNAL OF PROTEOME RESEARCH

Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes

(2015) Michael R. Hoopmann et al.   JOURNAL OF PROTEOME RESEARCH

A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides

(2015) Sven H. Giese et al.   MOLECULAR & CELLULAR PROTEOMICS

Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification

(2015) Matthew M. Makowski et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2015) Fan Liu et al.   NATURE METHODS

Mapping native disulfide bonds at a proteome scale

(2015) Shan Lu et al.   NATURE METHODS

Targeted cross-linking-mass spectrometry determines vicinal interactomes within heterogeneous RNP complexes

(2015) Christian Trahan et al.   NUCLEIC ACIDS RESEARCH

Structure of a yeast spliceosome at 3.6-angstrom resolution

(2015) Chuangye Yan et al.   SCIENCE

pQuant Improves Quantitation by Keeping out Interfering Signals and Evaluating the Accuracy of Calculated Ratios

(2014) Chao Liu et al.   ANALYTICAL CHEMISTRY

The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks

(2014) Andrea Sinz   Expert Review of Proteomics

Revisiting Peptide Identification by High-Accuracy Mass Spectrometry: Problems Associated with the Use of Narrow Mass Precursor Windows

(2014) Elena Bonzon-Kulichenko et al.   JOURNAL OF PROTEOME RESEARCH

A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database

(2014) Hansuk Buncherd et al.   Journal of Proteomics

JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy

(2014) Xusheng Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass spectrometry supported determination of protein complex structure

(2013) Thomas Walzthoeni et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Mechanism for Actin Filament Severing by Malaria Parasite Actin Depolymerizing Factor 1 via a Low Affinity Binding Interface

(2013) Wilson Wong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification

(2013) Michael J. Trnka et al.   MOLECULAR & CELLULAR PROTEOMICS

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

(2012) Viktor Granholm et al.   Journal of Proteomics

Evaluating protein interactions through cross-linking mass spectrometry

(2012) David L Tabb   NATURE METHODS

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

(2012) Thomas Walzthoeni et al.   NATURE METHODS

Identification of cross-linked peptides from complex samples

(2012) Bing Yang et al.   NATURE METHODS

StavroX—A Software for Analyzing Crosslinked Products in Protein Interaction Studies

(2011) Michael Götze et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

pParse: A method for accurate determination of monoisotopic peaks in high-resolution mass spectra

(2011) Zuo-F ei Yuan et al.   PROTEOMICS

Cleavable Cross-Linker for Protein Structure Analysis: Reliable Identification of Cross-Linking Products by Tandem MS

(2010) Mathias Q. Müller et al.   ANALYTICAL CHEMISTRY

Chemical Cross-Linking and Mass Spectrometry As a Low-Resolution Protein Structure Determination Technique

(2010) Pragya Singh et al.   ANALYTICAL CHEMISTRY

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes

(2010) Athit Kao et al.   MOLECULAR & CELLULAR PROTEOMICS

A new cross-linking strategy: protein interaction reporter (PIR) technology for protein–protein interaction studies

(2010) Xiaoting Tang et al.   Molecular BioSystems

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh et al.   JOURNAL OF PROTEOME RESEARCH

Enhancing Peptide Identification Confidence by Combining Search Methods

(2008) Gelio Alves et al.   JOURNAL OF PROTEOME RESEARCH

DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring

(2008) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Erratum: Corrigendum: Identification of cross-linked peptides from large sequence databases

(2008) Oliver Rinner et al.   NATURE METHODS