pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning

Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

(2020) Kaiyuan Liu et al.   ANALYTICAL CHEMISTRY

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics

(2020) Yi Yang et al.   Nature Communications

A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes

(2020) Rebecca Beveridge et al.   Nature Communications

An experimentally generated peptide database increases the sensitivity of XL-MS with complex samples

(2020) Iwan Parfentev et al.   Journal of Proteomics

A cross-linking mass spectrometry approach defines protein interactions in yeast mitochondria

(2020) Andreas Linden et al.   MOLECULAR & CELLULAR PROTEOMICS

Generating high quality libraries for DIA MS with empirically corrected peptide predictions

(2020) Brian C. Searle et al.   Nature Communications

Expanding the Depth and Sensitivity of Cross-Link Identification by Differential Ion Mobility Using High-Field Asymmetric Waveform Ion Mobility Spectrometry

(2020) Lennart Schnirch et al.   ANALYTICAL CHEMISTRY

In-cell architecture of an actively transcribing-translating expressome

(2020) Francis J. O’Reilly et al.   SCIENCE

Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation

(2020) Yi Yang et al.   JOURNAL OF PROTEOME RESEARCH

Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies

(2020) Kumar Yugandhar et al.   NATURE METHODS

Data-independent acquisition improves quantitative cross-linking mass spectrometry

(2019) Fränze Müller et al.   MOLECULAR & CELLULAR PROTEOMICS

Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents

(2019) Christian E. Stieger et al.   JOURNAL OF PROTEOME RESEARCH

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

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

(2019) Shivani Tiwary et al.   NATURE METHODS

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

(2019) Ralf Gabriels et al.   NUCLEIC ACIDS RESEARCH

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

(2019) Wen-Feng Zeng et al.   ANALYTICAL CHEMISTRY

A Simple Cross-Linking/Mass Spectrometry Workflow for Studying System-wide Protein Interactions

(2019) Michael Götze et al.   ANALYTICAL CHEMISTRY

pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics

(2019) Wen-Jing Zhou et al.   JOURNAL OF PROTEOME RESEARCH

Prediction of LC-MS/MS properties of peptides from sequence by deep learning

(2019) Shenheng Guan et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2019) Zhen-Lin Chen et al.   Nature Communications

An integrated workflow for crosslinking mass spectrometry

(2019) Marta L Mendes et al.   Molecular Systems Biology

PhoX: An IMAC-Enrichable Cross-Linking Reagent

(2019) Barbara Steigenberger et al.   ACS Central Science

Smart Cutter: An Efficient Strategy for Increasing the Coverage of Chemical Cross-Linking Analysis

(2019) Lili Zhao et al.   ANALYTICAL CHEMISTRY

MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks

(2019) Yang-Ming Lin et al.   BMC GENOMICS

In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria

(2019) Petra S. J. Ryl et al.   JOURNAL OF PROTEOME RESEARCH

MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity

(2019) Kumar Yugandhar et al.   MOLECULAR & CELLULAR PROTEOMICS

False discovery rate estimation and heterobifunctional cross-linkers

(2018) Lutz Fischer et al.   PLoS One

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

(2018) Hao Chi et al.   NATURE BIOTECHNOLOGY

Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification

(2017) Fan Liu et al.   Nature Communications

A Whole Proteome Inventory of Background Photocrosslinker Binding

(2016) Philipp Kleiner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2016) Dan Tan et al.   eLife

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction

(2015) Yaojun Wang et al.   BMC BIOINFORMATICS

Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics

(2015) Avinash K. Shanmugam 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

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

(2015) Fan Liu et al.   NATURE METHODS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

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

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

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

(2010) Sujun Li et al.   ANALYTICAL CHEMISTRY

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