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A synthetic peptide library for benchmarking crosslinking mass spectrometry search engines

https://doi.org/10.1101/821447
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Outgoing claims: the papers this work cites, builds on, or argues with.

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StavroX—A Software for Analyzing Crosslinked Products in Protein Interaction Studies
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Quaternary Diamines as Mass Spectrometry Cleavable Crosslinkers for Protein Interactions
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Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis
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Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0
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Chemical Cross-Linking Enables Drafting ClpXP Proximity Maps and Taking Snapshots of In Situ Interaction Networks
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Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines
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Cleavable Cross-Linker for Protein Structure Analysis: Reliable Identification of Cross-Linking Products by Tandem MS
inferredcites →https://doi.org/10.1021/acs.analchem.6b03745openalex-snapshot
Quirks of Error Estimation in Cross-Linking/Mass Spectrometry
inferredcites →https://doi.org/10.1021/acs.jproteome.8b00947openalex-snapshot
Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents
inferredcites →https://doi.org/10.1021/acs.jproteome.9b00085openalex-snapshot
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics
inferredcites →https://doi.org/10.1021/acscentsci.9b00416openalex-snapshot
PhoX: An IMAC-Enrichable Cross-Linking Reagent
inferredcites →https://doi.org/10.1021/jasms.9b00068openalex-snapshot
Quaternary Structure of the Tryptophan Synthase α-Subunit Homolog BX1 from Zea mays
inferredcites →https://doi.org/10.1021/pr070542gopenalex-snapshot
Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics
inferredcites →https://doi.org/10.1021/pr501321hopenalex-snapshot
Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes
inferredcites →https://doi.org/10.1038/nature19321openalex-snapshot
Structure of the voltage-gated calcium channel Cav1.1 at 3.6 Å resolution
inferredcites →https://doi.org/10.1038/ncomms15473openalex-snapshot
Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification
inferredcites →https://doi.org/10.1038/nmeth.2099openalex-snapshot
Identification of cross-linked peptides from complex samples
inferredcites →https://doi.org/10.1038/nmeth.2557openalex-snapshot
The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
inferredcites →https://doi.org/10.1038/nmeth.3603openalex-snapshot
Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry
inferredcites →https://doi.org/10.1038/s41467-018-06953-0openalex-snapshot
Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex
inferredcites →https://doi.org/10.1038/s41467-019-11337-zopenalex-snapshot
A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides
inferredcites →https://doi.org/10.1038/s41592-020-0959-9openalex-snapshot
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies
inferredcites →https://doi.org/10.1038/s41596-018-0068-8openalex-snapshot
A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein–protein interactions
inferredcites →https://doi.org/10.1038/s41596-018-0074-xopenalex-snapshot
Efficient and robust proteome-wide approaches for cross-linking mass spectrometry
inferredcites →https://doi.org/10.1038/s41596-018-0089-3openalex-snapshot
Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes
inferredcites →https://doi.org/10.1074/mcp.m110.002212openalex-snapshot
Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes
inferredcites →https://doi.org/10.1074/mcp.m113.034009openalex-snapshot
Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification
inferredcites →https://doi.org/10.1074/mcp.m114.042630openalex-snapshot
A New in Vivo Cross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells
inferredcites →https://doi.org/10.1093/nar/gky1106openalex-snapshot
The PRIDE database and related tools and resources in 2019: improving support for quantification data
inferredcites →https://doi.org/10.1101/739318openalex-snapshot
Flexible regions in the molecular architecture of Human fibrin clots structurally resolved by XL-MS and integrative structural modeling
inferredcites →https://doi.org/10.15252/embj.201797150openalex-snapshot
The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion
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