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Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity

https://doi.org/10.1101/097089
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Probability-based protein identification by searching sequence databases using mass spectrometry data
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Development and validation of a spectral library searching method for peptide identification from MS/MS
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Comet: An open‐source MS / MS sequence database search tool
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Application of a fast sorting algorithm to the assignment of mass spectrometric cross‐linking data
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In planta chemical cross‐linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis
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pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry
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StavroX—A Software for Analyzing Crosslinked Products in Protein Interaction Studies
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Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis
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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
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Molecular Architecture of the ATP-Dependent Chromatin-Remodeling Complex SWR1
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Isotope-labeled cross-linkers and fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex
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MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides
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InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra
inferredcites →https://doi.org/10.1021/ac801646fopenalex-snapshot
Characterization of Protein Cross-Links via Mass Spectrometry and an Open-Modification Search Strategy
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Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics
inferredcites →https://doi.org/10.1021/pr070234iopenalex-snapshot
Shotgun Cross-Linking Analysis for Studying Quaternary and Tertiary Protein Structures
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Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-Linked Peptides Using Tandem Mass Spectrometry
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Learning Score Function Parameters for Improved Spectrum Identification in Tandem Mass Spectrometry Experiments
inferredcites →https://doi.org/10.1021/pr4003867openalex-snapshot
Hekate: Software Suite for the Mass Spectrometric Analysis and Three-Dimensional Visualization of Cross-Linked Protein Samples
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Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis
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Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes
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A Fast SEQUEST Cross Correlation Algorithm
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The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and Their Assemblies Using Mass Spectrometry-Based Approaches
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Detecting Cross-Linked Peptides by Searching against a Database of Cross-Linked Peptide Pairs
inferredcites →https://doi.org/10.1021/pr9011816openalex-snapshot
xComb: A Cross-Linked Peptide Database Approach to Protein−Protein Interaction Analysis
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Architecture of the large subunit of the mammalian mitochondrial ribosome
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MS-GF+ makes progress towards a universal database search tool for proteomics
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Identification of cross-linked peptides from large sequence databases
inferredcites →https://doi.org/10.1038/nmeth.1254openalex-snapshot
Building consensus spectral libraries for peptide identification in proteomics
inferredcites →https://doi.org/10.1038/nmeth.2099openalex-snapshot
Identification of cross-linked peptides from complex samples
inferredcites →https://doi.org/10.1038/nmeth.2103openalex-snapshot
False discovery rate estimation for cross-linked peptides identified by mass spectrometry
inferredcites →https://doi.org/10.1038/nmeth.2139openalex-snapshot
Evaluating protein interactions through cross-linking mass spectrometry
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A mass spectrometry–based hybrid method for structural modeling of protein complexes
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Mapping native disulfide bonds at a proteome scale
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Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry
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Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
inferredcites →https://doi.org/10.1038/nmeth1113openalex-snapshot
Semi-supervised learning for peptide identification from shotgun proteomics datasets
inferredcites →https://doi.org/10.1038/nprot.2013.168openalex-snapshot
Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline
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Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry
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High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry
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Statistical significance for genomewide studies
inferredcites →https://doi.org/10.1074/mcp.m110.001420openalex-snapshot
An Isotopically Coded CID-cleavable Biotinylated Cross-linker for Structural Proteomics
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
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Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification
inferredcites →https://doi.org/10.1074/mcp.m700274-mcp200openalex-snapshot
Structural Analysis of Multiprotein Complexes by Cross-linking, Mass Spectrometry, and Database Searching
inferredcites →https://doi.org/10.1074/mcp.m800020-mcp200openalex-snapshot
CrossSearch, a User-friendly Search Engine for Detecting Chemically Cross-linked Peptides in Conjugated Proteins
inferredcites →https://doi.org/10.1074/mcp.o113.036327openalex-snapshot
Computing Exact p-values for a Cross-correlation Shotgun Proteomics Score Function
inferredcites →https://doi.org/10.1093/bioinformatics/bth092openalex-snapshot
TANDEM: matching proteins with tandem mass spectra
inferredcites →https://doi.org/10.1093/bioinformatics/btv083openalex-snapshot
Crossfinder-assisted mapping of protein crosslinks formed by site-specifically incorporated crosslinkers
inferredcites →https://doi.org/10.1111/j.1742-4658.2005.05053.xopenalex-snapshot
Computer‐assisted mass spectrometric analysis of naturally occurring and artificially introduced cross‐links in proteins and protein complexes
inferredcites →https://doi.org/10.1126/science.1221483openalex-snapshot
Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry
inferredcites →https://doi.org/10.1186/1471-2105-11-64openalex-snapshot
ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite
inferredcites →https://doi.org/10.1186/1471-2105-6-s2-s9openalex-snapshot
CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis
inferredcites →https://doi.org/10.1186/s12859-015-0844-1openalex-snapshot
Weakly supervised learning of biomedical information extraction from curated data
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ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/mas.21908openalex-snapshot
Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross‐Linking
inferred← citeshttps://doi.org/10.1002/pmic.202100145openalex-snapshot
Progress in methodologies and quality‐control strategies in protein cross‐linking mass spectrometry
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty526openalex-snapshot
Xolik: finding cross-linked peptides with maximum paired scores in linear time
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