cross linking mass spectrometry protocol

Identification of Subunit Subunit Interactions in

Chemical cross-linking analyzed by mass spectrometry was used to identify residue specific inter- and intra-subunit interactions in the P22 procapsids All the intersubunit cross-links occurred between residues clustered in a loop region (residues 157-207) which was previously identified by mass spectrometry based on hydrogen/deuterium

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Mass Spectrometry Proteomics

Modern proteomic tools are essential to understand biological questions The Mass Spectrometry Proteomics Core Facility provides IRB Barcelona researchers and external users with a number of mass spectrometry-(MS) and proteomics-based techniques that can help to further their knowledge of disease pathways targets and drug effects Set up in September 2007 the Facility currently offers

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eXL

The analysis of proteins and protein complexes by cross-linking mass spectrometry (XL-MS) has expanded in the past decade However mostly used approaches suffer important limitations in term of efficiency and sensitivity We describe here a new workflow based on the advanced use of the trifunctional cross-linker NNP9 NNP9 carries an azido group allowing the quantitative and selective

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A Click‐Chemistry‐Based Enrichable Crosslinker for

OSTI GOV Journal Article: A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry Journal Article: A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

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Chemical Cross

03 10 2011Cite this protocol as: Mller M Q Sinz A (2012) Chemical Cross-Linking and High-Resolution Mass Spectrometry to Study Protein–Drug Interactions In: Drewes G Bantscheff M (eds) Chemical Proteomics Methods in Molecular Biology (Methods and Protocols) vol 803 Humana Press Totowa NJ First Online 03 October 2011

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A comparative cross

Chemical cross-linking together with mass spectrometry (MS) The protocol involves first assigning cross-linked peptides in the complex without ligand binding or with post-translational modifications (PTMs) at natural abundance using a standard procedure with labeled cross-linkers

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Application and Refinement of a Zero

Chemical cross-linking and mass spectrometry (CX-MS) is a structural technique that has been gaining in popularity with the advent of instruments that provide increased access to high-resolution MS/MS data The Speicher laboratory is interested in zero-length cross-links which provide the highest-quality data but are the

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A General Method for Targeted Quantitative Cross

Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography NMR and cryo-electron microscopy[1] The extension of traditional quantitative proteomics methods

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Characterization of photochemically cross

The protocol can be divided into three parts: 1) Cross linking of the protein-nucleic acid complex by irradiation with ultraviolet light and subsequently verifying the crosslinking by mass spectrometry 2) Mass spectrometric peptide mapping of crosslinked protein-nucleic acid complexes to identify crosslinked peptide-nucleic acid hybrids 3) Tandem mass spectrometric sequencing of peptide

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Identification of Subunit Subunit Interactions in

Chemical cross-linking analyzed by mass spectrometry was used to identify residue specific inter- and intra-subunit interactions in the P22 procapsids All the intersubunit cross-links occurred between residues clustered in a loop region (residues 157-207) which was previously identified by mass spectrometry based on hydrogen/deuterium

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A Click‐Chemistry‐Based Enrichable Crosslinker for

OSTI GOV Journal Article: A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry Journal Article: A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

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The interactome of intact mitochondria by cross

08 12 2017Insights into the systemwide organization of proteins in intact mitochondria can potentially be obtained by cross-linking mass spectrometry (XL-MS) In XL-MS native protein contacts are captured using a cross-linker which is typically a small organic molecule composed of a spacer arm and two functional groups that are reactive toward specific residue side chains

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C X Interaction Analysis OVAL by High

Using cross-linking chemistry and High-Mass MALDI ToF mass spectrometry easy analysis of non-co-valent protein complexes becomes possible In the spectrum presented the protein complexes formed by HIV Integrase (IN) and cofactor LEDGF are charac-terized after cross-linking

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Visualizing the Ensemble Structures of Protein Complexes

Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry: Zhou Gong 1 Yue-He Ding 2 Xu Dong 1 Na Liu 2 E Erquan Zhang 2 Meng-Qiu Dong 2 Chun Tang 1: 1 CAS Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics Wuhan Institute of Physics and

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Protocol for Silver Staining of Gels

Optimized for Mass Spectrometry and Protein Identification GUIDELINES Silver staining is used for sensitive detection of proteins separated by 1D and 2D SDS PAGE with detection limits from 0 5-5 ng Many silver staining protocols and commercial staining kits are not compatible with mass spectrometry due to the use of cross-linking reagents

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Cross

Cross-linking mass spectrometry (CLMS) of Augmin (A) Methodology used for CLMS of Augmin isolated from extracts of Drosophila embryos expressing GFP-Msd1 (B) Relative abundance (mean area) of each Augmin subunit as identified by LC-MS/MS (C) Cross-links within and between Augmin subunits as identified by CLMS

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Using SIM

In this protocol we describe the key steps for using the Spectrum Identification Machine for Cross-linked Peptides (SIM-XL) a fast and sensitive XL search engine that is part of the PatternLab for proteomics environment (8) to analyze tandem mass spectrometry data derived from cross-linked peptides

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Combining Chemical Cross

After cross-linking the proteins are usually hydrolyzed with proteases and cross-linked di-peptides are analyzed by liquid chromatography-coupled mass spectrometry The identification of cross-linking products by database searching however requires the use of specialized software which concatenate peptide sequences of various proteins and disparate regions 17 18 19

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Research Article Imaging Mass Spectrometry by Matrix

Imaging Mass Spectrometry by Matrix-Assisted Laser Desorption/Ionization and Stress-Strain Measurements in Iontophoresis Transepithelial Corneal Collagen Cross-Linking PaoloVinciguerra 1 RitaMencucci 2 VitoRomano 3 EberhardSpoerl 4 FabrizioI Camesasca 1 EleonoraFavuzza 2 ClaudioAzzolini 5 RodolfoMastropasqua 6 andRiccardoVinciguerra 1 5

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C X Interaction Analysis OVAL by High

Using cross-linking chemistry and High-Mass MALDI ToF mass spectrometry easy analysis of non-co-valent protein complexes becomes possible In the spectrum presented the protein complexes formed by HIV Integrase (IN) and cofactor LEDGF are charac-terized after cross-linking

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