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ProteomicsDon’t Waste Time – Ensure Success in Your Cross-Linking Mass Spectrometry Experiments Before You Begin.
Cross-linking mass spectrometry (XL-MS) is becoming a more popular tool for researchers to turn towards for studying proteins and their complexes of interest especially in complex samples such as lysates or whole-cells. Studying a targeted proteins in a complex mixture can be difficult as data on ot...
ORGANISM(S): Neisseria meningitidis serogroup C (strain 8013) Bacteria 
2024-02-07 | PXD045792 | Pride
Cross-linking Mass spectrometry Protein abundance Ibaq 
ProteomicsCharacterizing protein conformers by cross-linking mass spectrometry and pattern recognition
Motivation: Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quali...
ORGANISM(S): Homo sapiens (Human) 
2025-01-03 | PXD022443 | Pride
Hsp90 Cross-link Quantification 
ProteomicsExpanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS
In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here we present a gas-phase sepa...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Gallus gallus (Chicken) Equus caballus (Horse) 
2020-07-22 | PXD019926 | Pride
Faims Whole proteome Cross-linking mass spectrometry Xl-ms Orbitrap fusion lumos Cx-ms 
ProteomicsReal-time library search assisted identification of cross-links increases resolution for structural modeling and interactome mapping
Cross-linking mass spectrometry (XL-MS) is a universal tool of molecular and structural biology for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental adva...
ORGANISM(S): Escherichia coli 
2023-03-20 | PXD037652 | Pride
Rtls E coli Cross-linking Diagnostic peaks Xl-ms Phox 
ProteomicsKinetic principles of chemical cross-link formation for protein-protein interactions
Proteins play a central role in most biological processes within the cell and deciphering how they interact is key to understand their function. Cross-linking coupled to mass spectrometry is an essential tool for elucidating protein-protein interactions. Despite its importance, we still know surpris...
ORGANISM(S): Homo sapiens (Human) 
2024-10-10 | PXD053500 | Pride
Human s26 proteasome Crosslinking mass spectrometry 
ProteomicsNon-covalently associated peptides are observed during liquid chromatography-mass spectrometry and affect cross-link analyses
Cross-Linking/mass spectrometry draws structural information out of covalently linked peptide pairs. When these links do not match to previous structural models they may indicate changes of protein conformation. Unfortunately, such links can also be the result of experimental errors or artefacts. He...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Gallus gallus (Chicken) 
2019-01-25 | PXD010895 | Pride
Cross-linking Hsa Sda 
ProteomicsStructural Analysis of a Prokaryotic Ribosome Using a Novel Amidinating Cross-Linker and Mass Spectrometry
The structure of the Escherichia coli ribosome, a 2.5 MDa ribonucleoprotein complex containing more than 50 proteins, was probed using the novel amidinating cross-linker diethyl suberthioimidate (DEST) and mass spectrometry. Peptide cross-links derived from this complex structure were identified at ...
ORGANISM(S): Escherichia coli 
2015-12-23 | PXD003381 | Pride
Amidination Dest E. coli Mass spectrometry Diethyl suberthioimidate Ribosome Protein cross-linking 
ProteomicsLarge-Scale Quantitative Cross-Linking and Mass Spectrometry Provides New Insight on Protein Conformational Plasticity within Organelles, Cells, and Tissues
Many proteins can exist in multiple conformational states in vivo to achieve distinct functional roles. These states include alternative conformations, variable PTMs, and association with interacting protein, nucleotide, and ligand partners. Quantitative chemical cross-linking of live cells, organel...
ORGANISM(S): Mus musculus (Mouse) 
2026-01-12 | PXD058490 | Pride
M.musculus qxl-ms 
ProteomicsLarge-Scale Quantitative Cross-Linking and Mass Spectrometry Provides New Insight on Protein Conformational Plasticity within Organelles, Cells, and Tissues
Many proteins can exist in multiple conformational states in vivo to achieve distinct functional roles. These states include alternative conformations, variable PTMs, and association with interacting protein, nucleotide, and ligand partners. Quantitative chemical cross-linking of live cells, organel...
ORGANISM(S): Mus musculus (Mouse) 
2026-01-12 | PXD058448 | Pride
M.mulsculus qxl-ms 
ProteomicsLarge-Scale Quantitative Cross-Linking and Mass Spectrometry Provides New Insight on Protein Conformational Plasticity within Organelles, Cells, and Tissues
Many proteins can exist in multiple conformational states in vivo to achieve distinct functional roles. These states include alternative conformations, variable PTMs, and association with interacting protein, nucleotide, and ligand partners. Quantitative chemical cross-linking of live cells, organel...
ORGANISM(S): Mus musculus (Mouse) 
2026-01-12 | PXD058430 | Pride
M.musculus qxl-ms 
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