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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 
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 
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 
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 
ProteomicsOpen search strategy for inferring the masses of cross-link adducts
Development of new reagents for protein cross-linking is continually ongoing. The chemical formulas of the linker adducts formed by these reagents are usually deduced from expert knowledge, and then validated by mass spectrometry. Clearly, it would have been more rigorous if the adduct masses are ...
ORGANISM(S): Bos taurus (Bovine) 
2021-09-09 | PXD020704 | Pride
Modifications Xl-ms Emcs Open search Cross-linking Mass spectrometry Glutaraldehyde 
ProteomicsCross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology
The specific functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartm...
ORGANISM(S): Homo sapiens (Human) 
2024-02-21 | PXD046382 | Pride
Synaptic vesicles Xl-ms Mitochondria Spatial proteomics Dsbso 
ProteomicsExpanding the cross-link coverage of a dihydrazide-based carboxyl-group specific chemical cross-linking strategy - Dataset 1: Model proteins
The conditions for chemical protein-protein cross-linking using the reagents pimelic dihydrazide (PDH) and 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) chloride were optimized using a set of five model proteins and two large complexes, the 20S proteasome and the 70S ribosome. Th...
ORGANISM(S): Bos taurus (Bovine) Oryctolagus cuniculus (Rabbit) Gallus gallus (Chicken) 
2021-01-04 | PXD019724 | Pride
Chemical cross-linking  pdh  dmtmm  model proteins  method optimization 
ProteomicsExpanding the cross-link coverage of a dihydrazide-based carboxyl-group specific chemical cross-linking strategy - Dataset 2: Bovine 20S proteasome
The conditions for chemical protein-protein cross-linking using the reagents pimelic dihydrazide (PDH) and 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) chloride were optimized using a set of five model proteins and two large complexes, the 20S proteasome and the 70S ribosome. Th...
ORGANISM(S): Bos taurus (Bovine) 
2021-01-04 | PXD019507 | Pride
Chemical cross-linking  pdh  dmtmm  20s proteasome  method optimization 
ProteomicsExpanding the cross-link coverage of a dihydrazide-based carboxyl-group specific chemical cross-linking strategy - Dataset 3: E. coli 70S ribosome
The conditions for chemical protein-protein cross-linking using the reagents pimelic dihydrazide (PDH) and 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) chloride were optimized using a set of five model proteins and two large complexes, the 20S proteasome and the 70S ribosome. Th...
ORGANISM(S): Escherichia coli 
2021-01-04 | PXD019508 | Pride
Chemical cross-linking  pdh  dmtmm  70s ribosome  method optimization 
ProteomicsA2M bait region engineering - autoconjugation product cross-link identification and PRM quantification
In-gel digest of a cross-linked product band was used to identify an internal isopeptide cross-link formed in A2M TR K704 upon bait region cleavage by trypsin. PRM was used to quantify the thiol ester in native PAGE bands of A2M nEXT and EXT mutants.
ORGANISM(S): Homo sapiens (Human) 
2021-09-10 | PXD023651 | Pride
Prm Protease inhibitor Protein engineering Cross-link A2m 
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