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ProteomicsQuantitative proteomics and in-cell cross-linking reveal cellular reorganisation during early neuronal differentiation of SH-SY5Y cells
The proteomes of undifferentiated and differentiated SH-SY5Y cells are characterised and compared. For this, neuronal differentiation using retinoic acid (RA) or a combination of RA and phorbol-12-myristat-13-acetate (RA/PMA) was explored. An MS-based label-free quantification approach is applied to...
ORGANISM(S): Homo sapiens (Human) 
2022-04-08 | PXD031054 | Pride
Proteomics Chemical cross-linking Mass spectrometry Protein networks Actin Sh-sy5y 
ProteomicsCharacterizing the dynamic oligomerization of Hsp90β using photo-cross-linking
Cross-linking mass spectrometry (XL-MS) is a powerful tool for probing protein structures. While conventional chemical cross-linkers react with specific residues with defined chemistry, photo-cross-linkers, despite their superior reactivity, have been hindered by incomplete mechanistic understanding...
ORGANISM(S): Homo sapiens (Human) 
2026-04-09 | PXD072009 | Pride
Hsp90 Cleavable cross-linkers Diazirine Photo-cross-linking 
ProteomicsIdentification of human PKD2 interaction partners from cytosolic protein fractions of HeLa cells by affinity enrichment cross-linking/MS
We investigated the interaction network of human PKD2 in the cytosol as well as in Golgi-enriched subcellular protein fractions, using an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins ...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003909 | Pride
Human Pkd2 Cross-linking/ms Affinity enrichment Orbitrap fusion 
ProteomicsIdentification of human PKD2 interaction partners from Golgi-enriched protein fractions of HeLa cells by affinity enrichment cross-linking/MS
We investigated the interaction network of human PKD2 in the cytosol as well as in Golgi-enriched subcellular protein fractions, using an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins ...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003913 | Pride
Human Pkd2 Hela cells Cross-linking/ms Affinity enrichment Golgi apparatus Orbitrap fusion 
ProteomicscapsPASEF – Collisional Cross Section Assisted Precursor Selection Applied to Cross-linking Mass Spectrometry
Ion mobility separates molecules in the gas-phase on their physico-chemical properties, providing information about their size as collisional cross-sections. The timsTOF Pro combines trapped ion mobility with a quadrupole, HCD cell and a time-of-flight mass spectrometer, to interrogate ions at high ...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2020-07-22 | PXD018189 | Pride
Ion mobility Cross-linking mass spectrometry Xl-ms Phox 
ProteomicsData independent acquisition cross-linking/mass spectrometry
Quantitative cross-linking/mass spectrometry (QCLMS) provides increasing structural detail on altered protein states in solution. Accurate quantitation is a value in itself but may also be central to elucidating small differences between protein states. Hence, QCLMS could benefit from data independe...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) Gallus gallus (Chicken) Equus caballus (Horse) 
2019-01-25 | PXD011036 | Pride
Xi Reproducibility Spectronaut Data independent acquisition Label-free Mass spectrometry Quantitation Cross-linking 
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 
ProteomicsCross-linking and mass spectrometry analysis of Trypanosoma brucei proteins
We performed in vivo cross-linking of T. brucei bloodstream forms expressing a V5-tagged phosphatidylinositol phosphate 5-phosphatase (PIP5Pase). Then, performed immunoprecipitations with anti-V5 antibodies to identify proteins that cross-links with PIP5Pase or its interacting partners.
ORGANISM(S): Trypanosoma brucei 
2025-11-11 | PXD059635 | Pride
Cross-linking Trypanosomes Nucleus 
ProteomicsSingle Nucleotide Resolution RNA-Protein Cross-Linking/MS: Simple Extension of the CLIR-MS Workflow
RNA-protein interactions mediate a vast number of intracellular processes. CLIR-MS (cross-linking of isotope labeled RNA and tandem mass spectrometry) is a mass spectrometric technique that allows the identification of RNA-protein interaction sites at single nucleotide/amino acid resolution in a sin...
ORGANISM(S): Homo sapiens (Human) 
2021-11-04 | PXD024010 | Pride
Protein rna cross-linking clir-ms uv xl 
ProteomicsComparison of OpenPepXL and xQuest on a Labeled Cross-Linking MS dataset
These data sets are part of a large study aimed at the comparison of experimental and computational workflows used in chemical cross-linking coupled to mass spectrometry. Bovine serum albumin (BSA) was used as a model protein. Two different cross-linking chemistries were used: disuccinimidyl suberat...
ORGANISM(S): Bos taurus (Bovine) 
2020-10-20 | PXD014523 | Pride
Chemical cross-linking  dss  pdh  dmtmm  structural proteomics  bovine serum albumin 
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