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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 
ProteomicsTranslational repression by 4E-T is crucial to maintain the prophase-I arrest in vertebrate oocytes
Meiotic maturation of vertebrate oocytes occurs in the near-absence of transcription. Thus, female fertility relies on timely translational activation of maternal transcripts stockpiled in full-grown prophase-I-arrested oocytes. However, how expression of these mRNAs is suppressed to maintain the lo...
ORGANISM(S): Xenopus laevis (African clawed frog) 
2025-07-18 | PXD062261 | Pride
4et Xenopus laevis Dia Knockdown Label-free quantification 4et-trim 
ProteomicsA comprehensive landscape of 60S ribosome biogenesis factors
We used quantitative proteomics and crosslinking mass spectrometry (XL-MS) to analyse a comprehensive set of purified pre-60S ribosomal particles, obtaining a detailed timeline of RBF engagement during 60S ribosome biogenesis as well as particle-specific crosslink networks for all analysed particles...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-12-07 | PXD021831 | Pride
Ribosome assembly factors (afs) Ribosome biogenesis factors (rbfs) Mi-filter False discovery rate (fdr) Crosslinking coupled to mass spectrometry (xl-ms) Ribosome biogenesis 
ProteomicsOptimized parameter settings enhance proteome-wide formation of crosslinks on low-abundant proteins
Studies using crosslinking coupled to mass spectrometry on the proteome-wide level have spurred great interest as they facilitate structural probing of protein interactions in living cells or even organisms. Here we show, by using both an in-vitro mimic of a crowded cellular environment and eukaryot...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-02-17 | PXD014759 | Pride
Proteome-wide xl-ms Reaction kinetics 
ProteomicsThe ubiquitin-like modifier FAT10 interferes with SUMO activation
In this study, the proteins SumoE1 and Fat10 or Fat10-AV mutant were crosslinked using the crosslinking reagent H12/D12 BS3 in order to determine specific interaction sites of Fat10 and SumoE1. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-XL-MS) was used to compare...
ORGANISM(S): Homo sapiens (Human) 
2019-10-08 | PXD012592 | Pride
Fat10 Q-xl-ms Xl-ms Sumoe1 
ProteomicsStructural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex
Deregulation of the ubiquitin ligase E6AP is causally linked to the development of human disease, including cervical cancer. In complex with the E6 oncoprotein of human papillomaviruses, E6AP targets the tumor suppressor p53 for degradation, thereby contributing to carcinogenesis. Moreover, E6 acts ...
ORGANISM(S): Human papillomavirus type 16 Homo sapiens (Human) 
2018-10-23 | PXD010002 | Pride
Xl-ms E6 oncoprotein Ubiquitin E6ap/ube3a P53 Papillomavirus 
ProteomicsHuman RNA ligase 1 as a novel regulator of ribosome function and translation under oxidative stress
Human RNA ligase 1 (Rlig1) is a recently identified human 5’-3’ RNA ligase essential for maintaining 28S rRNA integrity and promoting cell survival under oxidative stress. Although the enzymatic activity of Rlig1 implies a role in RNA maintenance or repair, its broader molecular context remains insu...
ORGANISM(S): Homo sapiens (Human) 
2026-05-25 | PXD067615 | Pride
Ribosome Xl-ms Rna repair Rlig1 
ProteomicsEarly Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC
In this study, NAC was UV-crosslinked using the photo-crosslinking amino acid p-benzoyl-L-phenylalanine (pBPA) in order to determine specific interaction sites of the alphaNAC N-terminus in the native protein structure. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-...
ORGANISM(S): Homo sapiens (Human) Caenorhabditis elegans 
2019-07-25 | PXD011995 | Pride
Nac Structural mass spectrometry Uv-crosslinking Q-xl-ms 
ProteomicsSite-specific ubiquitylation acts as a regulator of linker histone H1
Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. While this process is well studied for core histones and many of their PTMs, this is not the case for linker histone H1 in general and its ubiquitylation in part...
ORGANISM(S): Homo sapiens (Human) 
2021-06-07 | PXD025258 | Pride
Epigenetics Linker histone h1 Ubiquitin Posttranslational modification (ptm) Histone code Chromatin 
ProteomicsThe functional interactome of site-specifically ubiquitylated linker histone H1
Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. While this process is well studied for core histones and many of their PTMs, this is not the case for linker histone H1 in general and its ubiquitylation in part...
ORGANISM(S): Homo sapiens (Human) 
2021-07-20 | PXD020686 | Pride
Epigenetics Linker histone h1 Ubiquitin Posttranslational modification (ptm) Histone code Chromatin 
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