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ProteomicsDeep quantification of substrate turnover definesprotease subsite cooperativity. Working title: Massively parallel mapping of dipeptidyl peptidase cleavage sites reveals substrate motifs
Proteases play a crucial role in processing or breaking down proteins. They exhibit varying levels of substrate specificity that determine their physiological or pharmacological functions. However, this specificity is not well-understood. To address this, we have developed hiMAPS (high-throughput ma...
ORGANISM(S): Homo sapiens (Human) 
2024-11-01 | PXD042089 | Pride
Dpp4 Tmt Dipeptidyl peptidase Hela digest Multiplexing Proteome discoverer Sequence motif Himaps Einprot Dpf-3 
ProteomicsArgonaute Alg-1 IP Caenorhabditis elegans
The Argonautes (AGOs) are widely expressed, evolutionarily conserved RNA binding proteins that play an important role in gene expression regulation. The AGOs bind to small regulatory noncoding RNAs such as micro RNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs) etc. The ...
ORGANISM(S): Caenorhabditis elegans 
2025-03-06 | PXD060454 | Pride
Pulldown C. elegans Protein interactions Lc-ms Ip-ms Maxquant Argonautes Einprot Orbitrap fusion 
ProteomicsLarge-scale interactome screen for predicted transcription factors in fission yeast using IP-MS.
Large-scale interactome screen for 89 transcription factors (TFs) in fission yeast. TFs are tagged at the endogenous locus with a 3xFLAG affinity epitope. Cells cultured under optimal conditions (30°C, rich medium) were subjected to IP-MS at 150 mM an 500 mM NaCl.
ORGANISM(S): Schizosaccharomyces pombe 927 
2024-08-30 | PXD054070 | Pride
Pulldown Fission yeast Protein interactions Lc-ms Schizosaccharomyces pombe Ip-ms Maxquant Orbitrap fusion lumos Einprot Transcription factors 
ProteomicsNitrogen signaling factor triggers a respiration-like gene expression program
Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, nitrogen signaling factor (NSF) is part of such communication system, ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-06-25 | PXD047795 | Pride
Nsf Cell communication Nitrogen metabolism Nitrogen signaling 
ProteomicsA conserved chronobiological complex times C. elegans development; map LIN-42 interacting proteins
The mammalian PAS-domain protein PERIOD (PER) and its C. elegans orthologue LIN-42 have been proposed to constitute an evolutionary link between two distinct, circadian and developmental, timing systems. However, while the function of PER in animal circadian rhythms is well understood molecularly an...
ORGANISM(S): Caenorhabditis elegans 
2025-10-10 | PXD058601 | Pride
Kin-20 Lin-42 Ck1bd Phosphorylation Pas-domain protein period C. elegans development 
ProteomicsChAHP and ChAHP2 control diverse retrotransposons by complementary activities.
Retrotransposon control in mammals is an intricate process that is effectuated by a broad network of chromatin regulatory pathways. We previously discovered ChAHP, a protein complex with repressive activity against SINE retrotransposons, composed of the transcription factor ADNP, chromatin remodeler...
ORGANISM(S): Mus musculus (Mouse) 
2025-08-05 | PXD048314 | Pride
Adnp2 Mouse esc Hp1 Chd4 Retrotransposon control Adnp 
ProteomicsMetaproteomic analysis of non-IBD, UC and pouchitis patients stool samples berfore and on antibiotics treatment
Antibiotics (Abx) are critical in modern medicine but can induce intestinal dysbiosis, exacerbate inflammatory bowel diseases (IBD), and disrupt the gut microbiome. Moreover, Abx treatment was reported as a significant risk factor for developing IBD, yet the underlying mechanisms remain unknown. Her...
ORGANISM(S): Homo sapiens (Human) 
2026-04-29 | PXD066732 | Pride
Antibiotics Metaproteomics Ibd 
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