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ProteomicsFast Profiling of Protease Specificity reveals similar substrate specificities for cathepsins K, L and S
N-terminal COFRADIC analysis of cathespine K, L and S to obtain the substrate specificity profile of these cysteine cathepsins.
ORGANISM(S): Homo sapiens (Human) 
2015-02-10 | PXD001536 | Pride
Cathespins N-terminal cofradic 
ProteomicsA COFRADIC protocol to study protein ubiquitination
We here apply the COmbined FRActional DIagonal Chromatography (COFRADIC) technology to enrich for ubiquitinated peptides and identify sites of ubiquitination by mass spectrometry. Our technology bypasses the need to ectopically overexpress tagged variants of ubiquitin and the use of sequence-biased ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080780 | MassIVE
ProteomicsSubstrate specificity divergence of granzyme tryptases.
Elucidating the true physiological functions of granzymes has been challenging since the origin of the granzyme studied, the use of non-physiological granzyme concentrations and the interspecies use of granzymes, with extrapolation of all these data to orthologous granzymes has led to inconsistencie...
ORGANISM(S): Homo sapiens (Human) 
2015-09-30 | PXD000570 | Pride
Proteomics Granzyme N-terminal cofradic Protease Specificity profile 
ProteomicsPositional proteomics reveals differences in N-terminal proteoform stability.
To understand the impact of alternative translation initiation on a proteome, we performed the first large-scale study of protein turnover rates in which we distinguish between N-terminal proteoforms pointing to translation initiation events. Using pulsed SILAC combined with N-terminal COFRADIC we m...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-03-13 | MSV000083565 | MassIVE
ProteomicsAssessment of the epithelial/mesenchymal phenotype of pancreatic cancer cells based on data-independent acquisition – mass spectrometry.
Based on data-independent acquisition (DIA)-mass spectrometry (MS), we assessed the epithelial/mesenchymal phenotype of three pancreatic cancer cell lines: CAPAN-1, PANC-1 and MIA PaCa-2 in 2D cell culture.
ORGANISM(S): Homo sapiens (Human) 
2025-11-10 | PXD057259 | Pride
Cancer Pancreatic Human proteome Cell lines 
ProteomicsNovel surface functionalized superparamagnetic nanoparticles with engineered cellular uptake as a means for intracellular omics
Superparamagnetic nanoparticles (SPMNPs) are appealing for use in organelle isolation strategies. Yet, this potential remains largely unexplored because thus far research has focused on either physicochemical design or on their application in micron-sized beads. For their use in life sciences, the b...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-28 | MSV000080688 | MassIVE
ProteomicsDYn-2 based identification of Arabidopsis sulfenomes
Identifying the sulfenylation state (-SOH) of stressed cells. Here, we optimized an in vivo trapping method of sulfenic acids in hydrogen peroxide (H2O2) stressed plant cells. With click chemistry, the dimedone based alkyne functionalized DYn-2 probe was biotinylated for subsequent streptavidin enri...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2016-06-27 | PXD001562 | Pride
Arabidopsis Sulfenome Dyn-2 click chemistry H2o2 Ros Biotinylation 
ProteomicsThe dynamics of protein-bound methionine oxidation events in Arabidopsis thaliana during oxidative stress
Reactive oxygen species such as hydrogen peroxide can modify proteins via direct oxidation of their sulfur-containing amino acids, cysteine and methionine. Methionine oxidation, studied here, is a reversible posttranslational modification, which is increasingly suggested as a mechanism by which prot...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2015-03-24 | PXD001286 | Pride
Methionine oxidation Catalase mutant Oxidative stress Arabidopsis thaliana 
ProteomicsTriazolinedione protein modification: from an overlooked off-target effect to a tryptophan-based bioconjugation strategy
Labelling of tyrosine residues in peptides and proteins has been reported to selectively occur via a 'tyrosine-click' reaction with triazolinedione reagents (TAD). However, we here demonstrate that TAD reagents are actually not selective for tyrosine and that tryptophan residues are in fact also lab...
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD031607 | Pride
Site-selective protein modification Tad Tryptophan Protein modification 
ProteomicsVirotrap-based interactome analysis of 20 pairs of N-terminal proteoforms and their canonical protein
N-terminal proteoforms stem from the same gene but differ at their N-terminus, and most of these are found to be truncated, though some are N-terminally extended caused by ribosomes starting translation from codons in the annotated 5’UTR, and/or carry modified N-termini different from those of the c...
ORGANISM(S): Homo sapiens (Human) 
2023-06-08 | PXD039171 | Pride
Virotrap Protein-protein interaction N-terminal proteoform Lc-ms/ms 
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