[PDF][PDF] Personalized proteome profiles of healthy and tumor human colon organoids reveal both individual diversity and basic features of colorectal cancer

A Cristobal, HWP van den Toorn, M van de Wetering… - Cell reports, 2017 - cell.com
Diseases at the molecular level are complex and patient dependent, necessitating development
of strategies that enable precision treatment to optimize clinical outcomes. Organoid …

Toward an optimized workflow for middle-down proteomics

…, F Marino, H Post, HWP van den Toorn… - Analytical …, 2017 - ACS Publications
Mass spectrometry (MS)-based proteomics workflows can crudely be classified into two distinct
regimes, targeting either relatively small peptides (ie, 0.7 kDa < M w < 3.0 kDa) or small …

[HTML][HTML] The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the …

…, R Wang, JC Wright, HWP van den Toorn… - Molecular & Cellular …, 2012 - ASBMB
The original PRIDE Converter tool greatly simplified the process of submitting mass
spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user …

[HTML][HTML] Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

…, YE Bar-Epraïm, HWP van den Toorn… - Nature …, 2020 - nature.com
Tumor heterogeneity is a major cause of therapeutic resistance. Immunotherapy may exploit
alternative vulnerabilities of drug-resistant cells, where tumor-specific human leukocyte …

[HTML][HTML] Benefits of collisional cross section assisted precursor selection (caps-PASEF) for cross-linking mass spectrometry

B Steigenberger, HWP van den Toorn, E Bijl… - Molecular & Cellular …, 2020 - ASBMB
Ion mobility separates molecules in the gas-phase based on their physico-chemical properties,
providing information about their size as collisional cross-sections. The timsTOF Pro …

[HTML][HTML] Monitoring Human Milk β-Casein Phosphorylation and O-Glycosylation Over Lactation Reveals Distinct Differences between the Proteome and Endogenous …

KA Dingess, I Gazi, HWP van den Toorn… - International journal of …, 2021 - mdpi.com
Human milk is a vital biofluid containing a myriad of molecular components to ensure an
infant’s best start at a healthy life. One key component of human milk is β-casein, a protein …

[HTML][HTML] Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity

JH Ringrose, HW Van Den Toorn, M Eitel… - Nature …, 2013 - nature.com
Genome sequencing of arguably the simplest known animal, Trichoplax adhaerens, uncovered
a rich array of transcription factor and signalling pathway genes. Although the existence …

[HTML][HTML] In-depth characterization of the Staphylococcus aureus phosphoproteome reveals new targets of Stk1

N Prust, S van der Laarse, HWP van den Toorn… - Molecular & Cellular …, 2021 - ASBMB
Staphylococcus aureus is a major cause of infections worldwide, and infection results in a
variety of diseases. As of no surprise, protein phosphorylation is an important game player in …

[HTML][HTML] qcML: an exchange format for quality control metrics from mass spectrometry experiments

…, P Kelchtermans, P Pichler, HWP van den Toorn… - Molecular & Cellular …, 2014 - ASBMB
Quality control is increasingly recognized as a crucial aspect of mass spectrometry based
proteomics. Several recent papers discuss relevant parameters for quality control and present …

[HTML][HTML] Selectivity in Enrichment of cAMP-dependent Protein Kinase Regulatory Subunits Type I and Type II and Their Interactors Using Modified cAMP Affinity Resins …

TT Aye, S Mohammed, HWP van den Toorn… - Molecular & Cellular …, 2009 - ASBMB
cAMP regulates cellular functions primarily by activating PKA. The involvement of PKAs in
various signaling pathways occurring simultaneously in different cellular compartments …