Bead-based lysis

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Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
Illumina HiSeq 2000 (2)
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bacteria (1)

Modification

N6 (1)
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Lab affiliation

Merck (6)
ETH Zürich Institute of Molecular Systems Biology HPM F43 Otto-Stern-Weg 3 8093 Zürich Switzerland (5)
ETHZ IMSB (4)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (3)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (3)
Dr. Matthias Gstaiger ETH Zürich Institute of Molecular Systems Biology Otto-Stern-Weg 3 8093 Zürich Switzerland (3)
Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland (3)
North Carolina State University (3)
Amgen (2)
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Australia (2)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (2)
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (2)
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands (2)
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands. Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (2)
Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada (2)
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. (2)
Farnusch Kaschani, Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (2)
Head of Proteomics (2)
Koç University, Department of Molecular Biology and Genetic Cell Biology Lab head (2)
Laboratory of Pediatrics, UMCG, The Netherlands (2)
Max-Planck-Institute for Biology of Ageing Joseph-Stelzmann-Str. 9b 50931 Cologne, Germany (2)
Medical University of Vienna (2)
Molecular Genetics, RPTU Kaiserslautern, Germany (2)
Nanoparticle Systems Engineering Laboratory Department of Mechanical and Process Engineering ETH Zurich, Switzerland (2)
Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (part of Philip Morris International group of companies) (2)
Professor Laboratory Medicine and Pathology Mayo Clinic, Rochester, MN, USA (2)
UCSF (2)
1. Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway 2 Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain 3 Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain (1)
1.Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA 2.Department of Microbiology, Harvard Medical School, Boston, MA, USA 3.Howard Hughes Medical Institute, Boston, MA, USA (1)
1Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands 2Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands (1)

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Bead-based kinase phosphorylation profiling identifies SRC as a therapeutic target in glioblastoma

Here we describe a bead-based method capable of profiling tyrosine kinase phosphorylations in a multiplexed, high-throughput and low-cost manner. This approach allows for the discovery of tyrosine kinase-activating events, even when the DNA sequence is wild-type. In an effort to pilot the establishm...

ORGANISM(S): Homo sapiens

2010-06-24 | E-GEOD-13808 | biostudies-arrayexpress

A magnetic bead-based workflow for sensitive and streamlined cell surface proteomics

Cell-surface proteins represent an important class of molecules for therapeutic targeting and defining cellular phenotypes. However, their enrichment and detection via mass spectrometry-based proteomics remains challenging due to low abundance, posttranslational modifications, hydrophobic regions, a...

ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse)

2024-01-21 | PXD043678 | Pride

Refinement of paramagnetic bead–based digestion protocol for automatic sample preparation using an artificial neural network

Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction an...

ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Mus musculus (Mouse) Homo sapiens (Human) Escherichia coli Rattus norvegicus (Rat)

2024-05-31 | PXD048358 | Pride

Bile Magnetic beads Protein aggregation Sp3 protein digestion Artificial neural network

Streamlined instrument-free lysis for the detection of Candida auris.

Not available

S-EPMC10710429 | biostudies-literature

Pre-analytical Sample Quality Determines Performance of Plasma Proteomics Workflows for Biomarker Discovery

This dataset contains mass spectrometry-based proteomic analyses of human plasma samples processed through five distinct proteomics workflows: neat plasma, perchloric acid precipitation with neutralization (PCA-N), and three bead-based enrichment methods (SAX magnetic beads, Sera Sil 700 magnetic be...

ORGANISM(S): Homo sapiens (Human)

2025-08-21 | PXD063572 | Pride

Pre-analytical variables Lc-ms Plasma proteomics Bead-based enrichment Cellular contamination Sample quality

Pre-analytical Sample Quality Determines Performance of Plasma Proteomics Workflows for Biomarker Discovery part02

ORGANISM(S): Homo sapiens (Human)

2025-08-21 | PXD063593 | Pride

Pre-analytical variables Lc-ms Plasma proteomics Bead-based enrichment Cellular contamination Sample quality

Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer.

Not available

S-EPMC7232467 | biostudies-literature

Rapid Extraction of Viral Nucleic Acids Using Rotating Blade Lysis and Magnetic Beads.

Not available

S-EPMC9407373 | biostudies-literature

Using repeated lysis steps fractionates between heterotrophic and cyanobacterial DNA extracted from xenic cyanobacterial cultures.

Not available

S-EPMC12341861 | biostudies-literature

Evaluating Protein Extraction Techniques for Elucidating Proteomic Changes in Yeast Deletion Strains

Alterations in protein abundance profiles in yeast deletion strains are frequently utilized to gain insights into cellular functions and regulatory networks, most of which are conserved in higher eukaryotes. Here, we investigate the impact of protein extraction methodologies on proteomic analysis of...

ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast)

2025-08-04 | PXD063969 | Pride

Protein extraction Bead-based lysis Sumoylation Mass spectrometry Gene deletion Yeast proteomics

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