Sonication - OmicsDI

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Proteomics (3857)
Genomics (1626)
Unknown (1257)
Transcriptomics (1208)
Metabolomics (289)
Other (9)
Methylation profiling (4)
Genomic (1)

Organisms

Mus musculus (547)
Homo sapiens (540)
Drosophila melanogaster (526)
Caenorhabditis elegans (354)
Saccharomyces cerevisiae (111)
Schizosaccharomyces pombe (39)
Arabidopsis thaliana (39)
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Streptomyces coelicolor (23)
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Escherichia coli str. K-12 substr. MG1655 (12)
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Geobacter sulfurreducens PCA (7)
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Oryza sativa Japonica Group (7)
Listeria monocytogenes (6)
Bacillus subtilis subsp. subtilis str. 168 (5)
Macaca mulatta (5)
Streptomyces coelicolor A3(2) (5)
Vibrio cholerae (5)
Gallus gallus (5)
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Canis lupus familiaris (4)
Burkholderia cenocepacia (4)
Saccharomyces cerevisiae SK1 (3)

Organisms

Homo sapiens (89)
Mus musculus (83)
Saccharomyces cerevisiae (26)
Drosophila melanogaster (13)
Danio rerio (4)
Arabidopsis thaliana (4)
Human gammaherpesvirus 8 (3)
Schizosaccharomyces pombe (3)
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Halobacterium salinarum NRC-1 (2)
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Cicer arietinum (2)
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Caenorhabditis elegans (2)
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Colias eurytheme (1)
Saccharomyces cerevisiae W303 (1)

Repository

pride (3756)
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Tissue

Cell culture (768)
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Cell suspension culture (52)
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Cell line (5)
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Optic nerve (1)
Neurons (1)
Human intrahepatic cholangiocarcarcinoma cell line (1)
Prostate (1)

Disease

Breast cancer (104)
Disease free (80)
Acute leukemia (60)
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Alzheimer's disease (23)
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Lymphoma (20)
Malignant neoplasm of ovary (20)
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Non-small cell lung carcinoma (17)
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Lung cancer (13)
Plasmodium falciparum malaria (13)
Pancreatic cancer (12)
Brain cancer (10)
Malaria (9)
Triple-receptor negative breast cancer (4)
Normal (3)
Infiltrating ductal carcinoma (2)
Malignant glioma (1)
Post-stasis (1)
Symptom free (1)
Megakaryoblastic leukaemia (1)
Breast carcinoma (1)
Neuropathy (1)
Eye disease (1)

Technology Type

Mass Spectrometry (3758)
Shotgun proteomics (2089)
Bottom-up proteomics (845)
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Data-independent acquisition (296)
SWATH MS (164)
Mass spectrometry (162)
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Chemical cross-linking coupled with mass spectrometry proteomics (65)
DiaPASEF (37)
SRM/MRM (37)
All-ion fragmentation (24)
NMR spectroscopy (19)
HDMSE (16)
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MSE (15)
Metaproteomics (12)
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Proteogenomics (5)
NMR spectroscopy assay (4)
ESI (2)
Glycoproteomics (2)
Sodium dodecyl sulfate polyacrylamide gel electrophoresis (1)

Instrument Platform

Illumina HiSeq 2000 (56)
NextSeq 500 (49)
Illumina NovaSeq 6000 (44)
Illumina HiSeq 2500 (41)
Illumina HiSeq 4000 (27)
Illumina MiSeq (20)
Illumina Genome Analyzer IIx (14)
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AB 5500 Genetic Analyzer (2)
Affymetrix (2)
Ion Torrent PGM (2)
Ion Torrent Proton (2)
Illumina HiSeq 1000 (2)
QSonica Q800R (1)
Bio-Rad Mini-PROTEAN electrophoresis system and wet transfer cassettes, (1)
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Performed by Novogene; Illumina library preparation instrumentation (provider standard) (1)
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Publication Date

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2013 (642)
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2010 (221)
2018 (219)
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2017 (136)
2009 (33)
2008 (30)
2007 (17)
2006 (14)
2005 (10)
2004 (2)
2003 (1)

CHEBI ID

CHEBI:15741 (43)
CHEBI:16335 (42)
CHEBI:17368 (42)
CHEBI:15428 (37)
CHEBI:17596 (37)
CHEBI:18012 (35)
CHEBI:30769 (35)
CHEBI:15891 (34)
CHEBI:16449 (34)
CHEBI:17154 (33)
CHEBI:28300 (32)
CHEBI:25017 (32)
CHEBI:28044 (32)
CHEBI:16704 (32)
CHEBI:17568 (32)
CHEBI:16027 (32)
CHEBI:16750 (30)
CHEBI:15354 (30)
CHEBI:32816 (29)
CHEBI:16919 (29)
CHEBI:27266 (28)
CHEBI:17750 (28)
CHEBI:18237 (28)
CHEBI:17268 (28)
CHEBI:17822 (27)
CHEBI:18186 (27)
CHEBI:16708 (27)
CHEBI:24898 (27)
CHEBI:25094 (27)
CHEBI:26271 (26)

Metabolite Name

Hypoxanthine (58)
Uridine (53)
Adenosine (50)
Taurine (49)
Adenine (48)
Guanosine (46)
Creatine (46)
Inosine (46)
Xanthine (45)
Uracil (44)
Betaine (40)
Choline (40)
L-Histidine (39)
Azelaic acid (39)
Creatinine (39)
L-Phenylalanine (36)
Glycine (35)
Pantothenic acid (34)
Riboflavin (34)
L-Threonine (33)
Xanthosine (32)
Deoxycholic acid (32)
Phenylalanine (32)
Cytidine (32)
L-Tyrosine (32)
Citric acid (31)
Guanine (31)
L-Glutamine (31)
Glycerophosphocholine (31)
L-Valine (31)

First Public Date

2019 (35)
2024 (32)
2018 (32)
2017 (31)
2020 (30)
2014 (30)
2026 (27)
2025 (27)
2023 (25)
2021 (24)
2022 (23)
2016 (20)
2013 (18)
2015 (16)
2012 (5)

Classification

bacteria (6)
viruses (5)
protozoa (4)

Modification

4x(15)N labeled L-arginine (8)
2x(15)N labeled L-lysine (7)
4-tetrahydrothiazine-3-carboxylic acid (5)
15.994915 (3)
57.021464 (3)
N6-dimethyl-L-lysine (3)
Not available (3)
+3amu) (2)
15.99491 (2)
4 (2)
42.010565 (2)
57.02146 (2)
0.984 (1)
15.9949 (1)
27.994915 (1)
4'-dihydroxyphenylalanine (1)
45.029395 (1)
4x(2)H labeled dimethylated L-lysine (1)
4x(2)H labeled dimethylated residue (1)
57.0215 (1)
58.005479 (1)
Heavy form (1)
Heavy form - site K (1)
Medium form - site K (1)
Medium form - site N-term (1)
N6 (1)

Study type

ChIP-seq (1061)
ChIP-chip by tiling array (538)
RNA-seq of coding RNA (182)
Transcription profiling by array (151)
Methylation profiling by high throughput sequencing (104)
ChIP-chip by array (86)
Methylation profiling by array (59)
Other (49)
DNA-seq (34)
Comparative genomic hybridization by array (30)
Cell line - High-throughput sequencing (15)
Transcription profiling by tiling array (12)
Animal - High-throughput sequencing (9)
Bisulfite-seq (7)
RNA-seq of non coding RNA (7)
RNA-seq of total RNA (6)
High-throughput sequencing (5)
Genotyping by high throughput sequencing (5)
MeDIP-seq (4)
Hi-C (4)
RIP-seq (4)
RNA-seq of coding RNA from single cells (4)
FAIRE-seq (3)
Human - High-throughput sequencing (2)
Plant - High-throughput sequencing (2)
CLIP-seq (2)
MBD-seq (2)
Proteomic profiling by array (2)
GRO-seq (1)
Transcription profiling by SAGE (1)

Release Date

2013 (656)
2011 (344)
2015 (289)
2014 (284)
2010 (225)
2012 (205)
2022 (204)
2016 (200)
2023 (188)
2021 (179)
2025 (149)
2020 (146)
2019 (128)
2024 (114)
2018 (102)
2017 (64)
2026 (48)
2009 (40)
2008 (30)
2007 (24)
2006 (16)
2005 (10)
2004 (4)
2003 (4)
2002 (1)
2000 (1)
1998 (1)

Lab affiliation

Wageningen University (33)
The University of Melbourne (28)
Functional Proteomics, ICR (14)
The Institute of Cancer Research (14)
School of Life Sciences, Central China Normal University, Wuhan, Hubei province, China (13)
The University of Sydney (11)
Laboratoire de Spectrométrie de Masse BioOrganique, Analytical Science department, IPHC, CNRS, Strasbourg University, UMR7178, Strasbourg, France (10)
Proteomics Core Facility, Biozentrum, University of Basel, Switzerland (9)
DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (8)
Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital (8)
State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China (8)
University of Southampton (8)
Wellcome Trust Sanger Institute (8)
EDyP (7)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (7)
Michigan State University (7)
University of Alabama at Birmingham, Department of Pathology, Division MCP, O'Neal Comprehensive Cancer Center (7)
1) Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland 2) Faculty of Science, University of Zurich, Zurich, Switzerland (6)
Head of the Curie Institute Mass Spectrometry Platform (6)
Karolinska Institutet, Stockholm, Sweden (6)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (6)
Department of Biology, Institute of Microbiology, ETH Zürich, Switzerland (5)
Department of Chemistry, Scripps Research (5)
Molecular Genetics, RPTU Kaiserslautern, Germany (5)
Proteomics Center, Erasmus MC (5)
Proteomics, Leibniz-Institut für analytische Wissenschaften -ISAS - e.V., Germany (5)
State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences • Beijing, Beijing Institute of Lifeomics, Beijing, China (5)
The Institute of Cancer Research, London (5)
University of Edinburgh (5)
Administrerende Direktør • Novo Nordisk Foundation Center for Protein Research (4)

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Lipidomics Dataset of Sonication-Induced Traumatic Optic Neuropathy in Mice

Not available

ORGANISM(S): Mus musculus

ST001273 | MetabolomicsWorkbench

Influence of ultrasound treatment on the physical characteristics and metabolites of tempe

Tempe is a traditional fermented soybean food product that is rich in proteins. For centuries, the tempe production method has remained unchanged; however, modification of the tempe production process may improve its nutritional quality. In this study, we introduced and optimized ultrasound treat...

2024-08-22 | MTBLS2984 | MetaboLights

Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues

Tissue lysis using urea buffer was adopted in our previously published CPTAC protocol for mass spectrometry (MS)-based quantitative global proteomic and phosphoproteomic analysis. Herein, we reported an update to this initial protocol by implementing a sonication step into urea-based tissue lysis. S...

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

2025-07-28 | PXD050336 | Pride

ASAP – Automated Sonication free Acid assisted Proteomes from cells & FFPE tissues

Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for retrospective studies but protein extraction and subsequent sample processing steps have shown to be challenging for mass spectrometry (MS) analysis. Streamlined high-throughput sample preparation workflows are essential...

ORGANISM(S): Homo sapiens (Human)

2024-05-21 | PXD036910 | Pride

Pediatric tumors Trifluoroacetic acid Ffpe Sonication-free Clinical proteomics

Profiling chromatin state by single-cell itChIP-seq [sonication ChIP]

PRJNA431986 | ENA

ONT MinION sequencing of prosthetic joint infection sonication fluids

PRJEB23460 | ENA

Added diagnostic value of sonication of heart valves in infective endocarditis, a case-control study

PRJEB20613 | ENA

Sonication induced amorphisation in Ag nanowires.

Not available

S-EPMC6375950 | biostudies-literature