Activity based probes

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Transcriptomics (3917)
Unknown (1181)
Proteomics (202)
Genomics (148)
Other (3)
Metabolomics (3)
Models (2)
Methylation profiling (1)

Organisms

Homo sapiens (1592)
Mus musculus (649)
Drosophila melanogaster (162)
Arabidopsis thaliana (125)
Rattus norvegicus (105)
Caenorhabditis elegans (88)
Saccharomyces cerevisiae (78)
Sus scrofa (58)
Danio rerio (55)
Bos taurus (37)
Escherichia coli (29)
Gallus gallus (24)
Daphnia magna (21)
Oryza sativa (20)
Macaca mulatta (19)
Zea mays (16)
Pseudomonas putida (16)
synthetic construct (14)
Salmo salar (14)
Plasmodium falciparum (14)
Pimephales promelas (13)
Bifidobacterium breve UCC2003 (13)
Ovis aries (13)
Vitis vinifera (12)
Mycobacterium tuberculosis (12)
Oncorhynchus mykiss (12)
Apis mellifera (11)
Schizosaccharomyces pombe (11)
Escherichia coli str. K-12 substr. MG1655 (11)
Triticum aestivum (10)

Organisms

Homo sapiens (45)
Mus musculus (17)
Danio rerio (3)
Rattus norvegicus (3)
Pseudomonas aeruginosa UCBPP-PA14 (2)
Escherichia coli str. K-12 substr. MG1655 (2)
Listeria monocytogenes serotype 4b str. F2365 (1)
Fusarium fujikuroi IMI 58289 (1)
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (1)
Pseudomonas [fluorescens] SBW25 (1)
Burkholderia cepacia (1)
Porphyromonas gingivalis (1)
Yersinia pestis (1)
Cicer arietinum (1)
Mycobacterium tuberculosis (1)
Arabidopsis (1)
Pseudomonas aeruginosa (1)
Streptococcus pyogenes (1)
Drosophila melanogaster (1)
Bos taurus (1)
Phaseolus vulgaris (1)
Toxoplasma gondii (1)
Staphylococcus aureus (1)

Repository

biostudies-arrayexpress (3923)
pride (152)
ENA (102)
geo (45)
MassIVE (25)
iProX (17)
EGA (11)
jPOST (3)
MetaboLights (3)
Cell Collective (2)
LINCS (1)
PanoramaPublic (1)

Tissue

Cell culture (32)
Epithelial cell (13)
Brain (9)
Liver (8)
Lung (7)
Kidney cell (6)
B cell (5)
Lung epithelium (4)
Leaf (4)
Permanent cell line cell (4)
Blood (4)
Breast (3)
Melanocyte (3)
Cell suspension culture (3)
HeLa cell (3)
Fibroblast (3)
Primary cell (3)
Blood cell (3)
T cell (3)
Lymphocyte of B lineage (2)
Breast cancer cell line (2)
Whole body (2)
Hepatocyte (2)
Culture condition:-induced cell (1)
Stigma (1)
Skin cancer cell (1)
Luminal cell of prostate epithelium (1)
Endocervical epithelium (1)
Gastrointestinal mucosa (1)
Pancreatic acinar cell (1)

Disease

Normal (31)
Breast cancer (13)
Melanoma (6)
Breast adenocarcinoma (4)
Acute promyelocytic leukemia (3)
Neuroblastoma (3)
HHV-6B infected (2)
Primary tumor (2)
Leukemia (2)
Papillary thyroid carcinoma (2)
Head and neck squamous cell carcinoma (2)
Inoculated with P. syringae pv. tomato strain DC3000 + avrRps4 (1)
Toxicity (1)
MAS (1)
High grade glioblastoma (1)
Peripheral neuropathy (1)
Primary effusion lymphoma (PEL) (1)
Dermal neurofibroma (1)
Chronic lymphocytic leukemia (CLL) (1)
Epithelioid mesothelioma (1)
Large cell carcinoma (1)
Invasive pituitary adenoma (1)
Extranodal NK/T-Cell Lymphoma derived cell line (1)
B-cell chronic lymphocytic leukemia (1)
CUP (1)
Ependymoma (1)
Not applicable (1)
Keratoconus (1)
Unclassified carcinoid (1)
B. dendrobatidis infection (1)

Technology Type

Mass Spectrometry (152)
Affinity purification coupled with mass spectrometry proteomics (50)
Shotgun proteomics (48)
Bottom-up proteomics (44)
Data-dependent acquisition (31)
Data-independent acquisition (9)
Gel-based experiment (9)
Affinity proteomics (6)
Mass spectrometry (3)
SWATH MS (3)
DiaPASEF (2)
Top-down proteomics (2)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
ILLUMINA, NextSeq 500 (1)
Illumina Genome Analyzer IIx (1)
KiNativ (1)
Mass spectrometry (1)
RNA mass spectrometry (1)

Instrument Platform

Illumina NovaSeq 6000 (97)
NextSeq 500 (30)
Illumina NovaSeq X (20)
Illumina HiSeq 2500 (14)
Illumina HiSeq 2000 (13)
Illumina HiSeq 4000 (13)
NextSeq 2000 (11)
NextSeq 550 (10)
DNBSEQ-T7 (9)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (7)
GenePix 4000B [Axon Instruments] (7)
NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (6)
See manuscript (5)
GenePix 4000A [Axon Instruments] (5)
DNBSEQ-G400 (5)
FastPrep‑24 homogenizer (MP Biomedicals) (4)
None (4)
Affymetrix GeneChip Scanner 3000 7G (4)
418 [Affymetrix] (4)
ScanArray Express HT [PerkinElmer] (4)
Scanning hardware (4)
NA (4)
MinION (4)
ScanArray 5000 [PerkinElmer] (3)
G2505A DNA microarray scanner [Agilent] (3)
Axon GenePix 4000B scanning hardware (3)
Illumina MiSeq (3)
Illumina HiSeq 1500 (3)
Poly-T oligo-attached magnetic beads (2)
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)

Publication Date

2010 (660)
2013 (502)
2011 (475)
2012 (441)
2014 (405)
2015 (343)
2016 (189)
2008 (165)
2009 (157)
2025 (137)
2026 (132)
2007 (96)
2024 (79)
2006 (49)
2022 (47)
2023 (46)
2019 (39)
2018 (39)
2021 (38)
2017 (37)
2020 (34)
2005 (29)
2004 (14)
2003 (2)

CHEBI ID

CHEBI:27524 (1)
CHEBI:186165 (1)
CHEBI:165564 (1)
CHEBI:183136 (1)
CHEBI:1958 (1)
CHEBI:17282 (1)
CHEBI:170068 (1)
CHEBI:170157 (1)
CHEBI:170156 (1)
CHEBI:16485 (1)
CHEBI:63979 (1)
CHEBI:156190 (1)
CHEBI:170122 (1)
CHEBI:186499 (1)
CHEBI:86072 (1)
CHEBI:53013 (1)
CHEBI:88493 (1)
CHEBI:1014 (1)
CHEBI:16996 (1)
CHEBI:81564 (1)
CHEBI:46234 (1)
CHEBI:27584 (1)
CHEBI:78600 (1)
CHEBI:36405 (1)
CHEBI:17847 (1)
CHEBI:28125 (1)
CHEBI:30776 (1)
CHEBI:72733 (1)
CHEBI:73028 (1)
CHEBI:74640 (1)

Metabolite Name

N-acetyl-glutamic acid (1)
Maltose methoxyamine (1)
Glucose methoxyamine (1)
D(-)-Quinic acid (1)
Arabinose methoxyamine (1)
9,10,18-trihydroxyoctadecanoic acid (1)
Ceramide phosphoethanolamine (d31:0) (1)
Ceramide phosphoethanolamine (t35:0) (1)
1-octadecyl-sn-glycero-3-phosphoinositol-3-phosphate (1)
Phosphatidylinositol (12:0) (1)
18-hydroxycorticosterone (1)
Thiamine(1+) diphosphate (1)
Hesperetin sulfate (1)
Naringenin sulfate (1)
N-methylserotonin (1)
Cis-Caffeic acid (1)
3-phenylpropionic acid (1)
2-hydroxyoctanoic acid (1)
PA(15:0/20:2(11Z,14Z)) (1)
PA(20:2(11Z,14Z)/15:0) (1)
Hexanoic acid (1)
11-dehydrocorticosterone (1)
Hydroxylamine (1)
Hexadecenoylcarnitine (1)
P-cresol (1)
Hexadecanoic acid (1)
Ubiquinone-1 (1)
9,10,13-Trihydroxystearic acid (1)
3-Hydroxypyridine (1)
Lactic acid (1)

First Public Date

2014 (34)
2024 (12)
2023 (8)
2017 (7)
2026 (6)
2025 (5)
2019 (5)
2018 (5)
2016 (5)
2015 (5)
2022 (3)
2020 (3)
2021 (2)
2013 (2)

Classification

bacteria (13)
fungi (1)
protozoa (1)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (2)

Study type

Transcription profiling by array (2680)
Comparative genomic hybridization by array (296)
ChIP-chip by tiling array (212)
RNA-seq of coding RNA (148)
Methylation profiling by array (122)
Other (77)
RNA-seq of coding RNA from single cells (59)
Transcription profiling by tiling array (54)
Unknown experiment type (53)
ChIP-chip by array (37)
MicroRNA profiling by array (24)
RNA-seq of total RNA (22)
ChIP-seq (16)
RNA-seq of non coding RNA (11)
Animal - One-color microarray (10)
Genotyping by array (10)
Methylation profiling by high throughput sequencing (10)
Spatial transcriptomics by high-throughput sequencing (8)
Single nucleus RNA sequencing (8)
Transcription profiling by RT-PCR (6)
MicroRNA profiling by high throughput sequencing (5)
DNA-seq (5)
Human - One-color microarray (4)
Proteomic profiling by array (4)
Genotyping by high throughput sequencing (4)
Cell line - One-color microarray (3)
RNAi profiling by array (3)
Cell line - Methylation microarray (2)
Human - Two-color microarray (2)
One-color microarray (2)

Release Date

2010 (675)
2013 (531)
2011 (489)
2012 (468)
2014 (446)
2015 (389)
2016 (242)
2025 (226)
2008 (176)
2009 (170)
2024 (150)
2022 (134)
2021 (127)
2026 (122)
2019 (114)
2018 (113)
2020 (111)
2023 (106)
2007 (104)
2017 (89)
2006 (53)
2005 (33)
2004 (20)
2003 (5)
2002 (3)
2000 (3)
1998 (3)
1999 (2)

Lab affiliation

Scripps Research (5)
University of York (5)
Principal Investigator Centre for Targeted Protein Degradation, School of Life Sciences (4)
Moffitt Cancer Center Tampa, FL, USA (4)
Pacific Northwest National Laboratory, USA (4)
Moffitt Cancer Center (3)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (3)
Moffitt Cancer Center Tampa, FL (2)
GSK (2)
Professor of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, The Netherlands (2)
School of Health and Life Sciences, Teesside University, UK (2)
Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich (TUM), Ernst-Otto-Fischer-Stra?e 8, 85748 Garching, Germany (2)
Principal Investigator • Centre for Targeted Protein Degradation (2)
Technical University Munich, Department of Chemistry, Lichtenbergstrasse 4, 85748 Garching bei Muenchen, Germany (2)
Principal Investigator Centre for Targeted Protein Degradation (2)
Department of Biology, IISER Pune (2)
Pacific Northwest National Laboratory (2)
Technical University of Munich (TUM), TUM School of Natural Sciences, Department Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany (1)
Department of Chemistry, Scripps Research Institute, La Jolla (1)
Proteomics Group (1)
Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543 (1)
Biomolecular Mass Spectrometry and Proteomics, University Utrecht, Utrecht, The Netherlands (1)
Department of Molecular and Applied Microbiology Leibniz Institute for Natural Product Research and Infection Biology - Hans KnÃ¶ll Institute Jena (Leibniz-HKI) Jena, Germany (1)
1. Institute of Chemical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China; 2. School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China (1)
The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom (1)
Lipolysis and Bacterial Pathogenicity team, LISM UMR7255, CNRS, Aix-Marseille Univ. , IMM FR3479, Marseille, France (1)
Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching b. München 85747, Germany; Chair of Organic Chemistry II, Technische Universität München, Garching b. München 85747, Germany (1)
Department of Biological Chemistry, David Geffen School of Medicine, UCLA, USA (1)
National Center for Advancing Translational Sciences (NCATS) NIH (1)
Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany (1)

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Discovery of highly Potent and Selective Activity-Based Probes for the Deubiquitylating Enzyme USP30

Ubiquitin-specific protease 30 (USP30) is a deubiquitylating enzyme (DUB) localized in the mitochondrial membrane, which is related to PINK1/Parkin-mediated mitophagy, pexophagy, BAX/BAK-dependent apoptosis, and IKKβ-USP30-ACLY-regulated lipogenesis/tumorigenesis. Mission therapeutics pointed their ...

ORGANISM(S): Homo sapiens (Human)

2024-05-22 | PXD044792 | Pride

Pull down of enzymes using xylanase activity based probes (ABPs) from Bacillus subtilis secretome

This experiment aimed to identify GH5/10/30 arabinoxylan and glucuronoxylan-specific xylanases from secretomes produced by Bacillus subtilis using decorated activity based probes.

ORGANISM(S): Bacillus subtilis

2026-06-23 | PXD065065 | Pride

Activity based probes Xylan Bacillus subtilis Xylanases

Pull down of enzymes using alpha-amylase activity based probes from a complex compost sample

This experiment aimed to identify new GH13 alpha-amylaases from a complex compost sample using activity based probes. The substrate specificities of these novel enzymes could also be assigned by using -1 and -2 branched activity based probes.

ORGANISM(S): Parageobacillus toebii Pseudoxanthomonas suwonensis J47 Geobacillus thermodenitrificans Aeribacillus pallidus

2025-06-16 | PXD053848 | Pride

Alpha-amylases Tims-tof ht Activity-based probes Pull-down Glycoside hydrolase

SILAC E3 ligase activity-based profiling of interferon-stimulated THP-1 cells

Activity-based probes that covalently label proteins with transthiolating E3 ligase activity were used to determine differential changes in E3 ligase activity upon interferon stimulation of monocytic THP-1 cells.

ORGANISM(S): Homo sapiens (Human)

2026-05-22 | PXD065503 | Pride

Silac Activity-based probes

Pull down of enzymes using xylanase activity based probes from Clostridium thermocellum

This experiment aimed to identify GH10 xylanases from Clostridium thermocellum secretome sample using activity based probes.

ORGANISM(S): Acetivibrio thermocellus DSM 2360

2026-06-23 | PXD065060 | Pride

Clostridium thermocellum Activity-based probes Xylanases

Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes

Goal: To identify copy number variation in normal individuals using high density, non-polymorphic oligonucleotide probes Background DNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the ...

ORGANISM(S): Homo sapiens

2008-04-24 | E-GEOD-9053 | biostudies-arrayexpress

Xanthohumol Activity-Based Probes Targeting Flavonoid Catabolism

Xanthohumol, the principle prenylflavonoid found in hops (Humulus lupulus), is a potential anti-inflammatory agent in the gut. To investigate the interactions between xanthohumol and catabolic gut bacteria, and its role in the anti-inflammatory pathway, a suite of xanthohumol-derived activity-based ...

ORGANISM(S): Eubacterium Ramulus (ncbitaxon:39490) Escherichia Coli (ncbitaxon:562)

2022-02-04 | MSV000088789 | MassIVE

Glycosylated cyclophellitol-derived activity-based probes and inhibitors for cellulases

Cellulases and related β-1,4-glucanases are essential components of lignocellulose-degrading enzyme mixtures. The detection of β-1,4-glucanase activity typically relies on monitoring the breakdown of purified lignocellulose-derived substrates or synthetic chromogenic substrates, limiting the activit...

ORGANISM(S): Aspergillus niger NRRL3

2021-09-09 | PXD019930 | Pride

Abpp Activity-based probe Cellulases Cyclophellitol

Activity-based protein profiling of xylan-degrading glycoside hydrolases in Aspergillus secretomes

Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides towards breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined...

ORGANISM(S): Aspergillus Niger (ncbitaxon:5061)

2019-04-24 | MSV000083714 | MassIVE

Pull down of enzymes using alpha-amylase activity based probes from Bacteroides thetaiotaomicron lysate

This experiment aimed to identify GH13 alpha-amylaases from Bacteroides thetaiotaomicron lysate using activity based probes.

ORGANISM(S): Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)

2025-06-16 | PXD053850 | Pride

Alpha-amylases Tims-tof ht Activity-based probes Pull-down Glycoside hydrolase

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5466 Results

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