Visual proteomics

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Proteomics (376)
Unknown (304)
Transcriptomics (29)
Metabolomics (10)
Genomics (8)
Other (3)
Multiomics (1)

Organisms

Acidithiobacillus ferrooxidans ATCC 53993 (241)
Aerococcus urinae NBRC 15544 = CCUG 36881 (241)
Allexis (241)
Arabidopsis thaliana (241)
Candida albicans (241)
Cyanophora paradoxa (241)
Ensifer adhaerens (241)
Enterococcus faecalis (241)
Globicatella sanguinis (241)
Histomonas meleagridis (241)
Leishmania major strain Friedlin (241)
Homo sapiens (42)
Mus musculus (39)
Saccharomyces cerevisiae (2)
Danio rerio (2)
Larimichthys crocea (1)
Thermoplasma acidophilum DSM 1728 (1)
unidentified (1)
Bacillus subtilis (1)
Arabidopsis thaliana (1)
Macaca mulatta (1)
Rattus rattus (1)
Escherichia coli (1)
Gallus gallus (1)
Xenopus (1)
cellular organisms (1)
Labeo rohita (1)
Octopus berrima (1)
Pleuromamma xiphias (1)
Fusarium sinicum (1)

Organisms

Mus musculus (2)
Homo sapiens (1)

Repository

pride (241)
MassIVE (68)
biostudies-arrayexpress (39)
iProX (21)
jPOST (11)
PanoramaPublic (11)
MetaboLights (10)
geo (6)
PAXDB (6)
EGA (4)
ENA (4)
GPMDB (3)
PeptideAtlas (2)

Tissue

Cell culture (30)
Retina (25)
Brain (22)
Epithelial cell (11)
Skin (11)
Liver (10)
Blood plasma (8)
Whole body (8)
Vitreous humor (7)
Blood serum (5)
Cornea (5)
Malignant cell (5)
Optic nerve (5)
Permanent cell line cell (5)
Hepatocyte (4)
Kidney (4)
Plant cell (4)
Retinal cell (4)
B cell (3)
Colon (3)
Endothelial cell (3)
Eye (3)
Fibroblast (3)
Head (3)
Heart (3)
Keratinocyte (3)
Lens (3)
Lymph node (3)
Macrophage (3)
Eye (1)

Disease

Disease free (9)
Breast cancer (7)
Myopia (6)
Retinal degeneration (4)
Type 2 diabetes mellitus (4)
Not Available (3)
Wounds and Injuries (3)
Alzheimer's disease (2)
Autism spectrum disorder (2)
Colon cancer (2)
Exfoliation syndrome (2)
Glaucoma (2)
Lymphoma (2)
Multiple sclerosis (2)
Oculocutaneous albinism type III (2)
Optic atrophy 1 (2)
Pancreatic ductal adenocarcinoma (2)
Retinal disease (2)
Colon cancer metastasis (1)
Locally advanced rectal cancer (1)
Normal (1)
Age related macular degeneration (1)
Alpha 1-antitrypsin deficiency (1)
Amyotrophic lateral sclerosis type 21 (1)
Autosomal recessive congenital ichthyosis (1)
Barrett's esophagus (1)
Cataract (1)
Cervix carcinoma (1)
Charcot-Marie-Tooth disease (1)
Fuchs' endothelial dystrophy (1)

Technology Type

Mass Spectrometry (241)
Shotgun proteomics (112)
Bottom-up proteomics (70)
Data-dependent acquisition (25)
Gel-based experiment (23)
Data-independent acquisition (20)
Affinity purification coupled with mass spectrometry proteomics (9)
SWATH MS (8)
Mass spectrometry (7)
HDMSE (7)
Top-down proteomics (6)
Chemical cross-linking coupled with mass spectrometry proteomics (5)
NMR spectroscopy (3)
DiaPASEF (3)
SRM/MRM (3)
Illumina (2)
MSE (2)
Mass spectrometry imaging (2)
ILLUMINA, Illumina HiSeq 2500, Illumina HiSeq 2500 (ILLUMINA) (1)
Illumina HiSeq 2500 (ILLUMINA) (1)
All-ion fragmentation (1)

Instrument Platform

LTQ Orbitrap Elite (11)
Q Exactive (10)
Orbitrap Fusion Lumos (9)
LTQ Orbitrap Velos (8)
Orbitrap Fusion (6)
GC MS (4)
Q Exactive HF-X (4)
Instrument (3)
GC-MS (3)
Orbitrap Exploris 480 (3)
LTQ (2)
LTQ Orbitrap (2)
Q Exactive HF (2)
Agilent 7890A GC with 5975C inert XL MSD (1)
Compact (1)
LTQ Orbitrap XL (1)
LTQ Velos (1)
NanoACQUITY UPLC (1)
NanoElute (1)
OrbiTrap Exactive Q HF (1)
Orbitrap Eclipse (1)
Orbitrap HFX (1)
Q Exactive HFX (1)
Synapt G2 HDMS (1)
TimsTOF (1)
TimsTOF Pro2 (1)
TimsTOF SCP (1)
TimsTOF fleX (1)
TripleTOF 5600 (1)
TripleTOF 6600 (1)

Publication Date

2025 (54)
2022 (52)
2024 (48)
2023 (37)
2016 (30)
2026 (30)
2015 (26)
2021 (25)
2017 (24)
2020 (23)
2019 (18)
2018 (13)
2014 (11)
2013 (6)
2010 (4)
2012 (2)
2011 (2)
2009 (1)
2005 (1)
2003 (1)

UNIPROT ID/AC

143BA_DANRE (4)
143BB_DANRE (4)
A0A0G2L1F5_DANRE (4)
A0A0R4IB76_DANRE (4)
A0A0R4IFK0_DANRE (4)
A0A0R4IGN3_DANRE (4)
A0A0R4IHT0_DANRE (4)
A0A0R4IKF0_DANRE (4)
A0A0R4IPH2_DANRE (4)
A0A0R4IPV5_DANRE (4)
A0A0R4ITL8_DANRE (4)
A0A0R4IV67_DANRE (4)
A0A0R4IVC8_DANRE (4)
A0A140LGU1_DANRE (4)
A0A1L1QZF2_DANRE (4)
A0A2R8QA71_DANRE (4)
A0A2R8QDV2_DANRE (4)
A0A2R8RZR0_DANRE (4)
A0A2R9YJH5_DANRE (4)
A2BGR9_DANRE (4)
A2BHA3_DANRE (4)
A2CE51_DANRE (4)
A3KPR3_DANRE (4)
A5PMV7_DANRE (4)
A5PN55_DANRE (4)
A5WUQ7_DANRE (4)
A5WWI5_DANRE (4)
A5WWI6_DANRE (4)
A7MCR1_DANRE (4)
A7YT47_DANRE (4)

ENSEMBL ID

ENSDARG00000000103 (1)
ENSDARG00000000212 (1)
ENSDARG00000000380 (1)
ENSDARG00000000638 (1)
ENSDARG00000001431 (1)
ENSDARG00000001437 (1)
ENSDARG00000001578 (1)
ENSDARG00000001788 (1)
ENSDARG00000001915 (1)
ENSDARG00000001950 (1)
ENSDARG00000001993 (1)
ENSDARG00000001994 (1)
ENSDARG00000002021 (1)
ENSDARG00000002193 (1)
ENSDARG00000002400 (1)
ENSDARG00000002414 (1)
ENSDARG00000002467 (1)
ENSDARG00000002480 (1)
ENSDARG00000002502 (1)
ENSDARG00000002549 (1)
ENSDARG00000002589 (1)
ENSDARG00000002632 (1)
ENSDARG00000002696 (1)
ENSDARG00000002702 (1)
ENSDARG00000002768 (1)
ENSDARG00000002791 (1)
ENSDARG00000003032 (1)
ENSDARG00000003035 (1)
ENSDARG00000003077 (1)
ENSDARG00000003153 (1)

CHEBI ID

CHEBI:17822 (5)
CHEBI:30769 (5)
CHEBI:17992 (4)
CHEBI:27570 (4)
CHEBI:17234 (4)
CHEBI:28300 (4)
CHEBI:6650 (4)
CHEBI:18237 (4)
CHEBI:15741 (4)
CHEBI:32816 (4)
CHEBI:15428 (4)
CHEBI:18012 (4)
CHEBI:30915 (4)
CHEBI:27897 (4)
CHEBI:17368 (4)
CHEBI:26271 (3)
CHEBI:22660 (3)
CHEBI:30751 (3)
CHEBI:18186 (3)
CHEBI:26986 (3)
CHEBI:16708 (3)
CHEBI:16530 (3)
CHEBI:25017 (3)
CHEBI:28044 (3)
CHEBI:27266 (3)
CHEBI:18211 (3)
CHEBI:16704 (3)
CHEBI:15366 (3)
CHEBI:17750 (3)
CHEBI:15891 (3)

Metabolite Name

L-isoleucine (3)
Aspartic acid (3)
Histidine (2)
Pyruvic acid (2)
L-leucine (2)
Formic acid (2)
Glycine betaine (2)
Acetic acid (2)
3-hydroxybutyric acid (2)
3-methyl-2-oxobutanoic acid (2)
Leucine (2)
Fructose 6-phosphate (2)
Tryptophan (2)
Taurine (2)
Serine (2)
Hypoxanthine (2)
Guanosine (2)
Citrulline (2)
Glucose (2)
Choline (2)
Creatinine (2)
Glutamine (2)
L-alanine (2)
Uracil (2)
Glycine (2)
Citric acid (2)
Sucrose (2)
L-valine (2)
Valine (2)
L-tyrosine (2)

First Public Date

2026 (1)
2024 (1)
2021 (1)
2020 (1)

Modification

4x(15)N labeled L-arginine (5)
15.994915 (4)
10.008269 (3)
42.010565 (3)
45.029395 (3)
-17.026549 (2)
2x(15)N labeled L-lysine (2)
58.005479 (2)
+3amu) (1)
144.102062 (1)
4 (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
57.021464 (1)
6.020129 (1)
6x(2)H labeled dimethylated L-arginine (1)
Not available (1)

Study type

Transcription profiling by array (24)
Proteomic profiling by array (13)
Other (1)
RNA-seq of coding RNA (1)

Release Date

2025 (37)
2023 (33)
2015 (32)
2024 (32)
2022 (30)
2021 (26)
2016 (23)
2020 (23)
2019 (15)
2017 (12)
2014 (11)
2010 (11)
2013 (10)
2018 (10)
2012 (8)
2009 (7)
2026 (6)
2011 (6)
2008 (5)
2007 (3)
2005 (1)
2003 (1)
2002 (1)

Lab affiliation

Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (4)
Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine (3)
Center for Translational Vision Research, Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, 92697, USA; Department of Physiology and Biophysics, Department of Chemistry, Department of Molecular Biology and Biochemistry; University of California, Irvine, Irvine, CA, 92697, USA (3)
Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada (3)
Department of Biology University of California, Riverside (2)
Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA (2)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (2)
Duke University (2)
Lecturer/Associate Professor, School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland (2)
Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS). Helmholtz Centre for Infection Research (HZI). Department of Pharmacy at Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany. (2)
Pediatric, Developmental & Genetic Ophthalmology Section AND Ophthalmis Clinical Genetics Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute Intramural Research Program, NIH, US Government (2)
Proteomics Core Facility, University of Oslo and Oslo University Hospital (2)
Research Officer|Proteomics and Small Molecule Mass Spectrometry Laboratory | Central Analytical Research Facility (CARF)| Queensland University of Technology | Address: Level 6, P Block, Gardens Point Campus, 2 George St Brisbane QLD 4000 (2)
Research Unit Protein Science, Helmholtz Zentrum München (2)
University of Miami Bascom Palmer Eye Institute (2)
1. Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. 2. Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands. (1)
1. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany, 2. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom; (1)
1. Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA 2. Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA (1)
1. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; 2. Proteomics and Singal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (1)
1Brunason Center for Translational Vision Research, Department of Ophthalmology and Visual Sciences, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, 92697, USA; 2Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA; 3Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697, USA (1)
1Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD (1)
1Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, (1)
1Gavin Herbert Eye Institute –Brunson Center for Translational Vision Research, Department of Ophthalmology and Visual Sciences, University of California Irvine, Irvine, CA 92697, USA 2Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA 3Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA 4Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA (1)
1Laboratory of Plant Physiology, Institute of Biology, University of Neuchâtel, Switzerland,Neuchâtel (1)
2Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA (1)
2IDAEA-CSIC, Jordi Girona 18, 08034, Barcelona, Spain (1)
8Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden (1)
Associate Professor and Research Director Department of Ophthalmology and Visual Neuroscience University of Minnesota (1)
Associate Professor of Neurology Institute for Cell Engineering Johns Hopkins University School of Medicine (1)
Associate Professor, University of Maryland College Park, MD 20742 (1)

Tags

xref:PubMed:34865853 (1)
xref:PubMed:34001262 (1)

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Deep Visual Proteomics reveals DNA replication stress as a hallmark of Signet Ring Cell Carcinoma

Background and Aims: Signet-Ring (SR) cell carcinoma (SRCC) is an increasingly prevalent form of gastric cancer, known for its late presentation and poor treatment outcomes. Using our spatial proteomics pipeline, Deep Visual Proteomics (DVP), we aimed to comprehensively explore the SRCC proteome lan...

ORGANISM(S): Homo sapiens (Human)

2025-05-07 | PXD053079 | Pride

Bypassing Androgens: CNS-Targeted Estrogen Delivery Rescues the Gonadectomized Male Rat Visual Cortex Neuroproteome

Mass spectrometry-based proteomics has become instrumental for elucidating the molec-ular mechanisms of neurodegeneration, enabling the identification of disease-associated proteomic alterations and protein-level responses to therapeutic interventions. Building on our previous proteomic characteriza...

ORGANISM(S): Rattus norvegicus (Rat)

2026-09-14 | PXD080450 | Pride

Androgen deprivation bioinformatics dhed gonadectomy neuroprotection neuropro-teomics mass spectrometry oxidative stress visual cortex.

Bypassing Androgens: CNS-Targeted Estrogen Delivery Res-cues the Gonadectomized Male Rat Visual Cortex Neuropro-teome

ORGANISM(S): Rattus norvegicus (Rat)

2026-09-14 | PXD080391 | Pride

Androgen deprivation bioinformatics dhed gonadectomy neuroprotection neuropro-teomics mass spectrometry oxidative stress visual cortex.

Spatial characterization and stratification of colorectal adenomas by Deep Visual Proteomics

Background and Aims: Colorectal adenomas (CRAs) are precursor lesions that can progress to adenocarcinomas. Current clinical guidelines categorize patients into risk groups based on adenoma characteristics observed during index colonoscopy, but this may lead to overtreatment. Our aim was to establis...

ORGANISM(S): Homo sapiens (Human)

2024-08-04 | PXD046999 | Pride

Spatial Mass spectrometry Pathology Cancer Colorectal adenoma Proteomics Dvp

CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes from Azotobacter vinelandii

Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging vis...

ORGANISM(S): Azotobacter vinelandii Bacteria

2026-05-25 | PXD062624 | Pride

Nitrogen fixation Cryoet Visual proteomics Anerobic Cryoem

Multi-omics analysis identifies ALDH7A1 as a key regulator of the visual-olfactory bimodal learning in honeybee

Specific genes or encoded proteins are involved in regulating various learning models of different species through certain signaling pathways，but whether there are also regulatory genes during bimodal learning and memory is largely unknown. Using a multi-omics approach to examine gene expression cha...

ORGANISM(S): Apis mellifera (Honeybee)

2021-09-13 | PXD017008 | Pride

Visual-olfactory bimodal learning

Deep Visual Proteomics defines single-cell identity and heterogeneity.

Not available

S-EPMC9371970 | biostudies-literature

Deep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation

Intestinal epithelial damage predisposes to chronic disorders like inflammatory bowel disease. The organoid model allows the cultivation, expansion and analysis of primary intestinal epithelial cells and has been instrumental in studying epithelial behavior in homeostasis and disease. Recent advance...

ORGANISM(S): Homo sapiens (Human)

2025-09-11 | PXD052341 | Pride

Colon Spatial proteomics Deep visual proteomics Organoids Proteomics

AI-powered Deep Visual Proteomics unmasks critical molecular transitions in pancreatic cancer precursors

Pancreatic ductal adenocarcinoma (PDAC) evolves through precursors, yet the protein programs that govern early progression remain poorly defined. We applied Deep Visual Proteomics - computational pathology, laser microdissection, and mass spectrometry (MS) - to profile normal ducts, acinar-to-ductal...

ORGANISM(S): Homo sapiens (Human)

2026-03-31 | PXD072559 | Pride

Deep visual proteomics Laser microdissection Pathology foundation models Mass spectrometry Artificial intelligence Precursor Spatial Tumor Pancreatic ductal adenocarcinoma

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics

Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we introduced mipDVP, an advanced approach integrating highly multiplexed imaging, single-cell laser microdissection, and sensitive mass spectrometry to spatially prof...

ORGANISM(S): Homo sapiens (Human)

2024-12-19 | PXD057118 | Pride

Cancer Multiplex staining Mass spectrometry Deep visual proteomics Tumor microenvironment

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730 Results

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