Manually curated database

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Models (708)
Unknown (593)
Proteomics (190)
Metabolomics (25)
Genomics (9)
Transcriptomics (8)

Organisms

Homo sapiens (260)
cellular organisms (66)
Mammalia (54)
Saccharomyces cerevisiae (49)
Mus musculus (46)
Escherichia coli (19)
Rattus norvegicus (17)
Rattus (16)
Eukaryota (15)
Drosophila melanogaster (10)
Murinae (10)
Arabidopsis thaliana (10)
Arabidopsis (9)
Trypanosoma brucei (9)
Xenopus laevis (9)
Chordata (8)
Viridiplantae (4)
Neurospora crassa (4)
Schizosaccharomyces pombe (4)
Amphibia (4)
Bacillus subtilis (4)
Rattus rattus (3)
Opisthokonta (3)
Mus sp. (3)
Mus (3)
Bos taurus (2)
Mycobacterium tuberculosis (2)
Oryctolagus (2)
Escherichia coli K-12 (2)
Lactococcus lactis (2)

Organisms

Homo sapiens (2)
Cercospora beticola (1)
Cyanobacteriota (1)
Danio rerio (1)

Repository

BioModels (708)
pride (188)
MetaboLights (25)
ENA (9)
biostudies-arrayexpress (6)
geo (2)
iProX (1)
MassIVE (1)

Tissue

Blood (59)
Cell culture (25)
T cell (14)
B cell (13)
Epithelial cell (9)
Blood plasma (8)
Permanent cell line cell (8)
Plant cell (8)
Neutrophil (6)
Bone marrow (5)
Fibroblast (5)
Monocyte (5)
Brain (4)
Embryonic stem cell (4)
Leaf (4)
Peripheral blood mononuclear cell (4)
Photosynthetic cell (4)
Platelet (4)
Blood serum (3)
Cell suspension culture (3)
Dendritic cell (3)
Macrophage (3)
Natural killer cell (3)
Testis (3)
Cervicovaginal fluid (2)
Cytotoxic T cell (2)
Embryo (2)
Eosinophil (2)
Erythrocyte (2)
HeLa cell (2)

Disease

Alzheimer's disease (19)
Diabetes mellitus (14)
Parkinson's disease (14)
Crohn's disease (4)
Bacterial infectious disease (4)
Neurodegenerative disease (4)
Type 2 diabetes mellitus (4)
Osteoarthritis (4)
Influenza (3)
Cancer (3)
Rheumatoid arthritis (2)
Huntington's disease (2)
Non-small cell lung carcinoma (2)
Liver disease (2)
Calcium metabolism disease (2)
Polycythemia due to hypoxia (2)
Botulism (2)
Human immunodeficiency virus infectious disease (2)
Glucocorticoid-remediable aldosteronism (2)
Pertussis (2)
Osteoporosis (1)
Paget's disease of bone (1)
Andersen-Tawil syndrome (1)
Colorectal cancer (1)
Brugada syndrome (1)
Benign glioma (1)
Swine influenza (1)
Prion disease (1)
Primary bacterial infectious disease (1)
Tauopathy (1)

Technology Type

Mass Spectrometry (188)
Shotgun proteomics (65)
Top-down proteomics (64)
Bottom-up proteomics (29)
Data-dependent acquisition (24)
Mass spectrometry (18)
Affinity purification coupled with mass spectrometry proteomics (18)
Gel-based experiment (11)
Chemical cross-linking coupled with mass spectrometry proteomics (8)
SWATH MS (8)
Mass spectrometry assay (7)
Data-independent acquisition (5)
HDMSE (4)
SRM/MRM (4)
NMR spectroscopy (1)
Affinity proteomics (1)
All-ion fragmentation (1)
DiaPASEF (1)
Glycoproteomics (1)
Immunopeptidomics (1)
MSE (1)
Mass spectrometry imaging (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (8)
Liquid Chromatography MS - negative - reverse phase (6)
Liquid Chromatography MS - positive - reverse-phase (5)
Liquid Chromatography MS - positive - hilic (5)
Liquid Chromatography MS - negative - hilic (4)
Liquid Chromatography MS - (3)
Gas Chromatography MS - positive (3)
Liquid Chromatography MS - negative - reverse-phase (3)
Beadarray reader (2)
Gas Chromatography MS - (2)
Exactive (Thermo Scientific) (2)
Liquid Chromatography MS - alternating - hilic (2)
Orbitrap Fusion (1)
Liquid Chromatography Tandem MS (LC-MS/MS (Negative)) (1)
Liquid Chromatography Tandem MS (LC-MS/MS (Positive)) (1)
Flow injection analysis MS - (1)
Liquid Chromatography MS - Negative (LC-MS (Negative)) (1)
Gas Chromatography MS - Positive (GC-MS (Positive)) (1)
Liquid Chromatography Tandem MS (LC-MS/MS) (1)
Direct infusion MS - negative (1)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (1)
MS Imaging - (1)
Nuclear Magnetic Resonance (NMR) - (1)
Liquid Chromatography MS - negative (1)
Liquid Chromatography MS - positive (1)
Liquid Chromatography MS - alternating - reverse phase (1)
Liquid Chromatography MS - positive - HILIC (1)

Publication Date

2024 (677)
2022 (72)
2015 (38)
2026 (27)
2025 (24)
2023 (24)
2021 (13)
2019 (12)
2020 (10)
2016 (8)
2005 (8)
2018 (8)
2017 (5)
2011 (2)
2010 (1)
2009 (1)

UNIPROT ID/AC

Q02750 (37)
P04049 (35)
P28482 (28)
P04637 (21)
Q07889 (19)
P27361 (18)
P31749 (17)
P01133 (17)
P00533 (16)
P24864 (15)
P20936 (14)
P49841 (14)
P01112 (14)
Q00987 (13)
P01308 (13)
P51452 (11)
P24941 (11)
P06213 (11)
P60484 (11)
P62993 (11)
P67775 (10)
P35222 (10)
P01137 (10)
P35568 (10)
P42345 (10)
P05067 (10)
P07663 (9)
Q9LKL2 (9)
P15056 (9)
P47736 (9)

ENSEMBL ID

ENSG00000064012 (4)
ENSG00000165661 (4)
ENSG00000176654 (4)
ENSG00000204531 (4)
ENSG00000141510 (3)
ENSG00000135679 (3)
ENSG00000148200 (2)
ENSG00000165556 (2)
ENSG00000141448 (2)
ENSMUST00000021413 (2)
ENSMUST00000019997 (2)
ENSG00000139318 (1)
ENSG00000168646 (1)
ENSG00000180198 (1)
ENSG00000151468 (1)
ENSG00000100234 (1)
ENSG00000102265 (1)
ENSG00000184557 (1)
ENSG00000137745 (1)
ENSG00000196611 (1)
ENSG00000177606 (1)
ENSG00000170345 (1)
ENSG00000158859 (1)
ENSG00000149968 (1)
ENSG00000147889 (1)
ENSMUST00000025867 (1)
ENSMUST00000029812 (1)
ENSRNOP00000009359 (1)
ENSMUSG00000029711 (1)
ENSMUSG00000006235 (1)

CHEBI ID

CHEBI:15422 (110)
CHEBI:16761 (96)
CHEBI:16027 (76)
CHEBI:16908 (74)
CHEBI:17552 (74)
CHEBI:15996 (72)
CHEBI:18021 (64)
CHEBI:15846 (63)
CHEBI:16474 (60)
CHEBI:16526 (60)
CHEBI:17794 (59)
CHEBI:17754 (57)
CHEBI:16905 (56)
CHEBI:15379 (56)
CHEBI:16108 (55)
CHEBI:18367 (55)
CHEBI:15351 (55)
CHEBI:18009 (54)
CHEBI:29052 (53)
CHEBI:29108 (53)
CHEBI:15346 (52)
CHEBI:16001 (52)
CHEBI:16236 (52)
CHEBI:16595 (50)
CHEBI:15946 (50)
CHEBI:33699 (50)
CHEBI:32816 (50)
CHEBI:15343 (49)
CHEBI:17489 (48)
CHEBI:4170 (48)

Metabolite Name

Adenosine (3)
Isoleucine (3)
PE(32:1) (2)
PI(36:5) (2)
PC 38:1 (2)
PE 36:3 (2)
PC 40:8 (2)
PC 40:7 (2)
PC 40:6 (2)
PC 40:5 (2)
PC 40:4 (2)
PC 38:5 (2)
PC 38:3 (2)
PC 38:2 (2)
PC 36:5 (2)
PC 36:3 (2)
PC 36:2 (2)
PC 36:1 (2)
PC 34:2 (2)
PC 32:1 (2)
TG 54:0 (2)
TG 50:0 (2)
TG 53:4 (2)
TG 52:7 (2)
PE 34:2 (2)
CE 18:0 (2)
PI(36:1) (2)
PE(38:4) (2)
Lactic acid (2)
Glycolic acid (2)

First Public Date

2024 (3)
2025 (2)
2019 (1)
2017 (1)
2016 (1)
2014 (1)

Modelling Approach

Ordinary differential equation model (638)
Constraint-based model (17)
Delayed differential equation model (4)
Mathematical model (2)
Logical model (2)
Regression method (1)
Pharmacodynamics model (1)

Lab affiliation

Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States (60)
Laboratory of Molecular Parasitology, Institute of Parasitology, University of Zurich, Switzerland (3)
Department of Chemistry and Bioscience Aalborg University Denmark (2)
ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium (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)
School of Chemistry and Molecular Biosciences, The University of Queensland, Australia (2)
Sun yat-sen university cancer center (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)
Applied Science and Technology Department–BioSolar Lab, Politecnico di Torino,Italy (1)
Assistant Professor Department of Cellular and Molecular Medicine Florida International University | Herbert Wertheim College of Medicine (1)
Assistant Professor & K12 Scholar Translational Glycobiology Institute, Department of Translational Medicine Florida International University | Herbert Wertheim College of Medicine (1)
Assistant Professor (PI,ANRF-SERB project), Department of Botany, Ravenshaw University, Cuttack, Odisha- 753003 India (1)
Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, Germany (1)
Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada (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. Netherlands Proteomic Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands. (1)
Biomolecular Mass Spectrometry and Proteomics,Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands (1)
Boston University, Dept. of Biochemistry (1)
Broad Institute (1)
CEA (1)
CSIRO Agriculture and Food (1)
CSIRO Food Futures National Research Flagship, Division of Livestock Industries, Queensland Biosciences Precinct, St. Lucia, Queensland, Australia (1)
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK (1)
Carnegie Mass Spectrometry Facility at Stanford (1)
Centre for Epigenetics and Department of Biochemistry and Molecular Biology, University of Southern Denmark Campusvej 55 DK-5230 Odense M, Denmark (1)
Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic. (1)
Chemistry Department, University of Texas at Dallas, Richardson. TX (1)
Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA (1)
College of chemistry and molecular engineering, Peking University (1)
Department of Biochemistry and Pharmacology, School of Biomedical Sciences, The University of Melbourne, Australia (1)
Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil. (1)

IsPrivate

False (708)

Model Flag

Non Kinetic (54)
Non Miriam (2)

Submitter Keywords

Immuno-oncology (32)
FROG (12)
Ersilia (1)
FAIR-AIML (1)
Machine Learning Model (1)
TransQST (1)
Manuscript Accepted (1)

Modification

N6 (2)
4-tetrahydrothiazine-3-carboxylic acid (1)
N6-dimethyl-L-lysine (1)

Study type

Transcription profiling by array (4)
Unknown experiment type (1)
Other (1)

Release Date

2022 (68)
2023 (55)
2020 (45)
2019 (45)
2018 (43)
2021 (40)
2024 (38)
2025 (34)
2013 (29)
2016 (26)
2015 (26)
2017 (25)
2014 (21)
2012 (18)
2026 (15)
2011 (14)
2008 (13)
2010 (12)
2009 (12)
2006 (6)
2007 (5)
2005 (5)
2003 (2)
2004 (1)
2002 (1)

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The TriMet_DB: a manually curated database of the metabolic proteins of Triticum aestivum

Mass spectrometry-based wheat proteomics is challenging because the current interpretation of mass spectrometry data relies on public databases that are not exhaustive (UniProtKB/Swiss-Prot) or contain many redundant and poor or un-annotated entries (UniProtKB/TrEMBL). Here we report the development...

ORGANISM(S): Triticum aestivum (Wheat)

2023-03-11 | PXD037709 | Pride

A database of high-resolution MS/MS spectra for lichen metabolites

While analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited analytical methods, Thin Layer Chromatography being the gold standard. To meet the modern standards of metabolomics within lichenochem...

2019-07-22 | MTBLS999 | MetaboLights

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry d...

ORGANISM(S): Mus musculus (Mouse)

2017-01-11 | PXD005489 | Pride

Proteomics Mass spectrometry Histone Chromatin Histone variants

IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease.

Not available

S-EPMC10986744 | biostudies-literature

CCIDB: a manually curated cell-cell interaction database with cell context information.

Not available

S-EPMC10419333 | biostudies-literature

LBD: a manually curated database of experimentally validated lymphoma biomarkers.

Not available

S-EPMC9254641 | biostudies-literature