Dia-based proteomics

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Proteomics (1894)
Unknown (246)
Genomics (10)
Metabolomics (6)
Other (1)
Transcriptomics (1)
Multiomics (1)

Organisms

Homo sapiens (134)
Mus musculus (39)
Gallus gallus (8)
Escherichia coli (7)
Saccharomyces cerevisiae (6)
Aeromonas hydrophila subsp. hydrophila ATCC 7966 (3)
Arabidopsis thaliana (3)
Oryza sativa (3)
Rattus norvegicus (3)
Canis lupus familiaris (2)
Clostridium butyricum (2)
Glycine max (2)
Hordeum vulgare (2)
Human alphaherpesvirus 1 (2)
Rattus rattus (2)
Escherichia coli str. K-12 substr. MG1655 (1)
Aeromonas hydrophila 07-345-3437 (1)
Aeromonas hydrophila subsp. hydrophila AL09-71 (1)
Enterococcus casseliflavus ATCC 49996 (1)
Ephedrus lacertosus (1)
Escherichia coli 90.0091 (1)
Fragaria vesca subsp. vesca (1)
Klebsiella aerogenes KCTC 2190 (1)
Klebsiella pneumoniae JH1 (1)
Mus (1)
Rhinomonas reticulata (1)
Staphylococcus aureus (1)
Staphylococcus aureus bacteriophage Sb-1 (1)
Streptococcus mutans (1)
Vibrio alginolyticus NBRC 15630 = ATCC 17749 (1)

Organisms

Homo sapiens (4)

Repository

pride (1580)
iProX (161)
MassIVE (77)
jPOST (50)
PanoramaPublic (25)
ENA (7)
MetaboLights (6)
geo (4)
EGA (1)
PAXDB (1)

Tissue

Cell culture (355)
Blood plasma (102)
Epithelial cell (83)
Brain (81)
Liver (67)
Blood serum (56)
Blood (38)
Heart (37)
Lung (35)
Kidney (33)
Blood cell (31)
Permanent cell line cell (28)
Cerebrospinal fluid (24)
Fibroblast (24)
Plant cell (23)
Leaf (22)
Whole body (22)
T cell (20)
Hepatocyte (19)
Cell suspension culture (17)
Skin (17)
Skeletal muscle (16)
Stem cell (15)
B cell (14)
Bone marrow (14)
Colon (14)
Macrophage (14)
Spleen (11)
Urine (11)
HeLa cell (10)

Disease

Breast cancer (25)
Disease free (23)
Colon cancer (16)
Cervix carcinoma (15)
Acute leukemia (14)
COVID-19 (13)
Parkinson's disease (11)
Non-small cell lung carcinoma (10)
Type 2 diabetes mellitus (10)
Pancreatic ductal adenocarcinoma (9)
Prostate adenocarcinoma (9)
Alzheimer's disease (8)
Glioblastoma (7)
Lymphoma (7)
Cardiovascular system disease (6)
Malignant neoplasm of ovary (6)
Osteosarcoma (6)
Melanoma (5)
Bacterial sepsis (4)
Brain cancer (4)
Influenza (4)
Malaria (4)
Multiple myeloma (4)
Obesity (4)
Osteoarthritis (4)
Pulmonary tuberculosis (4)
Type 1 diabetes mellitus (4)
Wounds and Injuries (4)
Brain ischemia (3)
Cerebrovascular disease (3)

Technology Type

Mass Spectrometry (1580)
Data-independent acquisition (676)
Bottom-up proteomics (471)
SWATH MS (421)
Shotgun proteomics (352)
Data-dependent acquisition (111)
DiaPASEF (68)
All-ion fragmentation (60)
Affinity purification coupled with mass spectrometry proteomics (56)
Top-down proteomics (30)
HDMSE (29)
SRM/MRM (16)
Gel-based experiment (15)
MSE (14)
Affinity proteomics (7)
Chemical cross-linking coupled with mass spectrometry proteomics (5)
Immunopeptidomics (5)
Mass spectrometry (4)
Mass spectrometry assay (2)
Metaproteomics (1)
PAcIFIC (1)

Instrument Platform

Orbitrap Astral (14)
Orbitrap Exploris 480 (8)
Orbitrap Fusion Lumos (7)
Q Exactive (6)
TimsTOF Pro (6)
TripleTOF 5600 (6)
Orbitrap Fusion (5)
Orbitrap Eclipse (4)
Q Exactive HF-X (4)
Orbitrap Exploris 240 (3)
Q Exactive HF (3)
Q Exactive Plus (3)
TimsTOF (3)
TimsTOF Ultra (3)
ZenoTOF 7600 (3)
Liquid Chromatography MS - positive - hilic (3)
TimsTOF HT (2)
TimsTOF Pro 2 (2)
TimsTOF SCP (2)
Liquid Chromatography MS - negative - hilic (2)
MaXis II (1)
Orbitrap Fusion (Thermo Scientific instrument model) (1)
Q Exactive HF (Thermo Scientific instrument model) (1)
Q-Exactive H-FX (1)
Stellar MS Ion Trap (Thermo Scientific Instrument Model) (1)
Synapt G2 MS (1)
TimsTOF Ultra 2 (1)
TimsTOF fleX (1)
TripleTOF 6600 (1)
Xevo G2 Q-Tof (1)

UNIPROT ID/AC

3MG1_ECOLI (1)
3PASE_ECOLI (1)
5DNU_ECOLI (1)
6PGD_ECOLI (1)
6PGL_ECOLI (1)
A2MG_ECOLI (1)
AAAT_ECOLI (1)
AAER_ECOLI (1)
AAS_ECOLI (1)
AAT_ECOLI (1)
ACCA_ECOLI (1)
ACCC_ECOLI (1)
ACCD_ECOLI (1)
ACEA_ECOLI (1)
ACFD_ECOLI (1)
ACKA_ECOLI (1)
ACNA_ECOLI (1)
ACNB_ECOLI (1)
ACPH_ECOLI (1)
ACPS_ECOLI (1)
ACPT_ECOLI (1)
ACP_ECOLI (1)
ACRA_ECOLI (1)
ACRB_ECOLI (1)
ACSA_ECOLI (1)
ACUI_ECOLI (1)
ACYP_ECOLI (1)
ADD_ECOLI (1)
ADEC_ECOLI (1)
ADEP_ECOLI (1)

CHEBI ID

CHEBI:16680 (3)
CHEBI:18186 (3)
CHEBI:16811 (3)
CHEBI:16750 (3)
CHEBI:28044 (3)
CHEBI:28790 (3)
CHEBI:17509 (3)
CHEBI:73024 (3)
CHEBI:27732 (3)
CHEBI:27897 (3)
CHEBI:17596 (3)
CHEBI:16092 (2)
CHEBI:64681 (2)
CHEBI:28918 (2)
CHEBI:68447 (2)
CHEBI:16077 (2)
CHEBI:16765 (2)
CHEBI:64850 (2)
CHEBI:17992 (2)
CHEBI:89487 (2)
CHEBI:17822 (2)
CHEBI:25094 (2)
CHEBI:18237 (2)
CHEBI:16436 (2)
CHEBI:22660 (2)
CHEBI:22653 (2)
CHEBI:18323 (2)
CHEBI:27570 (2)
CHEBI:26986 (2)
CHEBI:28300 (2)

Metabolite Name

Citric acid (3)
P-Hydroxyphenyllactic acid (2)
Fraxidin (2)
Loganic acid (2)
4-Hydroxyhippuric acid (2)
Leucine (2)
3-Hydroxysuberic acid (2)
3-Dehydroquinic acid (2)
Homovanillic acid sulfate (2)
Orotic acid (2)
Indoxyl sulfate (2)
5-Methylcytidine (2)
Succinic acid (2)
N-Acetylneuraminic acid (2)
Taurocholic acid (2)
Gentisic acid (2)
Deoxycholic acid (2)
3-Hydroxysebacic acid (2)
Suberylglycine (2)
Sebacic acid (2)
Xylitol (2)
Mevalonic acid (2)
Azelaic acid (2)
Tryptophan (2)
Phenytoin Quinone (1)
4,5-Diphenylimidazole (1)
25-Hydroxyvitamin D2-25-Glucuronide (1)
Ms-275 (1)
Diguanosine Triphosphate (1)
Dihydronicotinamide Formycin Dinucleotide (1)

First Public Date

2023 (4)
2022 (1)
2021 (1)
2020 (1)

Modification

4x(15)N labeled L-arginine (2)
2x(15)N labeled L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
4x(2)H labeled dimethylated residue (1)
N6 (1)

Release Date

2025 (66)
2022 (36)
2024 (33)
2023 (33)
2021 (20)
2020 (17)
2019 (9)
2017 (9)
2016 (7)
2018 (6)
2015 (5)
2026 (4)
2013 (1)

Lab affiliation

Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (35)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (29)
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 (23)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (18)
TIGEM (9)
University of Edinburgh (8)
Professor, Deputy Head of Centre Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen, DENMARK (7)
Proteomics facility, Central Science Laboratory, University of Tasmania (7)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (6)
Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia (6)
Imperial College London (6)
Masaryk University, Faculty of Science (6)
Max-Planck-Institute for Biology of Ageing Department of Mitochondrial Proteostasis Joseph-Stelzmann-Str. 9b 50931 Cologne (6)
Instituto de Investigaciones Sanitarias de Santiago de Compostela (5)
Ludwig-Maximilians-Universität München Genzentrum Laboratory for Functional Genome Analysis Feodor-Lynen-Str. 25 D-81377 München (5)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (4)
Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry (4)
Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Office B25A/04/94 Rue du Bugnon 25a, CH-1005 Lausanne (4)
Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland (4)
Mass Spectrometry/Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands. (4)
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark (4)
Proteomics, Leibniz-Institut für analytische Wissenschaften -ISAS - e.V., Germany (4)
School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, CA, USA (4)
The University of Melbourne (4)
Tokyo Metropolitan Institute of Medical Science (4)
Yale University School of Medicine (4)
1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany (lab head) (3)
Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China (3)
DZNE Munich, Neuroproteomics, Feodor-Lynen-Str. 17, 81377 München, Germany (3)
Department of Cell & Developmental Biology, University of California, San Diego, CA 92093, USA. (3)

Publication date

2025 (531)
2026 (348)
2024 (316)
2023 (208)
2022 (150)
2021 (101)
2020 (60)
2019 (41)
2018 (22)
2017 (20)
2016 (8)
2015 (2)

Tags

xref:PubMed:34032011 (1)

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QuickProt: A bioinformatics and visualization tool for DIA and PRM mass spectrometry-based proteomics datasets.

Not available

S-EPMC11974799 | biostudies-literature

A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis.

Not available

S-EPMC11798701 | biostudies-literature

A DIA-MS-based proteomics approach to find potential serum prognostic biomarkers in glioblastoma patients.

Not available

S-EPMC12420366 | biostudies-literature

iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics.

Not available

S-EPMC7178409 | biostudies-literature

Astral-based DIA proteomics analysis reveals the effects of selenium on Pleurotus pulmonarius.

Not available

S-EPMC12297576 | biostudies-literature

Data-Independent Acquisition (DIA)-Based Proteomics for the Identification of Biomarkers in Tissue Washings of Endometrial Cancer.

Not available

S-EPMC12691889 | biostudies-literature

A DIA-MS-based proteomics approach to find potential serum prognostic biomarkers in glioblastoma patients

No blood-based protein biomarkers are currently available for routine clinical use to determine the prognosis of patients with glioblastoma (GB). We performed data-independent acquisition mass spectrometry (DIA-MS)-based proteomics on 96 presurgical serum samples from patients with GB and 30 serum s...

ORGANISM(S): Homo sapiens (Human)

2025-09-15 | PXD045467 | Pride

Benchmarking informatics workflows for data-independent acquisition single-cell proteomics.

Not available

S-EPMC12639053 | biostudies-literature

DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis.

Not available

S-EPMC11997033 | biostudies-literature

DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift.

Not available

S-EPMC7768684 | biostudies-literature

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2158 Results

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