Informed proteomics

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Proteomics (396)
Unknown (130)
Genomics (23)
Metabolomics (9)
Transcriptomics (8)
Genomic (4)
Other (3)
Multiomics (3)

Organisms

Bombyx mori (353)
Klebsiella pneumoniae (353)
Schizosaccharomyces pombe (353)
Streptomyces coelicolor A3(2) (353)
Human immunodeficiency virus 1 (353)
Oryza sativa Indica Group (353)
Sinorhizobium meliloti BL225C (353)
Vitis (353)
Sus scrofa domesticus (353)
Ostreococcus tauri (353)
Saccharomyces cerevisiae (353)
Synechocystis sp. PCC 6803 (353)
Olavius algarvensis Gamma 1 endosymbiont (353)
Vitis vinifera (353)
Saccharopolyspora erythraea (353)
Staphylococcus aureus (353)
Rattus norvegicus (353)
Rattus rattus (353)
Pseudomonas aeruginosa (353)
Olavius algarvensis Delta 4 endosymbiont (353)
Escherichia coli (353)
Candida albicans (353)
Cyanophora paradoxa (353)
Equus caballus (353)
Bursaphelenchus xylophilus (353)
Homo sapiens (29)
Mus musculus (3)
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (1)
Bos taurus (1)
Candidatus Nanopusillus acidilobi (1)

Organisms

Homo sapiens (15)
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (1)

Repository

pride (353)
ENA (21)
MassIVE (19)
biostudies-arrayexpress (12)
iProX (9)
MetaboLights (9)
geo (5)
dbGaP (4)
jPOST (4)
EGA (2)
GPMDB (2)
NODE (2)
PeptideAtlas (1)

Tissue

Blood plasma (48)
Cell culture (33)
Blood serum (29)
Brain (19)
Saliva (19)
Blood (18)
Epithelial cell (15)
Bone marrow (9)
Blood cell (9)
Colon (8)
T cell (8)
Blood platelet (7)
Heart (7)
Liver (6)
Placenta (5)
Skin (5)
Macrophage (5)
Cell suspension culture (5)
Lung (5)
Platelet (5)
Tear (4)
Cerebrospinal fluid (4)
Urine (4)
Fibroblast (4)
Ileum (3)
Sperm (3)
Pancreas (3)
Melanocyte (3)
Bone marrow cell (3)
Feces (3)

Disease

Disease free (10)
Colon cancer (6)
Acute leukemia (5)
Lung adenocarcinoma (4)
Melanoma (4)
Cardiovascular system disease (4)
Brain cancer (4)
Alzheimer's disease (4)
COVID-19 (4)
Multiple myeloma (3)
Pancreatic cancer (3)
Glioblastoma (3)
Crohn's disease (3)
Not Available (2)
Obsolete hepatitis B virus related hepatocellular carcinoma (2)
Brain glioma (2)
Metastatic melanoma (2)
Mucositis (2)
Severe acute respiratory syndrome (2)
Cholangiocarcinoma (2)
Inflammatory bowel disease (2)
Acute myeloid leukemia (2)
Parkinson's disease (2)
Periodontitis (2)
Osteoarthritis (2)
Ulcerative colitis (2)
Amyotrophic lateral sclerosis (2)
Malignant neoplasm of ovary (2)
Rheumatoid arthritis (2)
Breast cancer (2)

Technology Type

Mass Spectrometry (353)
Shotgun proteomics (208)
Bottom-up proteomics (59)
Data-independent acquisition (37)
Data-dependent acquisition (35)
Top-down proteomics (21)
SWATH MS (16)
Gel-based experiment (14)
SRM/MRM (11)
Mass spectrometry (8)
Affinity purification coupled with mass spectrometry proteomics (6)
Affinity proteomics (4)
DiaPASEF (4)
Olink affinity proteomics (3)
SomaScan affinity proteomics (2)
Metaproteomics (2)
Mass spectrometry imaging (2)
NMR spectroscopy (1)
Proteogenomics (1)
Glycoproteomics (1)
MSE (1)
All-ion fragmentation (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (4)
Orbitrap Fusion Lumos (3)
Instrument (2)
Orbitrap Exploris 480 (2)
Q Exactive HF-X (2)
LTQ Orbitrap Elite (2)
Q Exactive Plus (2)
LTQ Orbitrap Velos (2)
Liquid Chromatography MS - negative - reverse phase (2)
InnoScan 900 (1)
Illumina NovaSeq 6000 (1)
Autoflex (1)
Q-Exactive HF (1)
LTQ Orbitrap Pro (1)
Exactive (1)
Orbitrap Fusion (1)
Orbitrap Exploris 240 (1)
Q Exactive (1)
Matrix-assisted laser desorption-ionisation imaging MS - (1)
5975C Series GC/MSD (Agilent) (1)
MS Imaging - (1)
Exactive (Thermo Scientific) (1)
API 4000 QTRAP (AB Sciex) (1)
Nuclear Magnetic Resonance (NMR) - (1)
Liquid Chromatography MS - negative - hilic (1)
Liquid Chromatography MS - positive - hilic (1)
LTQ (1)

Publication Date

2025 (62)
2023 (49)
2026 (48)
2024 (44)
2022 (40)
2018 (32)
2021 (32)
2020 (31)
2019 (26)
2016 (19)
2015 (8)
2017 (8)
2014 (5)
2009 (3)
2011 (1)
2010 (1)

UNIPROT ID/AC

Q9Z2S7-4 (1)
Q9Z247 (1)
Q9Z1Q2 (1)
Q9Z0K8 (1)
Q9R014 (1)
Q9JKD3 (1)
Q9ET52 (1)
Q9EP52 (1)
Q9DAY2 (1)
Q9DAY1 (1)
Q9DAX0 (1)
Q9DAV5 (1)
Q9DAT7 (1)
Q9D164 (1)
Q9CR60 (1)
Q9CQV4 (1)
Q9CQC0 (1)
Q9CQ58 (1)
Q91ZF4 (1)
Q91ZD5 (1)
Q8VHQ1 (1)
Q8VDH1 (1)
Q8K078 (1)
Q8BSN5 (1)
Q8BMT0 (1)
Q80UY2 (1)
Q7TNL7 (1)
Q78Y73 (1)
Q78Y72 (1)
Q6ZQ73 (1)

ENSEMBL ID

ENSMUSG00000027651 (1)
ENSMUSG00000072849 (1)
ENSMUSP00000141097 (1)

CHEBI ID

CHEBI:17687 (4)
CHEBI:37024 (4)
CHEBI:15756 (4)
CHEBI:16919 (4)
CHEBI:89935 (3)
CHEBI:75454 (3)
CHEBI:72747 (3)
CHEBI:28733 (3)
CHEBI:72998 (3)
CHEBI:18183 (3)
CHEBI:16831 (3)
CHEBI:16196 (3)
CHEBI:4676 (3)
CHEBI:17895 (3)
CHEBI:15843 (3)
CHEBI:28610 (3)
CHEBI:28044 (3)
CHEBI:84505 (2)
CHEBI:88829 (2)
CHEBI:583580 (2)
CHEBI:7563 (2)
CHEBI:8832 (2)
CHEBI:173890 (2)
CHEBI:177599 (2)
CHEBI:182449 (2)
CHEBI:182253 (2)
CHEBI:182699 (2)
CHEBI:177514 (2)
CHEBI:177688 (2)
CHEBI:182667 (2)

Metabolite Name

Creatine (4)
Glycocholic acid (3)
(-)-Rhododendrin (2)
(2E)-2-Tridecene-4,6,8-triyn-1-ol (2)
(2E,4E,12Z)-N-Isobutyl-2,4,12-octadecatrienamide (2)
(2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-(2-phenylethoxy)oxane-3,4,5-triol (2)
(2R,3S,4S,5S,6R)-2-({7-hydroxy-4-[(3Z)-5-hydroxy-3-methylpent-3-en-1-yl]-4a,8,8-trimethyl-3-methylidene-decahydronaphthalen-2-yl}oxy)-6-(hydroxymethyl)oxane-3,4,5-triol (2)
(2S)-2-Amino-8-hydroxyoctanoic acid (2)
(4E)-1,7-Bis(4-hydroxyphenyl)-4-hepten-3-one (2)
(9Z)-9-Octadecenamide (2)
(E)-Dacarbazine (2)
(E)-p-coumaric acid (2)
(Z)-3-butylidene-7-hydroxyphthalide (2)
[(4Z)-5-(Methylsulfanyl)-4-penten-2-yn-1-yl]benzene (2)
1,2-Cyclohexadione (2)
1,3,7-Octanetriol (2)
1,4-Anhydro-6-O-dodecanoyl-2,3-bis-O-(2-hydroxyethyl)-D-glucitol (2)
2-linoleoylglycerol (2)
1-Monopalmitoylglycerol (2)
1-Hexyl-2-methylbenzene (2)
1-Linoleoyl-sn-glycero-3-phosphocholine (2)
1-oleoyl-sn-glycero-3-phosphoethanolamine (2)
1-Tetradecylamine (2)
2-((2E)-3,7-Dimethyl-2,6-octadienyl)-5,6-dimethoxy-3-methyl-1,4-benzenediol (2)
2-(12-Tridecyn-1-yl)furan (2)
2,2,6,6-Tetramethyl-1-piperidinol (2)
2,3,4,9-Tetrahydro-1H-beta-carboline-1,3-dicarboxylic acid (2)
2,6-di-tert-butyl-4-ethylphenol (2)
2,6-di-tert-butylhydroquinone (2)
1-[2,6-Dimethyl-4-(2-methyl-2-propanyl)-3,5-dinitrophenyl]ethanone (2)

First Public Date

2024 (7)
2020 (3)
2026 (2)
2022 (2)
2016 (2)
2025 (1)
2023 (1)
2021 (1)
2017 (1)
2015 (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (3)
4x(2)H labeled dimethylated residue (1)
4 (1)
4x(15)N labeled L-arginine (1)
Not available (1)

Study type

Transcription profiling by array (4)
Proteomic profiling by array (4)
Antigen profiling (2)
Proteomic profiling by mass spectrometer (1)
Spatial transcriptomics by high-throughput sequencing (1)

Release Date

2025 (30)
2024 (13)
2022 (13)
2019 (12)
2023 (11)
2021 (11)
2020 (10)
2017 (8)
2018 (6)
2015 (6)
2026 (5)
2014 (4)
2013 (3)
2012 (3)
2010 (2)
2009 (2)
2016 (2)
2011 (1)

Lab affiliation

University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (7)
Parasitology Laboratory, Institute of Natural Resources and Agrobiology (IRNASA, CSIC). Cordel de Merinas, 40-52, 37008 Salamanca, Spain. (4)
CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France (4)
1School of Natural Sciences, Macquarie University, Sydney, NSW, Australia 2Institute for Glyco-core Research (iGCORE), Nagoya University, Aichi, Japan (3)
Tianjin Medical University General Hospital (3)
Life and Environmental Sciences Department (Biomedical Section) - University of Cagliari (3)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (3)
Department of Molecular Biology and Genetics, Lab of Proteome Research, Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119992, Russia (2)
Clinical Protein Science & Imaging, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden (2)
Division of Cell Matrix Biology & Regenerative Medicine (L5) / Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester (2)
Translational Metabolic Laboratory, Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands (2)
Nanoparticle Systems Engineering Laboratory Department of Mechanical and Process Engineering ETH Zurich, Switzerland (2)
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA USA (2)
Radboud university medical center, Radboud Institute for Health Sciences, Department of Hematology The Netherlands (2)
Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel (2)
Institute of Bioinformatics, Bangalore - 560066, India (2)
The University of Sydney (2)
OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands (2)
Basilbiotech, Incheon 22002, Republic of Korea. (2)
University of Oxford (2)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (2)
Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, Zagreb, Croatia Drago Perović Department of Anatomy, School of Medicine, University of Zagreb, Zagreb, Croatia (1)
Johns Hopkins University, School of Medicine, Clinical Chemistry (1)
Department of Oncology-Pathology, Karolinska Institutet (1)
Cardiovascular Biochemistry Group, Research Institute of the Hospital de la Santa Creu i Sant Pau (IIB Sant Pau), Barcelona, Spain (1)
INSERM IRSD U1220 CHU PURPAN PLACE DU DOCTEUR BAYLAC CS 60039 31024 TOULOUSE CEDEX 3 FRANCE (1)
The Second Affiliated Hospital of Zhejiang University, Medicine Cancer Institute (1)
The Second Affiliated Hospital of Chengdu Medical College (China National Nuclear Corporation 416 Hospital), (1)
National Key Laboratory of Medical Molecular Biology and Department of Immunology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences (1)
Associate Professor, Department of Chemistry, Vanderbilt University (1)

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Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes Aegypti

PRJEB13078 | ENA

Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes aegypti

The incomplete genome annotation of non-model organisms hampers molecular and proteomic studies. Proteomics informed by transcriptomics (PIT) is suited to non-model organisms because peptides are identified using transcriptomic, not genomic, data. Aedes aegypti is the mosquito vector for the (re-)em...

ORGANISM(S): Aedes aegypti aegypti

2017-02-15 | PXD003799 | Pride

Informed-Proteomics: open-source software package for top-down proteomics.

Not available

S-EPMC5578875 | biostudies-literature

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.

Not available

S-EPMC4638048 | biostudies-literature

Generalized cell phenotyping for spatial proteomics with language-informed vision models.

Not available

S-EPMC11601246 | biostudies-literature

Proteomics informed deconvolution of 3 cell lines

The project aimed to investigate the possibility to use proteomics data to deconvolute cell line proportions in mixed samples. Samples containing either HEK 293, Caco-2, or A549 cells and mixtures of the three cell lines was analysed using the total protein approach. This was then used for proteomic...

ORGANISM(S): Homo sapiens (Human)

2023-10-24 | PXD027282 | Pride

Hek 293 A549 Caco-2

A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva.

Not available

S-EPMC8722417 | biostudies-literature

A Phylogeny-Informed Proteomics Approach for Species Identification within the Burkholderia cepacia Complex.

Not available

S-EPMC7587091 | biostudies-literature

Proteomics informed by transcriptomics for a qualitative and quantitative analysis of the sialoproteome of adult Ornithodoros moubata ticks.

Not available

S-EPMC8356541 | biostudies-literature

Simultaneous metagenome-informed metaproteomics of the human gut microbiome, host and dietary exposome uncover functional interactomes in health & IBD

Host-microbiome-dietary interactions play crucial roles in regulating human health, yet direct functional assessment of their interplays, cross-regulations and downstream disease impacts remains challenging. We adopted metagenome-informed metaproteomics (MIM), in both mice and humans, to simultaneou...

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

2025-08-08 | PXD057701 | Pride

Microbiome Diet Metagenomics-informed metaproteomics Proteomics Host Biomarker

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