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Genomics (3226)
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Repository

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pride (966)
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Tissue

Cell culture (179)
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Colorectal Neoplasms (1)

Technology Type

Mass Spectrometry (966)
Shotgun proteomics (491)
Bottom-up proteomics (188)
Affinity purification coupled with mass spectrometry proteomics (112)
Data-dependent acquisition (105)
Mass spectrometry (96)
Gel-based experiment (69)
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Mass spectrometry assay (33)
Top-down proteomics (29)
MSE (28)
SWATH MS (24)
SRM/MRM (17)
All-ion fragmentation (4)
DiaPASEF (4)
Affinity proteomics (3)
ILLUMINA, Illumina HiSeq 2500, NextSeq 500, Nanostring (1)
Illumina HiSeq 2000, PacBio RS II (1)
ILLUMINA, Illumina HiSeq 2000, Illumina MiSeq (1)
ILLUMINA, Illumina HiSeq 2500 (1)
ILLUMINA, Illumina HiSeq 2500, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000 (1)
Illumina Genome Analyzer II (1)
Glycoproteomics (1)
Mass spectrometry imaging (1)
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PAcIFIC (1)
Proteogenomics (1)

Instrument Platform

Illumina NovaSeq 6000 (36)
Illumina HiSeq 2000 (15)
Illumina HiSeq 2500 (14)
Illumina HiSeq 4000 (13)
NextSeq 500 (9)
NextSeq 550 (6)
Agilent G2505B scanner (4)
NextSeq 2000 (4)
Illumina NovaSeq X (3)
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)
Chromium 10x (2)
Sony SH800 (2)
DNBSEQ-G400 (2)
DNBSEQ-T7 (2)
Illumina MiSeq (2)
Illumina HiSeq 3000 (2)
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RNeasy 96-well plate kit (1)
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BRB-seq tool and pipeline (1)
NucleoSpin RNA kit (Macherey-Nagel) (1)
Gilson Minipuls 3 (1)
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STAR v2.5.3a, rpkmforgenes, RSeQC 2.6.1 (1)
Illumina Nextera XT index kits (Set A–D) (1)
Oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific), TapeStation 4200 or 2100 Bioanalyzer with a DNA High Sensitivity chip (Agilent Biotechnologies) (1)
Aria III (BD Biosciences) (1)
Chromium Next GEM Chip G (1)
10X v3 (1)
CytoFLEX SRT Benchtop Cell Sorter (1)

Publication Date

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2010 (184)
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2012 (183)
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2013 (171)
2019 (153)
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2018 (146)
2011 (133)
2017 (111)
2008 (59)
2009 (45)
2007 (30)
2005 (22)
2006 (9)
2004 (4)

UNIPROT ID/AC

Q00987 (10)
P27361 (10)
P04049 (10)
P04637 (10)
P31749 (9)
P28482 (8)
Q02750 (8)
P20936 (7)
P25054 (7)
Q07889 (7)
P01112 (7)
P00533 (7)
P01133 (7)
Q05655 (6)
O14640 (6)
O15169 (6)
P01024 (6)
Q13905 (6)
P15056 (6)
P47736 (6)
P62070 (6)
P67775 (6)
P30086 (6)
Q15418 (6)
Q9UJU2 (6)
P35222 (6)
P62834 (6)
P49841 (6)
P60484 (6)
Q9LKL2 (5)

ENSEMBL ID

ENSG00000151468 (1)
ENSG00000003402 (1)
ENSG00000171791 (1)
ENST00000333681.5 (1)
ENSSSCT00065044848.1 (1)
ENST00000371199.8 (1)
ENST00000612899.5 (1)
ENSG00000101966 (1)
ENST00000216797.10 (1)
ENSG00000100906 (1)
ENSG00000118503 (1)
NewID (1)
ENSMUSG00000021039 (1)
ENSMUSG00000027651 (1)
ENSMUSG00000098557 (1)
ENSMUSP00000069525 (1)
ENSMUSP00000140201 (1)
ENSMUSP00000141097 (1)
ENSMUSP00000141637 (1)

CHEBI ID

CHEBI:16027 (12)
CHEBI:33699 (9)
CHEBI:36080 (8)
CHEBI:0016618 (6)
CHEBI:0018348 (6)
CHEBI:24875 (3)
CHEBI:15422 (3)
CHEBI:18248 (2)
CHEBI:144829 (2)
CHEBI:15996 (2)
CHEBI:17552 (2)
CHEBI:16991 (2)
CHEBI:26667 (1)
CHEBI:73623 (1)
CHEBI:50183 (1)
CHEBI:9168 (1)
CHEBI:5939 (1)
CHEBI:26490 (1)
CHEBI:22194 (1)
CHEBI:25115 (1)
CHEBI:26806 (1)
CHEBI:27232 (1)
CHEBI:30867 (1)
CHEBI:68689 (1)
CHEBI:78679 (1)
CHEBI:53071 (1)
CHEBI:77131 (1)
CHEBI:57768 (1)
CHEBI:57754 (1)
CHEBI:61995 (1)

Metabolite Name

L-Tryptophan (22)
Xanthine (21)
Hypoxanthine (21)
L-Arginine (20)
Adenosine (20)
Guanine (20)
Uridine (20)
L-Tyrosine (20)
Adenine (19)
L-Phenylalanine (19)
Inosine (19)
Citric acid (18)
L-Proline (17)
Azelaic acid (17)
Guanosine (17)
5'-Methylthioadenosine (16)
Uracil (16)
Uric acid (16)
Pyroglutamic acid (15)
L-Histidine (15)
Linoleic acid (15)
L-Glutamine (15)
Hexadecanedioic acid (15)
Creatinine (15)
Citrulline (14)
Glycine (14)
Allantoin (14)
Choline (14)
Adipic acid (14)
Thymidine (14)

First Public Date

2025 (521)
2026 (501)
2024 (388)
2023 (239)
2021 (183)
2014 (171)
2020 (154)
2022 (143)
2018 (131)
2019 (129)
2017 (111)
2015 (66)
2016 (63)
2013 (45)
2011 (4)
2012 (1)

Modelling Approach

Ordinary differential equation model (127)
Logical model (11)
Constraint-based model (5)
Computational model (4)
Differential equation model (4)
Petri net (3)
Other (3)
Partial differential equation model (3)
Boolean model (2)
Agent-based model (2)
Markov model (1)
Multi-value logic model (1)

Study status

Recruiting (2)

Lab affiliation

Cellzome (6)
Department of Chemical & Systems Biology, Stanford University (6)
Research Unit for Molecular Medicine, Department of clinical Medicine, Aarhus University, Aarhus, Denmark (5)
CEA-Marcoule, ProGenoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Ceze, France (4)
Department of Molecular Biology, Princeton University (4)
LIST-ERIN-BEAP Bascharage1 Luxembourg (4)
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (4)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (4)
Biozentrum, University of Basel, Switzerland (3)
CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France (3)
Department of Biochemistry and Molecular Biology, University of Southern Denmark (3)
Department of Chemistry & Chemical Biology, Northeastern University (3)
Department of Chemistry and Chemical Biology, Harvard University (3)
Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic (3)
Keck MS & Proteomics Resource Yale School of Medicine (3)
Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. (3)
Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China. (3)
Teagasc (3)
Utrecht University (3)
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 2. Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands (2)
1. University of Victoria Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada 2. Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada 3. Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada 4. Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, Canada (2)
Academia Sinica (2)
Associate Professor of Genetics Stanford University USA (2)
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 Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands (2)
Cancer Research Center of Toulouse, INSERM UMR 1037, 31037 Toulouse, France Université Toulouse III Paul Sabatier, 31330 Toulouse, France (2)
College of Plant Science and Technology, Huazhong Agricultural University (2)
Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany (2)
Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada; Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada; The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada (2)
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia (2)
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia. (2)

Keyword

Tumor heterogeneity (1)
Tumor evolution (1)
Targeted therapy (1)
Chemotherapy (1)

IsPrivate

False (167)

Model Flag

Non Kinetic (11)

Submitter Keywords

Ersilia (4)
Machine Learning Model (4)
Immuno-oncology (4)
Manuscript Accepted (2)
FROG (2)
Oncology (1)
TransQST (1)
Not Peer Reviewed (1)

Classification

bacteria (84)
viruses (13)
protozoa (13)
fungi (7)
helminths (1)

Modification

N6 (6)
2x(15)N labeled L-lysine (5)
4x(15)N labeled L-arginine (5)
N6-dimethyl-L-lysine (2)
Not available (2)
-17.026549 (1)
-18.010565 (1)
15.9949 (1)
15.99491 (1)
15.994915 (1)
4 (1)
4'-dihydroxyphenylalanine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
42.010565 (1)
57.02146 (1)
57.021464 (1)
57.0215 (1)
Heavy form - site K (1)
Light form - site K (1)

Study type

Transcription profiling by array (729)
RNA-seq of coding RNA (150)
ChIP-chip by tiling array (58)
ChIP-seq (47)
Methylation profiling by array (42)
RNA-seq of coding RNA from single cells (32)
Comparative genomic hybridization by array (31)
Other (26)
Transcription profiling by tiling array (19)
ChIP-chip by array (19)
Unknown experiment type (14)
Methylation profiling by high throughput sequencing (14)
Genotyping by array (8)
RNAi profiling by array (6)
Transcription profiling by RT-PCR (4)
RNA-seq of non coding RNA (4)
Animal - High-throughput sequencing (3)
MicroRNA profiling by array (3)
Cell line - Single-cell sequencing (2)
RIP-seq (2)
ScATAC-seq (2)
Single nucleus RNA sequencing (2)
DNA-seq (2)
Proteomic profiling by array (2)
RNA-seq of total RNA (2)
Transcription profiling by SAGE (1)
Animal - Two-color microarray (1)
Baseline (1)
Differential (1)
Animal - One-color microarray (1)

Release Date

2025 (7347)
2022 (6325)
2024 (5814)
2023 (5801)
2021 (5510)
2020 (4190)
2019 (3447)
2018 (3105)
2017 (2792)
2016 (2587)
2015 (2383)
2014 (2161)
2013 (1617)
2012 (1562)
2011 (1295)
2010 (1188)
2026 (1129)
2009 (824)
2008 (751)
2007 (539)
2006 (412)
2005 (260)
2004 (205)
2003 (149)
2002 (79)
2001 (59)
2000 (40)
1999 (30)
1998 (19)
1997 (7)

Location

Sweden (1)
Japan (1)

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Biological Potential of Lophosoria quadripinnata Fern Extract: Integration of UHPLC/ESI/QToF/MS Analysis, Antioxidant Activity, Molecular Docking and Molecular Dynamics Simulation

Lophosoria quadripinnata (J.F.Gmel.) C.Chr., a fern species from the Dicksoniaceae family, is widely distributed in Central and South America. This study aimed to identify the bioactive compounds in the aqueous extract of L. quadripinnata, evaluate its antioxidant potential through in vitro analy...

2025-06-27 | MTBLS9336 | MetaboLights

Epimedium-Derived Extracellular Vesicles Alleviate Cisplatin-induced Acute Kidney Injury: Integrated Multi-Omics Analysis and Molecular Simulations Reveal Flavonoid Interactions with PPARα

This study explores the protective effects and potential underlying mechanisms of Epimedium-derived extracellular vesicles (EpEVs) against cisplatin-induced acute kidney injury (CIAKI) in mice. EpEVs were isolated and purified via differential centrifugation combined with sucrose and iodixanol gradi...

2026-09-02 | MTBLS15534 | MetaboLights

Metabolomics reveals molecular signatures for psoriasis biomarkers and drug targets discovery

Psoriasis is a chronic skin disease that affects multiple systems and can be influenced by immunological, environmental, and genetic factors. The discovery of plasma biomarkers of psoriasis and the regulation of metabolic pathways helps us understand psoriasis and may assist clinicians in the diagno...

2024-09-26 | MTBLS5185 | MetaboLights

Unveiling molecular changes in guabiju during Aspergillus brasiliensis cultivation: insights from untargeted metabolomics

Black aspergilli exhibit remarkable bioconversion potential by transforming plant matrices into bioactive compounds, although their metabolic processes remain underexplored. This study investigated the biotransformation of metabolites during the solid-state cultivation of guabiju (Myrcianthes...

2025-08-08 | MTBLS12436 | MetaboLights

Elucidating the molecular mechanisms of Daifu decoction in ulcerative colitis treatment through a multi-omics framework and experimental verification

Background: Ulcerative colitis (UC) is a significant and challenging condition in the digestive system, necessitating the development of effective therapeutic interventions. The Daifu decoction (DFD) is derived from the Lizhong decoction, a classic traditional Chinese Medicine (TCM) formula used ...

2026-03-18 | MTBLS13973 | MetaboLights

Comprehensive Evaluation of Anti-hyperuricemic Effect of Red Kidney Bean Anthocyanins and Molecular Screening of the Lead Candidate

Hyperuricemia (HUA) has emerged as an increasingly prevalent metabolic disorder worldwide. This study aimed to investigate the effects of red kidney bean (Phaseolus vulgaris L.) anthocyanins (RKBA) on alleviating HUA and screen the lead candidate. RKBA effectively inhibited XOD in vitro. In vivo ...

2025-10-29 | MTBLS13234 | MetaboLights

Unravelling age-driven molecular transitions underlying Pacific Oyster Mortality Syndrome permissiveness in Magallana gigas

Ageing is a progressive and irreversible biological process characterized by the deterioration of physiological functions and increased vulnerability to mortality. Although extensively studied in vertebrates, ageing in long-lived invertebrates remains comparatively unexplored. While ageing typica...

2025-12-08 | MTBLS13463 | MetaboLights

Molecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics

Sweet cherry (Prunus avium L.) is a stone fruit widely consumed and appreciated for its organoleptic properties, as well as its nutraceutical potential. We here investigated the characteristics of six non-commercial Tuscan varieties of sweet cherry maintained at the Regional Germplasm Ba...

2021-10-29 | MTBLS1803 | MetaboLights

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

PRJNA492896 | ENA

Molecular Dynamics Simulation-directed Ionic Liquid Screening for Deep Coverage Proteome Analysis

In-depth coverage of proteomic analysis could enhance our understanding to the mechanism of the protein functions. Unfortunately, many highly hydrophobic and low-abundance proteins are easily lost during sample preparation, mainly attributed to the fact that very few extractants can simultaneously s...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2019-05-19 | MSV000083818 | MassIVE