Comprehensive proteomics

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Proteomics (4636)
Unknown (3969)
Genomics (283)
Transcriptomics (135)
Multiomics (82)
Metabolomics (81)
Other (33)
Genomic (3)
Methylation profiling (2)
Models (1)

Organisms

Homo sapiens (799)
Mus musculus (188)
Rattus norvegicus (24)
Bos taurus (13)
Drosophila melanogaster (9)
Staphylococcus aureus (6)
Ovis aries (4)
Gallus gallus (3)
synthetic construct (3)
Shigella flexneri 2a str. 301 (2)
Bartonella henselae (2)
Xenopus laevis (2)
Agrobacterium tumefaciens (1)
Methanococcus maripaludis (1)
Geobacter sulfurreducens PCA (1)
Bacillus subtilis (1)
Solanum tuberosum (1)
Staphylococcus aureus subsp. aureus N315 (1)
Human mastadenovirus A (1)
Staphylococcus aureus subsp. aureus Mu50 (1)
Escherichia coli DH1 (1)
Staphylococcus aureus subsp. aureus COL (1)
Staphylococcus aureus subsp. aureus NCTC 8325 (1)
Staphylococcus aureus subsp. aureus MW2 (1)
Staphylococcus aureus subsp. aureus MSSA476 (1)
Staphylococcus aureus subsp. aureus MRSA252 (1)
Staphylococcus aureus subsp. aureus USA300 (1)
Escherichia coli B (1)
Ctenopharyngodon idella (1)
Sus scrofa domesticus (1)

Organisms

Homo sapiens (117)
Mus musculus (40)
Drosophila melanogaster (7)
Rattus norvegicus (4)
Ovis aries (2)
Escherichia coli B (1)
Shigella flexneri 2a str. 301 (1)
Bartonella henselae (1)
Streptococcus equi subsp. equi (1)
Escherichia coli DH1 (1)
Staphylococcus aureus (1)
Macleaya microcarpa (1)
Macleaya cordata (1)
Leiocassis longirostris (1)
unidentified (1)
Chlamydomonas reinhardtii (1)
Sus scrofa domesticus (1)
Schmidtea mediterranea (1)
Ctenopharyngodon idella (1)
Phyllostachys edulis (1)
Xenopus laevis (1)
Schizosaccharomyces pombe (1)
Bos taurus (1)
Saccharomyces cerevisiae (1)

Repository

pride (2862)
iProX (616)
MassIVE (502)
PeptideAtlas (276)
ENA (246)
jPOST (171)
geo (170)
PAXDB (140)
MetaboLights (74)
biostudies-arrayexpress (42)
PanoramaPublic (41)
GPMDB (21)
GNPS (7)
dbGaP (3)
EGA (2)
BioModels (1)

Tissue

Cell culture (595)
Epithelial cell (190)
Brain (182)
Liver (122)
Blood plasma (97)
Blood (85)
Kidney (83)
Permanent cell line cell (83)
Lung (79)
Others (75)
Breast (72)
Blood serum (68)
B cell (60)
Heart (60)
Whole body (59)
Leaf (56)
Plasma Non-glyco (17)
Digestive System (11)
Heart (6)
Liver (6)
Male Reproductive System (6)
Brain (5)
Female Reproductive System (5)
Lung (4)
Adrenal Gland (3)
Eye (3)
Kidney (3)
Pancreas (2)
Urinary Bladder (2)
Urine (1)

Disease

Disease free (74)
Breast cancer (71)
Breast Carcinoma (36)
Colon cancer (36)
Acute leukemia (33)
Alzheimer's disease (24)
Type 2 diabetes mellitus (22)
Not Available (21)
Lymphoma (17)
Glioblastoma (14)
Malignant neoplasm of ovary (14)
Cardiovascular system disease (13)
Lung cancer (12)
COVID-19 (11)
Influenza (11)
Osteosarcoma (11)
Prostate adenocarcinoma (11)
Cervix carcinoma (10)
Pancreatic ductal adenocarcinoma (10)
Huntington Disease (9)
Melanoma (9)
Non-small cell lung carcinoma (9)
Pancreatic cancer (9)
Plasmodium falciparum malaria (9)
Wounds and Injuries (9)
Brain glioblastoma multiforme (8)
Chronic kidney disease (8)
Brain cancer (7)
Cervical cancer (1)
Non-small Cell Lung Carcinoma (1)

Technology Type

Mass Spectrometry (2862)
Shotgun proteomics (1458)
Bottom-up proteomics (684)
Data-dependent acquisition (345)
Data-independent acquisition (269)
Affinity purification coupled with mass spectrometry proteomics (257)
SWATH MS (153)
Gel-based experiment (145)
Top-down proteomics (90)
Mass spectrometry (59)
SRM/MRM (36)
Chemical cross-linking coupled with mass spectrometry proteomics (35)
DiaPASEF (24)
HDMSE (23)
All-ion fragmentation (21)
MSE (16)
Mass spectrometry assay (14)
Proteogenomics (12)
Immunopeptidomics (7)
Metaproteomics (6)
RNA mass spectrometry (6)
Affinity proteomics (5)
Glycoproteomics (4)
Mass spectrometry imaging (3)
NMR spectroscopy (2)
Olink affinity proteomics (1)
SomaScan affinity proteomics (1)

Instrument Platform

Q Exactive (120)
LTQ Orbitrap Velos (110)
LTQ Orbitrap Elite (99)
Orbitrap Fusion Lumos (56)
Orbitrap Fusion (33)
Orbitrap Eclipse (29)
TripleTOF 5600 (28)
Q Exactive HF (27)
Orbitrap Exploris 480 (25)
Q Exactive HF-X (21)
Instrument (21)
LTQ Orbitrap (21)
Q Exactive Plus (20)
Orbitrap Astral (15)
LTQ (15)
TimsTOF Pro (10)
TripleTOF 6600 (10)
GC-MS (9)
GC MS (6)
Orbitrap Fusion ETD (6)
Illumina HiSeq 2000 (4)
Exactive (Thermo Scientific) (3)
Illumina HiSeq 2500 (2)
Coulter Automated Workstation Biomek i7 Hybrid (1)
RNeasy 96-well plate kit (1)
None (1)
NextSeq 2000 (1)
Illumina HiSeq 4000 (1)
7890A GC coupled to a 5975C inert XL MSD, with a 7683 series injector (G2614A) (1)
Q-Exactive HF (1)

Publication Date

2025 (689)
2026 (459)
2024 (455)
2022 (397)
2023 (395)
2021 (377)
2020 (375)
2019 (225)
2018 (209)
2015 (189)
2014 (175)
2017 (172)
2016 (164)
2013 (83)
2012 (17)
2009 (9)
2011 (8)
2010 (6)
2005 (5)
2008 (3)
2003 (3)
2006 (3)
2007 (1)
2004 (1)

UNIPROT ID/AC

1433G_MOUSE (8)
1433Z_MOUSE (8)
ACTB_MOUSE (8)
ACTN4_MOUSE (8)
ALDOA_MOUSE (8)
AMPL_MOUSE (8)
CAP1_MOUSE (8)
CATA_MOUSE (8)
COF1_MOUSE (8)
COR1B_MOUSE (8)
DEST_MOUSE (8)
EF1A1_MOUSE (8)
ENPL_MOUSE (8)
ESTD_MOUSE (8)
G3P_MOUSE (8)
GDIB_MOUSE (8)
GDIR1_MOUSE (8)
GELS_MOUSE (8)
GSTM1_MOUSE (8)
GSTO1_MOUSE (8)
H4_MOUSE (8)
HBA_MOUSE (8)
HINT1_MOUSE (8)
HS90B_MOUSE (8)
HSP74_MOUSE (8)
HSP7C_MOUSE (8)
IF5A1_MOUSE (8)
KPYM_MOUSE (8)
LDHA_MOUSE (8)
LONM_MOUSE (8)

ENSEMBL ID

ENSG00000170477 (189)
ENSG00000229353 (126)
ENSG00000147251 (123)
ENSG00000204131 (86)
ENSG00000247315 (74)
ENSG00000176092 (35)
ENSMUSP00000141097 (15)
ENSMUSG00000027651 (14)
ENSMUSG00000021039 (11)
ENSMUSG00000098557 (10)
ENSMUSG00000090272 (6)
ENSMUSP00000106991 (6)
ENSMUSP00000111587 (6)
ENSMUSP00000141542 (4)
ENSG00000214897 (3)
ENSMUSG00000072849 (2)
ENSMUSG00000076695 (2)
ENSMUSG00000094546 (2)
ENSMUSG00000094652 (2)
ENSMUSP00000141637 (2)
ENSMUSG00000076514 (1)
ENSMUSG00000076532 (1)
ENSMUSG00000076562 (1)
ENSMUSG00000076668 (1)
ENSMUSG00000093894 (1)
ENSMUSG00000093896 (1)
ENSMUSG00000094075 (1)
ENSMUSG00000094194 (1)
ENSMUSG00000094356 (1)
ENSMUSG00000094502 (1)

CHEBI ID

CHEBI:28044 (19)
CHEBI:16708 (17)
CHEBI:30769 (17)
CHEBI:18186 (14)
CHEBI:27897 (14)
CHEBI:15741 (13)
CHEBI:16737 (13)
CHEBI:16919 (13)
CHEBI:15428 (12)
CHEBI:16335 (12)
CHEBI:28300 (12)
CHEBI:7916 (12)
CHEBI:30915 (12)
CHEBI:17568 (12)
CHEBI:16467 (11)
CHEBI:6650 (11)
CHEBI:18012 (11)
CHEBI:17509 (11)
CHEBI:17992 (11)
CHEBI:16750 (11)
CHEBI:17895 (11)
CHEBI:17295 (11)
CHEBI:17596 (11)
CHEBI:16857 (10)
CHEBI:17154 (10)
CHEBI:27266 (10)
CHEBI:16811 (10)
CHEBI:28790 (10)
CHEBI:16040 (10)
CHEBI:25017 (10)

Metabolite Name

Adenine (13)
Phenylalanine (12)
Cytosine (10)
Citric acid (10)
Creatine (10)
Uracil (9)
Hypoxanthine (9)
Ornithine (8)
Succinic acid (8)
Glucose (8)
Uric acid (8)
Sucrose (8)
Creatinine (8)
Leucine (7)
Glycine (7)
Spermidine (7)
Pantothenic acid (7)
Methionine (7)
Choline (7)
Itaconic acid (7)
Adenosine (7)
Azelaic acid (7)
Uridine (7)
L-Tyrosine (7)
Adenine (6)
Valine (6)
Succinic acid (6)
Serine (6)
Fumaric acid (6)
Tyrosine (6)

First Public Date

2025 (50)
2026 (37)
2023 (32)
2021 (26)
2022 (24)
2024 (20)
2018 (11)
2017 (11)
2019 (10)
2020 (8)
2015 (7)
2013 (5)
2014 (4)
2016 (1)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

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 (24)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (20)
Cellzome (14)
Chair of Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany (9)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (8)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (8)
University of Alabama at Birmingham, Department of Pathology, Division MCP, O'Neal Comprehensive Cancer Center (8)
CRUK Scotland Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (7)
Professor, Deputy Head of Centre Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen, DENMARK (7)
Department of Inflammation and Immunity, Gastroenterology and Hepatology. Cleveland Clinic, Cleveland Ohio, USA (6)
Head of the Curie Institute Mass Spectrometry Platform (6)
Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Germany (6)
Institutes of Biomedical Sciences and department of Chemistry, Fudan University, Shanghai, China (6)
University of Wisconsin-Madison (6)
Associate Professor, Department of Biology, Massachusetts Institute of Technology and Whitehead Institute of Biomedical Research (5)
Baylor College of Medicine (5)
DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (5)
Institute for Systems Biology, Seattle, WA, USA (5)
Neuroproteomics Group Department of Molecular Neurobiology Max Planck Institute for Multidisciplinary Sciences Hermann-Rein-Str. 3 37075 Goettingen Germany (5)
The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 USA (5)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (4)
Associate Professor Department of Biochemistry Room 220, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2 (4)
Biological Chemistry Department David Geffen School of Medicine UCLA (4)
Dpt. of Immunobiology University of Lausanne (UNIL), Boveresses 155 CH-1066 Epalinges (4)
Fraunhofer Institute for Molecular Biology and Applied Ecology IME Auf dem Aberg 1 | 57392 Schmallenberg | Germany (4)
Harvard Medical School (4)
Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria. (4)
Karolinska Institutet, Stockholm, Sweden (4)
Lineberger Comprehensive Cancer Center at UNC Chapel Hill (4)
Max Planck Institute of Immunobiology and Epigenetics Proteomics Unit Stuebeweg 51 79108 Freiburg Germany (4)

IsPrivate

False (1)

Classification

bacteria (6)

Modification

Not available (14)
N6 (13)
N6-dimethyl-L-lysine (6)
2x(15)N labeled L-lysine (4)
4x(15)N labeled L-arginine (4)
15.994915 (3)
-17.026549 (2)
4-tetrahydrothiazine-3-carboxylic acid (2)
42.010565 (2)
57.021464 (2)
-18.010565 (1)
144.105918 (1)
15.99491 (1)
4 (1)
4x(2)H labeled dimethylated residue (1)
57.02146 (1)
6-dioxaoctanediamine derivatized cysteine (1)
6x(2)H labeled dimethylated L-arginine (1)
71.037114 (1)
79.966331 (1)

Study type

RNA-seq of coding RNA (14)
Transcription profiling by array (11)
Proteomic profiling by array (7)
Proteomic profiling by mass spectrometer (3)
Transcription profiling by tiling array (2)
RNA-seq of non coding RNA (2)
Transcription profiling by SAGE (1)
Unknown experiment type (1)
Antigen profiling (1)

Release Date

2025 (574)
2024 (444)
2023 (413)
2022 (393)
2021 (362)
2020 (279)
2019 (236)
2018 (192)
2016 (183)
2017 (177)
2015 (147)
2014 (142)
2013 (92)
2026 (76)
2012 (59)
2011 (57)
2009 (54)
2010 (51)
2008 (33)
2007 (24)
2006 (8)
2004 (5)
2005 (4)
2003 (2)
2001 (2)
2002 (1)

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ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis

Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the...

2021-09-01 | MTBLS1903 | MetaboLights

Mechanism of Hepatotoxicity Induced by Ethanol Extract of Emilia sonchifolia (L.) DC Revealed by Proteomics and Metabolomics

Objective: Hepatotoxicity has been reported for Emilia sonchifolia (L.) DC (Emilia sonchifolia). The plant material is typically prepared using two extraction methods for practical application: water extraction and ethanol extraction. However, our previous research only investigated its wate...

2025-10-30 | MTBLS13237 | MetaboLights

MetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Standard mixture assay)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identit...

2021-11-05 | MTBLS1311 | MetaboLights

MetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Mouse liver assays)

2021-11-02 | MTBLS1266 | MetaboLights

Deciphering the Anti-Biofilm Mechanism of Anthraquinone-2-Carboxylic Acid Against MRSA by Comprehensive Multi-Omics Analysis

Background: Methicillin-resistant Staphylococcus aureus (MRSA) biofilms exhibit high levels of drug resistance and cause nosocomial infections in humans, thus posing a sustainable global health threat. This underscores the critical need to develop novel antibiofilm therapeutics with high efficacy...

2025-09-18 | MTBLS13012 | MetaboLights

Comprehensive systems biology analysis of a seven-month cigarette smoke inhalation study in C57BL/6 mice

Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences in mice of smoke derived from a prototype modified risk tobacco product (pMRTP) as compare...

2015-11-19 | MTBLS143 | MetaboLights

Metabolomic alterations in invasive ductal carcinoma of breast: A comprehensive metabolomic study using tissue and serum samples

Invasive ductal carcinoma (IDC) is the most common type of breast cancer and the leading cause of breast cancer related mortality. In the present study, metabolomic profiles of 72 tissue samples and 146 serum samples were analysed using targeted liquid chromatography multiple reaction monitoring mas...

2018-10-16 | MTBLS552 | MetaboLights

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.

Not available

S-EPMC4739683 | biostudies-literature

Kinase inhibitor pulldown assay (KiP) for clinical proteomics.

Not available

S-EPMC10790396 | biostudies-literature

Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.

Not available

S-EPMC12506516 | biostudies-literature