Benchmark datasets

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Unknown (2047)
Genomics (97)
Proteomics (62)
Transcriptomics (61)
Other (6)
Metabolomics (5)
Models (3)
Methylation profiling (1)

Organisms

Homo sapiens (60)
Bartonella quintana JK 31 (43)
Bombyx mori (43)
Onchocerca volvulus (43)
Klebsiella pneumoniae (43)
Musca domestica (43)
Brugia malayi (43)
Schizosaccharomyces pombe (43)
Mus musculus (29)
Canis lupus familiaris (15)
Rattus norvegicus (5)
Danio rerio (2)
Sus scrofa (2)
Scenedesmus vacuolatus (1)
unidentified (1)
Bacteroides fragilis (1)
Enterococcus casseliflavus (1)
Klebsiella aerogenes (1)
Citrobacter freundii complex (1)
Escherichia coli ATCC 25922 (1)
Morganella morganii (1)
Enterobacter asburiae (1)
Saccharomyces cerevisiae S288C (1)
Lactobacillus acidophilus (1)
Pseudomonas aeruginosa (1)
Klebsiella pneumoniae (1)
Clostridium butyricum (1)
Enterococcus faecalis (1)
Saccharomyces cerevisiae (1)
Drosophila melanogaster (1)

Organisms

Homo sapiens (28)
Mus musculus (5)
Rattus norvegicus (2)
Scenedesmus vacuolatus (1)
Salmonella enterica subsp. enterica (1)
Salmonella enterica subsp. enterica serovar Typhi (1)
root metagenome (1)
Severe acute respiratory syndrome coronavirus 2 (1)
mouse gut metagenome (1)

Repository

ENA (90)
geo (53)
pride (43)
biostudies-arrayexpress (19)
MassIVE (12)
iProX (5)
MetaboLights (5)
BioModels (3)
EGA (3)
jPOST (1)
PAXDB (1)

Tissue

Cell culture (11)
Feces (2)
Blood plasma (2)
HeLa cell (2)
Permanent cell line cell (2)
Epithelial cell (2)
Blood cell (2)
Blood (2)
Pancreatic ductal cell (1)
Epithelial cell of prostate (1)
JURKAT cell (1)
Cerebrospinal fluid (1)
Brain (1)
Fibroblast (1)
Colon (1)
T cell (1)

Disease

Plasmodium falciparum malaria (1)
Prostate adenocarcinoma (1)
Pancreatic ductal adenocarcinoma (1)
Cervix carcinoma (1)
Malaria (1)
Malignant neoplasm of ovary (1)
Disease free (1)

Technology Type

Mass Spectrometry (43)
Shotgun proteomics (24)
Bottom-up proteomics (12)
SWATH MS (8)
Data-independent acquisition (8)
Data-dependent acquisition (6)
Mass spectrometry (5)
All-ion fragmentation (2)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
DiaPASEF (1)
SRM/MRM (1)
Gel-based experiment (1)
Affinity purification coupled with mass spectrometry proteomics (1)

Instrument Platform

Q Exactive (4)
PromethION (3)
Sequel IIe (2)
MinION (2)
Illumina NovaSeq 6000 (2)
Illumina HiSeq 2000 (2)
Illumina HiSeq 3000 (2)
Orbitrap Astral (2)
TripleTOF 5600 (2)
Orbitrap Exploris 480 (2)
Q Exactive HF-X (2)
LTQ Orbitrap (2)
Q Exactive HF (2)
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)
Illumina NovaSeq X (1)
NextSeq 2000 (1)
BGISEQ-500 (1)
Illumina HiSeq 4000 (1)
Q Exactive HFX (1)
6550 iFunnel Q-TOF LC/MS (1)
Orbitrap Fusion ETD (1)
TripleTOF 5600+ (1)
LTQ Orbitrap Velos (1)
TimsTOF Pro (1)
Orbitrap Fusion (1)
Orbitrap Eclipse (1)
Orbitrap Fusion Lumos (1)

Publication Date

2019 (24)
2025 (21)
2026 (19)
2023 (15)
2022 (10)
2024 (8)
2018 (7)
2021 (6)
2020 (6)
2017 (6)
2016 (4)
2013 (3)
2014 (2)
2012 (2)
2008 (2)
2011 (1)
2010 (1)
2009 (1)
2006 (1)

UNIPROT ID/AC

NAP1_YEAST (1)
GGC1_YEAST (1)
CBK1_YEAST (1)
MCFS1_YEAST (1)
ARI1_YEAST (1)
HCH1_YEAST (1)
YKT6_YEAST (1)
H3_YEAST (1)
OYE2_YEAST (1)
ACON_YEAST (1)
TPS2_YEAST (1)
YIR7_YEAST (1)
DRS1_YEAST (1)
GATB_YEAST (1)
PGM3_YEAST (1)
DCP2_YEAST (1)
THTR_YEAST (1)
RPA2_YEAST (1)
DUG2_YEAST (1)
NUP60_YEAST (1)
PSA6_YEAST (1)
DHYS_YEAST (1)
SF3B1_YEAST (1)
TYW1_YEAST (1)
MS116_YEAST (1)
ARMT1_YEAST (1)
4932.YMR051C (1)
EIF3J_YEAST (1)
SOK1_YEAST (1)
END3_YEAST (1)

Metabolite Name

NSI-189 (1)
S7p (1)
SM (d16:3/28:0) (1)
Dl-Lanthionine (1)
PC (22:5e/18:3) (1)
SM (d28:1/15:0) (1)
Bisphenol TMC (1)
N-{6-[(5-chloro-3-pyridyl)oxy]-3-pyridyl}-N'-methylurea (1)
N-(2,4-difluorophenyl)-N'-(1,3-diphenyl-1H-pyrazol-4-yl)urea (1)
MLK (1)
5α-Dihydrotestosterone glucuronide (1)
ACar 22:3 (1)
ACar 22:2 (1)
Neodiosmin (1)
Morphine-d3 (1)
HRH (1)
Methyl 6-{[4-(trifluoromethyl)anilino]carbonyl}nicotinate (1)
PC (20:5e/2:0) (1)
4-[1-(fur-2-oyl)pyrazol-5-yl]-5-methyl-1-phenylpyrazole (1)
11β-Hydroxyandrosterone (1)
VNH (1)
MKK (1)
4-[2-(trifluoromethyl)phenyl]-5-undecyl-4H-1,2,4-triazole-3-thiol (1)
Υ-Glutamylcysteine (1)
3-Methoxy prostaglandin F1α (1)
6β-Naltrexol (1)
TAG (18:1-18:1-18:2) (1)
1-(3,4-dihydroxyphenyl)-7-(4-hydroxyphenyl)heptan-3-one (1)
Β-Cortolone (1)
11-Deoxy prostaglandin F1α (1)

IsPrivate

False (3)

Submitter Keywords

Ersilia (3)
FAIR-AIML (3)
Machine Learning Model (3)

First Public Date

2019 (23)
2026 (16)
2025 (13)
2018 (10)
2023 (9)
2024 (6)
2022 (4)
2021 (4)
2014 (2)
2020 (1)
2017 (1)
2013 (1)

Classification

bacteria (2)
viruses (1)

Modelling Approach

Computational model (2)
Machine learning (1)

Study type

RNA-seq of coding RNA from single cells (7)
Transcription profiling by array (4)
RNA-seq of total RNA (2)
RNA-seq of coding RNA (2)
Animal - High-throughput sequencing (1)
Other (1)
ChIP-seq (1)
Methylation profiling by array (1)

Release Date

2025 (411)
2024 (299)
2023 (264)
2022 (263)
2021 (177)
2020 (124)
2019 (101)
2018 (79)
2026 (67)
2017 (65)
2016 (41)
2014 (35)
2015 (33)
2010 (23)
2012 (22)
2013 (19)
2008 (12)
2011 (10)
2009 (9)
2007 (8)
2006 (2)
2005 (2)

Lab affiliation

Department of Proteomics and Signal Transduction, Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany (2)
Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia (2)
ProGenTomics, Laboratory of Pharmaceutical Biotechnology,Ghent University (2)
Lee Kong Chian School of Medicine, School of Biological Sciences, Nanyang Technological University, Singapore (2)
Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands. (1)
Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia (1)
Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany (1)
Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil (1)
Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany. (1)
Lehigh University (1)
University of Manchester, Faculty of Life Sciences,B1072 Michael Smith Building, Oxford Road, Manchester, M13 9PT (1)
CSIC/UAB Proteomics Laboratory, IIBB-CSIC, Barcelona, Spain (1)
Department of Pathology, Department of Urology, Department of Oncology, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231 (1)
Institute for Microbiology Department of Microbial Proteomics and Mass Spectrometry Ernst-Moritz-Arndt-University Greifswald F.-L.-Jahn-Str. 15 17489 Greifswald phone: ++49 3834 864073 (1)
Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna (1)
University of Applied Sciences Upper Austria, Bioinformatics Research Group, Softwarepark 11, 4232 Hagenberg, Austria (1)
Head of research group Quantitative and Systems Biology; Max Planck Institute for Biophysical Chemistry; Goettingen; Germany (1)
Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States (1)
Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology (1)
Institute for Molecular Pathology, Vienna, Austria. Institute of Molecular Biotechnology, Vienna Austria (1)
DTU Bioengineering (1)
University of California, San Diego (1)
Proteomics Team Leader of Nestlé Institute of Health Sciences (1)
Cellzome - a GSK company Target Discovery Meyerhofstrasse 1 69117 HEIDELBERG (1)
The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia (1)
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA (1)
Professor, Department of Biochemistry and Molecular Biology, University of Southern Denmark (1)
Columbia University, Dept. Biochemistry/Mol. Biophysics (1)
Professor. Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark (1)
Institute of Aquaculture, University of Stirling (1)

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Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry

Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives ...

2016-07-27 | MTBLS176 | MetaboLights

Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control

Direct-infusion mass spectrometry (DIMS) metabolomics is an important approach for characterising molecular responses of organisms to disease, drugs and the environment. Increasingly large-scale metabolomics studies are being conducted, necessitating improvements in both bioanalytical and computatio...

2022-05-16 | MTBLS79 | MetaboLights

MaxLFQ label-free quantification algorithm benchmark datasets

We developed a set of algorithms for label-free quantification, termed MaxLFQ, embedded into MaxQuant. This contains two datasets to benchmark MaxLFQ: The proteome benchmark dataset consists of of HeLa and E. coli lysates mixed at defined ratios. The dynamic range benchmark dataset consists of UPS1...

ORGANISM(S): Homo sapiens (Human) Escherichia coli

2014-09-17 | PXD000279 | Pride