Shotgun-ms - OmicsDI

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Proteomics (1511)
Unknown (515)
Transcriptomics (309)
Genomics (87)
Metabolomics (41)
Other (11)
Multiomics (3)

Organisms

Homo sapiens (145)
Mus musculus (84)
Drosophila melanogaster (64)
Arabidopsis thaliana (15)
Rattus norvegicus (8)
Danio rerio (7)
Saccharomyces cerevisiae (5)
Bos taurus (5)
Escherichia coli K-12 (3)
Gallus gallus (3)
Cervus nippon (2)
Streptococcus thermophilus (2)
Caenorhabditis elegans (2)
Candida albicans (2)
Cereibacter sphaeroides (1)
Drosophila hawaiiensis (1)
Ephydatia fluviatilis (1)
Ixodes ricinus (1)
Methyloversatilis universalis FAM5 (1)
Miniopterus schreibersii (1)
Mycobacterium avium subsp. paratuberculosis K-10 (1)
Yersinia pseudotuberculosis YPIII (1)
Triticum turgidum subsp. durum (1)
Tetrahymena thermophila (1)
Boreogadus saida (1)
Capra hircus (1)
Populus tremuloides (1)
Citrus reticulata (1)
Setaria viridis (1)
Nothobranchius furzeri (1)

Organisms

Mus musculus (5)
Homo sapiens (2)
Lactiplantibacillus plantarum WCFS1 (1)
Erysipelotrichaceae bacterium OTU0002 (1)
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (1)
Akkermansia muciniphila (1)
Limosilactobacillus reuteri (1)
feces metagenome (1)
Bacillus subtilis subsp. subtilis str. 168 (1)
human gut metagenome (1)
Arabidopsis thaliana (1)
mouse gut metagenome (1)
lake water metagenome (1)
sediment metagenome (1)

Repository

pride (1307)
biostudies-arrayexpress (327)
MassIVE (118)
ENA (48)
MetaboLights (34)
PeptideAtlas (29)
iProX (21)
jPOST (18)
PAXDB (16)
EGA (14)
geo (9)
GNPS (7)
GPMDB (7)
LINCS (3)
PanoramaPublic (1)

Tissue

Cell culture (225)
Brain (61)
Blood plasma (59)
Epithelial cell (55)
Liver (50)
Blood serum (36)
Leaf (32)
Blood (30)
Permanent cell line cell (30)
Lung (28)
Fibroblast (26)
Plant cell (26)
Heart (23)
Cerebrospinal fluid (21)
Kidney (21)
Whole body (21)
Blood cell (19)
Macrophage (19)
Skin (19)
Others (17)
Colon (15)
HeLa cell (15)
T cell (15)
Cell suspension culture (13)
Early embryonic cell (13)
Root (12)
Saliva (12)
Breast (11)
Brain (1)
Urine (1)

Disease

Breast cancer (38)
Disease free (24)
Colon cancer (19)
Malignant neoplasm of ovary (13)
Alzheimer's disease (9)
Melanoma (8)
Not Available (7)
Acute leukemia (7)
COVID-19 (7)
Cardiovascular system disease (7)
Parkinson's disease (7)
Atherosclerosis (6)
Neuroblastoma (6)
Prostate adenocarcinoma (6)
Brain cancer (5)
Cervix carcinoma (5)
Hepatocellular carcinoma (5)
Lung cancer (5)
Lymphoma (5)
Multiple myeloma (5)
Type 2 diabetes mellitus (5)
Osteosarcoma (4)
Type 1 diabetes mellitus (4)
Aortic valve stenosis (3)
Aortic valve stenosis (3)
Glioblastoma (3)
Intracerebral hemorrhage (3)
Mastitis (3)
Non-small cell lung carcinoma (3)
Osteoarthritis (3)

Technology Type

Mass Spectrometry (1307)
Shotgun proteomics (990)
SWATH MS (387)
Bottom-up proteomics (177)
Data-dependent acquisition (104)
Affinity purification coupled with mass spectrometry proteomics (68)
SRM/MRM (54)
Gel-based experiment (52)
Top-down proteomics (29)
Mass spectrometry (24)
Data-independent acquisition (24)
Chemical cross-linking coupled with mass spectrometry proteomics (11)
Mass spectrometry assay (10)
Mass spectrometry imaging (8)
HDMSE (7)
All-ion fragmentation (6)
MSE (6)
Mass spectrometry (3)
Shotgun-MS (3)
PAcIFIC (3)
RNA mass spectrometry (3)
Illumina HiSeq 2000 (1)
Affinity proteomics (1)
Immunopeptidomics (1)
Metaproteomics (1)
Proteogenomics (1)

Instrument Platform

Illumina NovaSeq 6000 (19)
Illumina HiSeq 2500 (16)
NextSeq 500 (14)
Illumina HiSeq 4000 (13)
Illumina HiSeq 2000 (12)
Illumina NovaSeq X (7)
NextSeq 550 (5)
Helicos HeliScope (4)
Illumina HiSeq 3000 (3)
Sequel II (2)
10x Chromium (2)
NextSeq 2000 (2)
MinION (2)
BGISEQ-500 (2)
Illumina HiSeq 1500 (2)
Maxwell® RSC 48 Instrument (Promega, AS8500) (1)
Transrectal ultrasound-guided systematic sampling of prostate tissue (TRUS biopsy) (1)
Accuracode RNA-seq Kit (1)
Microprep kit (1)
Small RNA Sample Prep Kit v1.5 (1)
RNAeasy kit (NimbleGen) (1)
Illumina TruSeq stranded ribo-minus Plant (1)
MS10 plates (1)
MagNA Lyser (1)
Linux computer (1)
Linux Beowulf cluster; AMD Opteron Linux Beowulf cluster; AMD Opteron 6168 (1)
Trizol (1)
GeneChip IVT Labelling Kit (1)
Qiagen RNeasy Plant Mini Kit (1)
Affymetrix ATH1 Gene Chip (1)

Publication Date

2022 (201)
2023 (180)
2024 (174)
2021 (160)
2025 (156)
2019 (144)
2020 (136)
2016 (114)
2026 (108)
2018 (101)
2017 (99)
2015 (86)
2014 (62)
2012 (56)
2013 (43)
2010 (28)
2011 (16)
2008 (11)
2009 (3)
2007 (1)
2006 (1)

UNIPROT ID/AC

1433B_MOUSE (4)
1433G_MOUSE (4)
1433S_MOUSE (4)
1433Z_MOUSE (4)
2A5A_MOUSE (4)
2A5E_MOUSE (4)
2AAA_MOUSE (4)
2AAB_MOUSE (4)
2ABA_MOUSE (4)
2ABD_MOUSE (4)
3HIDH_MOUSE (4)
4EBP2_MOUSE (4)
4ET_MOUSE (4)
4F2_MOUSE (4)
6PGD_MOUSE (4)
6PGL_MOUSE (4)
8ODP_MOUSE (4)
A16A1_MOUSE (4)
A16L1_MOUSE (4)
AAGAB_MOUSE (4)
AAK1_MOUSE (4)
AAKB1_MOUSE (4)
AAMDC_MOUSE (4)
AAR2_MOUSE (4)
AASD1_MOUSE (4)
AATC_MOUSE (4)
AATF_MOUSE (4)
AATM_MOUSE (4)
ABCE1_MOUSE (4)
ABCF1_MOUSE (4)

ENSEMBL ID

ENSG00000170477 (19)
ENSG00000147251 (5)
ENSG00000247315 (3)
ENSG00000229353 (1)

CHEBI ID

CHEBI:64433 (5)
CHEBI:26271 (5)
CHEBI:15356 (5)
CHEBI:18186 (5)
CHEBI:15428 (5)
CHEBI:16449 (5)
CHEBI:65302 (4)
CHEBI:84661 (4)
CHEBI:84665 (4)
CHEBI:64516 (4)
CHEBI:66849 (4)
CHEBI:64566 (4)
CHEBI:64561 (4)
CHEBI:17822 (4)
CHEBI:25094 (4)
CHEBI:18237 (4)
CHEBI:16811 (4)
CHEBI:25017 (4)
CHEBI:28044 (4)
CHEBI:73001 (4)
CHEBI:27266 (4)
CHEBI:27897 (4)
CHEBI:64567 (4)
CHEBI:64563 (4)
CHEBI:30769 (4)
CHEBI:86974 (3)
CHEBI:85688 (3)
CHEBI:71720 (3)
CHEBI:66860 (3)
CHEBI:136220 (3)

Metabolite Name

Uracil (4)
Adenosine (4)
Guanosine (4)
Glu-Asn (3)
Cryptotanshinone (3)
Quercetin (3)
Diosmin (3)
Linoleamide (3)
L-Alanine (3)
Erucamide (3)
Thymine (3)
L-Proline (3)
Piperidine (3)
Xanthosine (3)
Tyrosol (3)
Citric acid (3)
Oxypurinol (3)
Oleamide (3)
Ile-Glu (3)
Guanine (3)
Citrate (3)
Ala-Leu (3)
Caffeine (3)
L-Leucine (3)
Inosine (3)
Pro-Arg-Pro (2)
Piceol (2)
Caproic Acid (2)
Phe-Gly-Tyr (2)
Glu Ile (2)

First Public Date

2024 (13)
2026 (9)
2019 (7)
2018 (5)
2014 (3)
2025 (2)
2022 (2)
2020 (2)
2017 (2)
2023 (1)
2021 (1)
2016 (1)

Classification

bacteria (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (8)
15.994915 (5)
57.021464 (5)
15.99491 (3)
57.02146 (3)
0.984 (2)
0.984016 (2)
N6-dimethyl-L-lysine (2)
-17.026549 (1)
-18.010565 (1)
14.01565 (1)
19.989829 (1)
28.0313 (1)
2x(15)N labeled L-lysine (1)
3.994915 (1)
4-dinitrophenyl modified residue (1)
42.010565 (1)
43.00581 (1)
45.029395 (1)
4x(15)N labeled L-arginine (1)
4x(2)H labeled dimethylated residue (1)
79.966331 (1)
N6 (1)

Study type

RNA-seq of coding RNA (203)
RNA-seq of non coding RNA (42)
ChIP-seq (18)
Transcription profiling by array (14)
RNA-seq of total RNA (10)
Other (9)
RNA-seq of coding RNA from single cells (8)
Methylation profiling by high throughput sequencing (5)
Differential (2)
Plant - High-throughput sequencing (2)
Animal - High-throughput sequencing (2)
Cell line - High-throughput sequencing (2)
ATAC-seq (2)
Single nucleus RNA sequencing (2)
ChIP-chip by tiling array (1)
Proteomic profiling by mass spectrometer (1)
RIP-seq (1)
MicroRNA profiling by array (1)
DNA-seq (1)
Methylation profiling by array (1)

Release Date

2016 (76)
2012 (74)
2015 (69)
2014 (64)
2022 (63)
2021 (59)
2020 (49)
2019 (44)
2018 (44)
2025 (40)
2013 (40)
2023 (38)
2010 (36)
2024 (35)
2017 (32)
2011 (25)
2026 (18)
2009 (17)
2008 (7)
2007 (7)
2005 (3)
2006 (1)
2004 (1)

Lab affiliation

University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (23)
Instituto de Investigaciones Sanitarias de Santiago de Compostela (18)
College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China (9)
Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 (7)
Department of Biotechnology, TU Delft, The Netherlands (7)
General and molecular microbiology, Institute for chemistry and biology of the marine environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany (7)
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 (6)
Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA. Systems Biology Institute, Yale University, New Haven, CT 06516, USA (6)
Department of Entomology,Institute of Vegetables and Flowers,Chinese Academy of Agriculture Sciences,Beijing,100081,China (6)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (4)
DIVAS, University of Milan (4)
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland (4)
Department of Biotechnology, Delft University of Technology, The Netherlands. (4)
Department of Cardiovascular Medicine, Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Army Medical University; Chongqing, China. (4)
Institute for Systems Biology (4)
Institute of Plant Genetics, Leibniz Universitaet Hannover, Germany (4)
Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg,CNRS, IPHC UMR 7178, 67087 Strasbourg,France (4)
Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes (URMITE) UMR 6236, Faculté de médecine 27 Bd Jean Moulin 13385 MARSEILLE Cedex 05 FRANCE (4)
Aarhus University Department of Biomedicine DK-8000 Aarhus C (3)
Biological Mass Spectrometry Lab Department of Translational Medicine (DiMeT) Center for Translational Research on Autoimmune & Allergic Diseases - CAAD University of Piemonte Orientale Novara, Italy (3)
Center for Neuroscience and Cell Biology – University of Coimbra (3)
Chemical and Biological Engineering, The Hong Kong University of Science and Technology (HKUST), Hong Kong (3)
Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA. Systems Biology Institute, Yale University, New Haven, CT 06516, USA (3)
Department of Plant Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea (3)
Department of Proteomics and Signal Transduction, Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany (3)
ETH Zurich Prof. Dr. Ruedi Aebersold Institute of Molecular Systems Biology Head of Department of Biology HPT E 78 Auguste-Piccard-Hof 1 CH-8093 Zurich Switzerland (3)
Federal University of Uberlandia (3)
Globe Institute, University of Copenhagen, Denmark (3)
Head of Laboratory of Neuro-Oncology, Neurology, Clinical & Cancer Proteomics (3)
IBMC (3)

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LipidHunter Identifies Phospholipids by High-Throughput Processing of LC-MS and Shotgun Lipidomics Datasets (Rat cardiomyocyte assay)

Lipids are dynamic constituents of biological systems, rapidly responding to any changes in physiological conditions. Thus, there is a large interest in lipid-derived markers for diagnostic and prognostic applications, especially in translational and systems medicine research. As lipid identificatio...

2018-07-31 | MTBLS483 | MetaboLights

Proteomic analysis of protein interactions between Eimeria maxima sporozoites and chicken jejunal epithelial cells by shotgun LC-MS/MS

Identification of Eimeria maxima sporozoites soluble proteins that could bind to chicken jejunal epithelial cells using co-immunoprecipitation and shotgun LC-MS/MS

ORGANISM(S): Gallus Gallus Eimeria Maxima

2018-04-09 | PXD009075 |

Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures.

Not available

S-EPMC3487405 | biostudies-literature

Shotgun MS proteomic analysis of bronchoalveolar lavage fluid in normal subjects.

Not available

S-EPMC4239657 | biostudies-literature

Adapted MS/MS^ALL Shotgun Lipidomics Approach for Analysis of Cardiolipin Molecular Species.

Not available

S-EPMC6369710 | biostudies-literature

Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data.