Dia-umpire - OmicsDI

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Proteomics (41)
Unknown (9)
Multiomics (1)
Metabolomics (1)

Organisms

Andropogon gerardi (34)
Bacteria (34)
Bartonella quintana JK 31 (34)
Canis lupus familiaris (34)
Cnidaria (34)
Ensifer adhaerens (34)
Halictus scabiosae (34)
Human alphaherpesvirus 1 strain 17 (34)
Human alphaherpesvirus 1 strain KOS (34)
Human betaherpesvirus 5 (34)
Human herpesvirus 2 strain 186 (34)
Mesocricetus auratus (34)
Miscanthus x giganteus (34)
Mus musculus (34)
Panicum virgatum (34)
Platyhelminthes (34)
Pseudomonas aeruginosa PA103 (34)
Rabies virus Nishigahara RCEH (34)
Rattus norvegicus (34)
Rattus rattus (34)
Rhodococcus jostii RHA1 (34)
Rhodopseudomonas palustris (34)
Shigella (34)
Sorghastrum nutans (34)
Streptococcus dysgalactiae subsp. equisimilis SK1249 (34)
Streptococcus pneumoniae (34)
Streptomyces coelicolor A3(2) (34)
Synechocystis sp. PCC 6803 (34)
Tripsacum dactyloides (34)
Homo sapiens (2)

Repository

pride (34)
MassIVE (6)
iProX (1)
MetaboLights (1)

Tissue

Cell culture (9)
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Seed (1)
Stem cell (1)
X-organ-sinus-gland complex (1)

Disease

Disease free (4)
Breast cancer (3)
COVID-19 (1)
Colon cancer (1)
Influenza (1)
Parasitic infectious disease (1)
Perinatal necrotizing enterocolitis (1)
Type 1 diabetes mellitus (1)

Technology Type

Mass Spectrometry (34)
SWATH MS (28)
Shotgun proteomics (10)
Data-independent acquisition (5)
Bottom-up proteomics (3)
Immunopeptidomics (2)
Mass spectrometry (1)

Instrument Platform

Q Exactive (2)
TripleTOF 5600 (2)
Orbitrap Fusion (Thermo Scientific instrument model) (1)
Orbitrap Fusion ETD (1)
Q Exactive HF-X (1)
TripleTOF 5600 (AB Sciex) (1)

Publication Date

2022 (6)
2017 (5)
2023 (5)
2021 (4)
2025 (4)
2024 (4)
2020 (3)
2018 (3)
2016 (3)
2026 (2)
2015 (1)

CHEBI ID

CHEBI:75194 (1)
CHEBI:91040 (1)
CHEBI:72081 (1)
CHEBI:72080 (1)
CHEBI:72088 (1)
CHEBI:137221 (1)
CHEBI:72090 (1)
CHEBI:72097 (1)
CHEBI:91036 (1)
CHEBI:134238 (1)
CHEBI:72092 (1)
CHEBI:72091 (1)
CHEBI:140469 (1)
CHEBI:72396 (1)
CHEBI:50680 (1)
CHEBI:140470 (1)
CHEBI:85215 (1)
CHEBI:121071 (1)
CHEBI:92804 (1)
CHEBI:95324 (1)
CHEBI:83308 (1)
CHEBI:88612 (1)
CHEBI:50172 (1)
CHEBI:80645 (1)
CHEBI:49402 (1)
CHEBI:74372 (1)
CHEBI:74238 (1)
CHEBI:48845 (1)
CHEBI:65088 (1)
CHEBI:139043 (1)

Metabolite Name

6-Hydroxyflavone-beta-D-glucoside (1)
Monobehenin (1)
6,3',4'-Trimethoxyflavanone (1)
1,2-Di-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1'-myo-inositol) (1)
3-Dehydroepiandrosterone sulfate (1)
3-Methoxyprostaglandin F1alpha (1)
1-Hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoserine (1)
8-Carboxy-3-methylflavone (1)
7-Hydroxycoumarin-4-acetic acid (1)
LysoPE 20:3 (1)
LysoPE 16:1 (1)
2,6-Di-tert-butyl-4-methoxyphenol (1)
N-Nonanoyl-L-homoserine lactone (1)
Plasmenyl-PE 36:5 (1)
5-trans U-44069 (1)
13,14-Dehydro-15-cyclohexyl Carbaprostacyclin (1)
Plasmenyl-PE 40:5 (1)
17,20,21-Trihydroxypregn-1-ene-3,11-dione (1)
2'-Hydroxy-2,5,6'-trimethoxychalcone (1)
Uric acid, 1,3-dimethyl- (1)
7-Benzyl-1-ethyl-4-oxo-1,8-naphthyridine-3-carboxylic acid (1)
16-Phenoxy tetranor prostaglandin F2alpha (1)
Plasmenyl-PE 42:6 (1)
Plasmenyl-PE 36:4 (1)
PS 42:3 (1)
2'-Hydroxy-4-methoxychalcone (1)
PS 37:0 (1)
1-(9Z-Octadecenoyl)-sn-glycero-3-phosphoethanolamine (1)
(R)-Butaprost, free acid (1)
PS 44:5 (1)

Release Date

2022 (3)
2016 (3)
2023 (1)
2020 (1)
2015 (1)

Lab affiliation

Boston University Medical Campus 670 Albany St., Rm. 509 Boston, MA 02118 USA (2)
Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Office B25A/04/94 Rue du Bugnon 25a, CH-1005 Lausanne (2)
Xiamen University (2)
Biological Mass Spectrometry Lab,Department of Translational Medicine (DiMeT),Center for Translational Research on Autoimmune & Allergic Diseases - CAAD, University of Piemonte Orientale, Novara (NO),Italy. (1)
Boston University School of Medicine (1)
CRG,UPF (1)
Centro de Investigación Príncipe Felipe, Av. Eduardo Primo Yúfera 3, 46012 Valencia, Spain (1)
Department of Cardiology, Smidt Heart Institute and Proteomics and Metabolomics Core Facility (1)
Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, Hu Bei Province, 430060, China (1)
Department of Sciences and Technological Innovation, University of Piemonte Orientale, Italy (1)
Département d'immunologie et de biologie cellulaire, Faculté de médecine et des sciences de la santé, Université de Sherbrooke (1)
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 (1)
FMSS, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, Canada (1)
Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón (Spain) (1)
Heart Institute, Cedars-Sinai Medical Center (1)
Infection Medicine Proteomics Lab, Division of Infection Medicine (BMC), Faculty of Medicine, Lund University, Lund, Sweden (1)
Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany (1)
International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, Gdansk, Poland (1)
ManukaMed LP (1)
Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain (1)
Proteomics Unit Centre for Genomic Regulation University Pompeu Fabra Dr Aiguader 88, 08003 Barcelona, Spain (1)
Proteomics and Metabolomics Lab, Department of Translational Medicine (DiMeT), Center for Translational Research on Autoimmune & Allergic Diseases - CAAD, University of Piemonte Orientale, Novara (NO), Italy (1)
Regenerative Medicine Institute, Department of Biomedical Sciences (1)
Sichuan Agricultural University (1)
State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, China (1)
University of Bern, Department of Clinical Research, Proteomics and Mass Spectrometry Core Facility, 3010 Bern, Switzerland (1)
University of Eastern Piedmont (1)
University of Freiburg Faculty of Biology Biochemistry and Functional Proteomics Schänzlestrasse 1 79104 Freiburg Germany (1)
University of Michigan (1)
University of Michigan, Ann Arbor, MI, US (1)

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DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics

This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational fra...

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

2015-01-21 | PXD001587 | Pride

Swath Dia

Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire

ORGANISM(S): Homo sapiens (Human)

2016-06-16 | PXD003179 | Pride

Human Dia Dia-umpire

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

Not available

S-EPMC4399776 | biostudies-literature

DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

2017-04-27 | MSV000081023 | MassIVE

Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire

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

2017-04-01 | MSV000080875 | MassIVE

LFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification

The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...

ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast)

2016-09-27 | PXD002952 | Pride

Lfqbench Lfq Swath-ms Benchmark

Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.

Not available

S-EPMC5476226 | biostudies-literature

Extensive and accurate benchmarking of DIA acquisition methods and softwares using a complex

In order to compare workflows for acquisition and treatment of proteomic data analyzed in Data Independent Acquisition (DIA) mode, a proteomic standard has been generated by spike-in the 48 human proteins of UPS1 (Sigma) in a whole cell extract of E.coli at 8 different concentrations ranging from 0....

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

2021-06-09 | MSV000087597 | MassIVE

Data Independent Acquisition analysis in ProHits 4.0.

Not available

S-EPMC5079801 | biostudies-literature

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.

Not available

S-EPMC10338508 | biostudies-literature

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51 Results

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