Ddapasef - OmicsDI

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Proteomics (87)
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Aerococcus urinae NBRC 15544 = CCUG 36881 (82)
Andropogon gerardi (82)
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pride (82)
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Technology Type

Mass Spectrometry (82)
Bottom-up proteomics (29)
Data-dependent acquisition (26)
Shotgun proteomics (25)
Data-independent acquisition (20)
Affinity purification coupled with mass spectrometry proteomics (12)
DiaPASEF (7)
SWATH MS (6)
All-ion fragmentation (3)
Top-down proteomics (2)

Instrument Platform

TimsTOF fleX (2)
TimsTOF fleX MALDI-2 (1)

Publication Date

2024 (28)
2025 (22)
2026 (16)
2023 (12)
2022 (4)
2021 (4)

Release Date

2025 (4)

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 (18)
Department of Animal and Poultry Sciences and the School of Neuroscience, Virginia Tech, Blacksburg, VA, USA (3)
Department of Cell & Developmental Biology, University of California, San Diego, CA 92093, USA. (3)
Imperial College London (3)
Queen's University Belfast (3)
Crick-GSK LinkLabs, UK (2)
Department of Chemistry & Biochemistry, University of Maryland at College Park (2)
Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States (2)
Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry (2)
Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems,Germany (2)
1, Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China 2, School of Medicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China 3, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China (1)
1. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; 2. Proteomics and Singal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (1)
Associate Professor Department of Biological Sciences University of Denver (1)
Center of Experimental Rheumatology, Department of Rheumatology, University Hospital, University of Zurich, Zurich, Switzerland (1)
Department for Drug Design and Pharmacology, University of Copenhagen (1)
Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (1)
Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich; Zurich, Switzerland (1)
Department of Neurology, University Hospital of Zurich (USZ) and University of Zurich (UZH) (1)
Department of Pediatrics, the Affiliated Huai’an No.1 People’s Hospital of Nanjing Medical University, Huai’an , China (1)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany. & NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (1)
Dept. CMIM y Química Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz (1)
Discovery Proteomics Facility, Target Discovery Institute,University of Oxford (1)
Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK (1)
Friedrich-Alexander-Universität Erlangen-Nürnberg, Chair of Food Chemistry (1)
Friedrich-Loeffler-Institut (1)
Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot, Spain (1)
Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology ETH, Zurich (1)
Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riem,Germany (1)
Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany (1)
Max Delbrück Center Robert-Rössle-Straße 10 13125 Berlin, Germany (1)

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Electrophoresis-Correlative Framing of Ion Mobility Deepens Single-Cell Mass Spectrometry Proteomics

This project developed electrophoresis-correlative (Eco) mass spectrometry (MS) to measure the proteome of single cells on a trapped ion mobility mass spectrometer (timsTOF PRO). Eco-MS identified 962 protein groups in a <20 min of electrophoresing a single-HeLa-cell-equivalent (~200 pg) proteome am...

ORGANISM(S): Homo sapiens (Human) Xenopus laevis (African clawed frog)

2025-05-07 | PXD057685 | Pride

Electrophoresis-Correlative Framing of Ion Mobility Deepens Single-Cell Mass Spectrometry Proteomics

ORGANISM(S): Homo sapiens (Human) Xenopus laevis (African clawed frog)

2025-02-06 | PXD053023 | Pride

Proteomics Xenopus laevis Mass spectrometry Single cell Capillary electrophoresis

diaPASEF optimization for peptide profiling of hydrolyzed infant formula by microLC-timsTOF Pro

This study optimized identification rate and reproducibility of an untargeted diaPASEF approach for quantitative peptide profiling of hydrolyzed infant formula. For this, the impact of variable window widths as well as major acquisition parameters, such as the precursor coverage, number of diaPASEF ...

ORGANISM(S): Bos taurus (Bovine)

2026-03-05 | PXD066057 | Pride

Hydrolyzed infant formula Lc-qtof-ms/ms Diapasef Spectral library Quantitative proteomics Peptide profiling

Differences of uniquely identified peptides between ddaPASEF and diaPASEF

Recent advancements in mass spectrometry-based proteomics have made it possible to conduct comprehensive protein analysis. In particular, the emergence of the data-independent acquisition (DIA) method powered by machine learning has significantly improved protein identification effi-ciency. However,...

ORGANISM(S): Homo Sapiens (human)

2024-12-01 | PXD056754 | JPOST Repository

Prospective ICH Q2(R2)-aligned validation of label-free untargeted proteomics for host cell protein quantification in biotherapeutics

This dataset contains raw and processed LC–MS/MS data generated for a prospective validation of label-free untargeted proteomics for host cell protein (HCP) quantification in biotherapeutic matrices. A stable isotope-labeled CHO whole-proteome standard was spiked into the NIST monoclonal antibody re...

ORGANISM(S): Mus musculus (Mouse)

2026-06-08 | PXD075694 | Pride

Host cell proteins Hcp quantification Biotherapeutics Timstof Analytical validation Untargeted proteomics Ddapasef Ich q2(r2) Lc–ms/ms

Deep Visual Proteomics defines single-cell identity and heterogeneity

Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven ima...

ORGANISM(S): Homo sapiens (Human)

2022-04-27 | PXD023904 | Pride

Microscopy Digital pathology Proteomics Laser microdissection

Spatial distribution of the proteome in human body and cancers

The ddaPASEF and diaPASEF data were acquired from over 60 types of human specimens. Based on these, the consensus spectral libraries were generated and used in subsequent DIA analysis to demonstrate a quantitative human proteome map and discover potential cancer biomarkers.

ORGANISM(S): Homo Sapiens

PXD077178 |

Spatial characterization and stratification of colorectal adenomas by Deep Visual Proteomics

Background and Aims: Colorectal adenomas (CRAs) are precursor lesions that can progress to adenocarcinomas. Current clinical guidelines categorize patients into risk groups based on adenoma characteristics observed during index colonoscopy, but this may lead to overtreatment. Our aim was to establis...

ORGANISM(S): Homo sapiens (Human)

2024-08-04 | PXD046999 | Pride

Spatial Mass spectrometry Pathology Cancer Colorectal adenoma Proteomics Dvp

Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes.

Not available

S-EPMC12687359 | biostudies-literature

Distinct Impact of Neuronal and Astrocytic IFNAR1 Loss in Parkinson-like Dementia

Interferon-alpha/beta-receptor (IFNAR) signal defects were recently identified to contribute to sporadic Parkinson’s disease (PD) with dementia (PDD). Mice lacking interferon-beta (IFNβ) develop PDD-like disease; however, the phenotypic, cellular, and molecular impacts of IFNAR1 loss in vivo have no...