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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 (19)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (8)
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Penn State College of Medicine, Department of Medicine, Penn State Cancer Institute. (3)
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Department of Cell & Developmental Biology, University of California, San Diego, CA 92093, USA. (3)
Cancer Research Center of Toulouse, INSERM UMR 1037, 31037 Toulouse, France Université Toulouse III Paul Sabatier, 31330 Toulouse, France (2)
Crick-GSK LinkLabs, UK (2)
UMR_S1134 Inserm/Université Paris Cité, Paris, France (2)
Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA (2)
Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA. (2)
Faculty of Chemistry and Center for Synthetic Microbiology (SYNMIKRO) Head of the Core-Facility for Mass Spectrometry Marburg University Hans-Meerwein-Str. 4 35032 Marburg GERMANY (2)
Professor, Microbiology, Immunology, and Pathology Mycobacteria Research Laboratories Scientific Director, Rocky Mountain Regional Biocontainment Laboratory Editor-in-chief, BMC Mycobacteria (2)
Université Paris Cité, INSERM, CNRS, Institut Cochin, F-75014 Paris, France (2)
Colorado State University (2)
CRIBL Unit, UMR CNRS 7276 INSERM 1262, University of Limoges (2)
Group Leader, Quattrocolo Lab, Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway (2)
Department of Immunology and Cell Biology, Sherbrooke, QC, Canada (2)
Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna (2)
School of Engineering, Westlake University (2)
head of Laboratory of Regenerative Biomedicine, Institute of Cytology, Russian Academy of Sciences (2)
Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (2)
Translational Metabolic Laboratory, Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands (2)
University of Missouri-Columbia (2)
Institut Cochin, Inserm U 1016, CNRS UMR 8104, Université Paris Cité. (2)
University of Copenhagen Faculty of Health and Medical Sciences Department of Biomedical Sciences (2)
Institute for Systems Biology, Seattle, WA, USA (2)
Laboratory of Molecular, Translational and Digital Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia (2)

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xref:PubMed:41423049 (1)

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Benchmarking Software for DDA-PASEF Immunopeptidomics

PRJEB98909 | ENA

A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer

Generation of a new library of targeted mass spectrometry assays for accurate protein quantification in triple negative breast cancer (TNBC) tissues. Primary tumor tissue lysates from 105 TNBC patients treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic, were used to generate...

ORGANISM(S): Homo sapiens (Human)

2024-05-31 | PXD047793 | Pride

Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF.

Not available

S-EPMC8844217 | biostudies-literature

Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry.

Not available

S-EPMC11480776 | biostudies-literature

Thunder-DDA-PASEF boosted by MS2rescore enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCoV-2 spike protein epitopes

Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highl...

ORGANISM(S): Homo sapiens (Human)

2024-03-19 | PXD046543 | Pride

Ms2rescore Immunopeptidomics Thunder-dda-pasef Timstof pro

Thunder-DDA-PASEF boosted by MS2rescore enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCoV-2 spike protein epitopes

ORGANISM(S): Homo sapiens (Human)

2024-03-19 | PXD046535 | Pride

Ms2rescore Immunopeptidomics Thunder-dda-pasef Timstof pro

DDA-PASEF and diaPASEF acquired A549/K562 proteomic datasets with deliberate batch effects

We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: A549 vs K562), allowi...

ORGANISM(S): Homo sapiens (Human)

2023-11-21 | PXD041421 | Pride

Dda Pasef Dia K562 A549 Batch effects

DDA-PASEF and diaPASEF acquired HCC1806/HS578T proteomic datasets with deliberate batch effects

ORGANISM(S): Homo sapiens (Human)

2023-11-21 | PXD041391 | Pride

Dda Pasef Dia Hcc1806 Hs578t Batch effects

A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer.

Not available

S-EPMC11258311 | biostudies-literature

Comprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer

The zebrafish (Danio rerio) retina has been increasingly used for studying vertebrate visual processing and ocular growth regulation as it has a high anatomical and physiological similarity to the human eye. Recently, the integration of trapped ion mobility spectrometry (TIMS) with parallel accumula...

ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio)

2026-06-17 | PXD076440 | Pride

Dia Retina Zebrafish Dda

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