tims-dda - OmicsDI

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University of Copenhagen Faculty of Health and Medical Sciences Department of Biomedical Sciences (2)
Université Paris Cité, INSERM, CNRS, Institut Cochin, F-75014 Paris, France (2)
1) Department of Analytical Chemistry and Biochemistry, AGH University of Krakow, Krakow, Poland 2) Laboratory of Proteomics and Mass Spectrometry, Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland (1)
1) Department of Analytical Chemistry and Biochemisty, AGH University of Krakow 2) Laboratory of Proteomics and Mass Spectrometry, Maj Institute of Pharmacology, Polish Academy of Sciences (1)
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.Semmelweis University, Department of Pharmacology and Pharmacotherapy, Budapest, Hungary. 2.Pharmahungary Group, Szeged, Hungary (1)
1Cancer Research Program, Hospital del Mar Research Institute, Doctor Aiguader 88, Barcelona 08003, Spain. Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain. (1)
1Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106 (1)
1Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA 2Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA 3Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA (1)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)
Not available (1)

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TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore - Plasma proteomics

The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields – such as plasma pro...

ORGANISM(S): Homo sapiens (Human)

2025-02-17 | PXD053748 | Pride

Plasma Data-driven rescoring

Ion mobility fractionation coupled to PASEF for enhanced proteome coverage

Data provided report the use of trapped ion mobility spectrometry (TIMS) to fractionate ions in the gas phase based on their ion mobility (V⋅s/cm2) followed by parallel accumulation serial fragmentation (PASEF) in a quadrupole time-of-flight instrument. TIMS fractionation coupled to DDA-PASEF allowe...

ORGANISM(S): Homo sapiens (Human)

2022-08-12 | PXD033129 | Pride

Timstof pro Pasef Dia Segmented Tims fractionation Fractionation Optimized Deep coverage Dda Ion mobility

Enhancement of Proteome Coverage by Ion Mobility Fractionation Coupled to PASEF on a TIMS-QTOF Instrument.

Not available

S-EPMC10653119 | biostudies-literature

Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with novel MS2PIP timsTOF fragmentation prediction model

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)

2024-03-18 | PXD040385 | JPOST Repository

Optimized Time-Segmented Acquisition Expands Peptide and Protein Identification in TIMS-TOF Pro Mass Spectrometry.

Not available

S-EPMC11811991 | biostudies-literature

Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments.

Not available

S-EPMC10370902 | biostudies-literature

LC-MS/MS analysis of KIF11-binding proteins

This data includes the raw data of LC-MS/MS analysis on KIF11-binding proteins

ORGANISM(S): Homo sapiens (Human)

2026-02-13 | PXD074456 | Pride

Lc-ms/ms analysis Kif11 Co-immunoprecipitation

Deep proteome coverage of microglia using a streamlined data independent acquisition-based proteomic workflow: method consideration for a phenotypically diverse cell type

As the immune cells of the brain, microglia play a key role in various homeostatic and disease-related processes. In order to carry out their numerous functions, microglia are able to adopt a wide range of phenotypic states. The proteomic landscape represents a more accurate molecular representation...

ORGANISM(S): Mus musculus (Mouse)

2025-03-31 | PXD056436 | Pride

Dia-pasef Dda library generation Deep proteomics Microglia Dia methods development

Mapping heat stress-induced core histone post-translational modifications in <i>Acropora cervicornis</i>.

Not available

S-EPMC12418939 | biostudies-literature

A novel strategy to characterize the pattern of β-lactam antibiotic-induced drug resistance in Acinetobacter baumannii.

Carbapenem-resistant Acinetobacter baumannii (CRAb) is an urgent public health threat, according to the CDC. This pathogen has few treatment options and causes severe nosocomial infections with >50% fatality rate. Although previous studies have examined the proteome of CRAb, there have been no focus...

ORGANISM(S): Acinetobacter baumannii A424 Bacteria

2023-07-20 | PXD042336 | Pride

Tims tof pro2 Acinetobacter baumannii Dda lfq

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