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ProteomicsComparison of DDA (Orbitrap Exploris 480) and DIA (timsTOF Pro 2) phosphoproteomics
In this experiment, 3 replicate phosphopeptide enrichments using titanium dioxide spin tips (GL Science) of the filamentous fungus Magnaporthe oryzae were measured on a) Orbitrap Exploris 480 in DDA and b) timsTOF Pro 2 in DIA for comparison of model/acquisition type differences.
ORGANISM(S): Cellular Organisms 
PXD038605 | JPOST Repository
ProteomicsTear Fluid Proteomics: A Comparative Study of DIA and DDA Mass Spectrometry
Background: Mass spectrometry is a powerful technique for tear fluid proteomics, offering critical insights into its complex molecular composition. Data-dependent acquisition (DDA), the most commonly used approach, preferentially selects high-abundance proteins, limiting reproducibility and the quan...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2025-10-20 | PXD062422 | Pride
Tear fluid  schirmer strip  proteomics  biomarkers  mass spectrometry 
ProteomicsTear Fluid Proteomics: A Comparative Study of DIA and DDA Mass Spectrometry
Background: Mass spectrometry is a powerful technique for tear fluid proteomics, offering critical insights into its complex molecular composition. Data-dependent acquisition (DDA), the most commonly used approach, preferentially selects high-abundance proteins, limiting reproducibility and the quan...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2025-10-20 | PXD062423 | Pride
Tear fluid  schirmer strip  proteomics  biomarkers  mass spectrometry 
ProteomicsImmunopeptidomics DIA and DDA Dynamic Range Experiment
The peptide identification sensitivity of the affinity purified immunopeptidome of a JY cell line (Epstein–Barr virus-immortalized B cell lymphoblastoid line, ECACC 94022533, IHW9287) for DDA and DIA experiments was assessed by a linear concentration series. JY cells are homozygous for all HLA-I loc...
ORGANISM(S): Homo sapiens (Human) 
2025-09-04 | PXD024809 | Pride
Dynamic range Dia Immunopeptidomics Hla 
ProteomicsComparative DDA and DIA-PASEF proteomics profiling of cross-kingdom macrophage infection reveals new mechanisms driving pathogen virulence
Opportunistic infections of the respiratory tract often succeed under a weakened immune response caused by an underlying illness or hospitalization. The human fungal pathogen, Cryptococcus neoformans, and the bacterial pathogen, Klebsiella pneumoniae, are both well-characterized microbes that cause...
ORGANISM(S): Mus musculus (Mouse) Klebsiella pneumoniae subsp. pneumoniae CIP 52.145 = B5055 Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (Filobasidiella neoformans var. grubii) 
2024-08-13 | PXD054527 | Pride
Cryptococcus neoformans Virulence Dia-pasef Klebsiella pneumoniae Macrophages Druggable targets Mass spectrometry-based proteomics Dda 
UnknownBlood proteome profiling for biomarker discovery in broilers with necrotic enteritis.
Not available
S-EPMC12000508 | biostudies-literature
ProteomicsAnalysis of 1,508 plasma samples of the DiOGenes study - Robust, single shot capillary flow data-independent acquisition to decipher proteomic profiles of weight loss and maintenance
Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies (1, 2), we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (D...
ORGANISM(S): Homo sapiens (Human) 
2019-04-05 | PXD013231 | Pride
Plasma proteomics Swath Library Single shot Clinical proteomics Stable isotope-based quantification High throughput Label-free quantification Data-independent acquisition 
ProteomicsComparison of Targeted MS Methods in Activity-Based Protein Profiling 1: DDA
To examine the different mass spectrometry approaches to monitoring kinases after enrichment with desthiobiotinylating probes for activity-based protein profiling (ABPP), two experiments were performed with H1993 lung cancer cells. First, cell lysates were pre-treated with DMSO vehicle, dasatinib, ...
ORGANISM(S): Homo sapiens (Human) 
2017-11-27 | PXD006095 | Pride
Dda Activity-based protein profiling Dia Prm Srm/mrm Lung cancer 
ProteomicsComparison of Targeted MS Methods in Activity-Based Protein Profiling 2: DIA
To examine the different mass spectrometry approaches to monitoring kinases after enrichment with desthiobiotinylating probes for activity-based protein profiling (ABPP), two experiments were performed with H1993 lung cancer cells. First, cell lysates were pre-treated with DMSO vehicle, dasatinib, ...
ORGANISM(S): Homo sapiens (Human) 
2017-11-27 | PXD006096 | Pride
Dda Activity-based protein profiling Dia Prm Srm/mrm Lung cancer 
ProteomicsDeep plasma proteomics with data-independent acquisition: A fastlane towards biomarkers identification
Plasma proteomic is a precious tool in human disease research, but requires extensive sample preparation in order to perform in-depth analysis and biomarker discovery using traditional Data-Dependent Acquisition (DDA). Here, we highlight the efficacy of combining moderate plasma prefractionation and...
ORGANISM(S): Homo sapiens (Human) 
2024-09-24 | PXD047901 | Pride
Dia-nn Data-independent acquisition Deep proteome analysis Plasma proteomics Fractionation Clinical proteomics Covid-19 Biomarkers 
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