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Proteomicsdia-PASEF HeLa dilution series 0.2ng - 200ng on Bruker timsTOF Pro 2
Different sample preparation methods were tested for HeLa proteome analysis. A sample obtained using sodium deoxycholate-based lysis allowed identification of the highest number of proteins. For this sample, a dilution series was acquired in triplicates ranging from 0.2ng to 200ng. All measurements ...
ORGANISM(S): Homo sapiens (Human) 
2022-06-20 | PXD029836 | Pride
Dia-pasef diapasef dia-nn hela 
ProteomicsThree-dimensional spheroid and bioprinted cervical cancer models exhibit non-interchangeable proteomic states
This dataset supports a comparative proteomic study of HeLa and SiHa cervical cancer cells cultured as adherent monolayers, scaffold-free spheroids, and 3D bioprinted alginate/gelatin constructs. The study integrated morphological assessment, resazurin-based relative metabolic activity measurements,...
ORGANISM(S): Homo sapiens (Human) 
2026-10-23 | PXD084972 | Pride
Cervical cancer  hela  siha  spheroids  3d bioprinting  alginate/gelatin hydrogel  dia-pasef  label-free quantitative proteomics  cell–matrix interaction  metabolic remodeling 
ProteomicsHigh-throughput mixed-species quantitative benchmark with varying sample amounts
Samples were generated by mixing commercially available tryptic digests (human: K562, HeLa; yeast (S.cerevisiae); E.coli) in defined proportions, to create a dataset with known ground truth, for benchmarking of the quantitative performance and scalability of DIA raw data processing software. Acquisi...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2025-12-09 | PXD055981 | Pride
ProteomicsA semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis
Initial discovery-based analysis using data independent acquisition (DIA) can obtain deep proteome coverage with high data completeness; however, the development of targeted PRM assays based on subsequent bioinformatic predictions can be tedious and time-consuming because of the complexity of the ou...
ORGANISM(S): Homo sapiens (Human) 
2024-09-06 | PXD049405 | Pride
Dia Timstof Script Bruker Sem-automated Prm 
ProteomicsIdentification of cellular factors associated with HIV-1 virions isolated by filtration and ultracentrifugation. (Viral particles)
The aim of this project was to identify cellular factors enriched with HIV-1 virions after filtration and ultracentrifugation of culture surpernatants of HIV-1 producer cells compared to a control. To this end, HeLa cells were transfected with HIV-1 NL4-3 provirus and, 48 hours after transfection, ...
ORGANISM(S): Homo sapiens (Human) 
2025-10-08 | PXD057129 | Pride
Hiv-1 Virion purification Atg proteins Cellular factors 
ProteomicsIdentification of cellular factors associated with HIV-1 virions isolated by filtration and ultracentrifugation. (Total lysate)
The aim of this project was to identify cellular factors enriched with HIV-1 virions after filtration and ultracentrifugation of culture surpernatants of HIV-1 producer cells compared to a control. To this end, HeLa cells were transfected with HIV-1 NL4-3 provirus and, 48 hours after transfection, ...
ORGANISM(S): Homo sapiens (Human) 
2025-10-08 | PXD057162 | Pride
Hiv-1 Virion purification Atg proteins Cellular factors 
ProteomicsThe effect of ADAR1 depletion on mitochondrial proteins
In this study, we found that ADAR1 reduces the levels of double-stranded RNAs (dsRNAs) derived from both nuclear and mitochondrial transcripts. To elucidate how ADAR1 controls mitochondrial dsRNA (mt-dsRNA) accumulation, we performed quantitative mass spectrometry on mitochondrial protein fractions ...
ORGANISM(S): Homo sapiens (Human) 
2026-01-23 | PXD069896 | Pride
ProteomicsUnraveling the impact of VHL Exon 2 mutations identified in Erythrocytosis or von Hippel-Lindau disease, identified hnRNP F and hnRNP AB as new RNA-Binding Proteins involved in VHL splicing.
This study explores the impact of mutations in the exon 2 of the von Hippel-Lindau (VHL) gene, associated with erythrocytosis or von Hippel-Lindau disease. We analyzed 15 genetic variants, including missense and synonymous mutations, to assess their effects on VHL protein stability and splicing. Usi...
ORGANISM(S): Homo sapiens (Human) 
2025-09-25 | PXD056515 | Pride
Dia Rna-binding proteins Von hippel-lindau disease Erythrocytosis 
ProteomicsCos-7 neonatal Fc receptor proteomics
Enteroviruses enter cells by endocytosis; however, the exact strategy is not known. There is an existing knowledge of enterovirus particles binding to the neonatal Fc receptor in vitro. To assess the feasibility of Enterovirus particles using the neonatal Fc receptor in vivo, with the subsequent con...
ORGANISM(S): Cercopithecus aethiops (Green monkey) (Grivet) 
2026-06-29 | PXD068859 | Pride
Neonatal fc receptor Fibroblast African green monkey 
ProteomicsPlasma Proteomics Benchmarking and Optimisation/ Plasma proteomics across three generations of mass spectrometry instruments: lessons for optimising biomarker discovery
In biomarker discovery phases clinical proteomics provides large-scale identification and quantification of proteins in donor samples. For these studies plasma is the most frequently used biofluid, as it reflects both physiological and pathological states of the circulating proteome. However, the va...
ORGANISM(S): Homo sapiens (Human) 
2026-04-21 | PXD069060 | Pride
Plasma proteomics Astral Clinical proteomics Lcms 
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