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ProteomicsMicroflow SWATH data analysed with DIA-NN
We have developed DIA-NN, an integrated software suite for fully-automated processing of raw SWATH/DIA data. DIA-NN enables deep and confident proteome coverage with fast chromatographic methods, paving the way for a new generation of high-throughput proteomics. This data set illustrates the capabil...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2019-11-06 | PXD014690 | Pride
Gas-phase fractionation Dia K562 Swath Yeast Plasma High-throughput proteomics 
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 
ProteomicsProteomes of yeast kinase knock-outs analysed by SWATH-MS
It proves so far difficult to predict the metabolome, even when genome, transcriptome or proteome of a cell are known. In order to globally map enzyme-metabolite relationships, we systematically quantified enzyme expression and metabolite concentrations in Saccharomyces cerevisiae kinase knock-out s...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-09-13 | PXD010529 | Pride
Swath Yeast Kinase High-throughput proteomics 
ProteomicsPho-Tip: one-pot dephosphorylation for rapid and sensitive analysis of DIA phosphoproteomics data
Here we introduce Pho-Tip, a low-loss one-pot dephosphorylation strategy. We show that Pho-Tip enables comprehensive mapping of phosphorylated peptide sequences, facilitating streamlined creation of experiment-focused in silico predicted spectral libraries and thus rapid and sensitive analysis of DI...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2026-02-17 | PXD070420 | Pride
Phosphorlyation Dia Human S. cerevisiae Yeast Hela High-throughput Phosphopeptides Quantitative proteomics 
ProteomicsFast proteomics with dia-PASEF and analytical flow-rate chromatography
The presented approach is a combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and raw data processing using the DIA-NN software suite, to conduct fast, low-cost proteomic experiments that only require moderate sample amount...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) 
2024-10-24 | MSV000096202 | MassIVE
ProteomicsProtein profiling of WERI RB1 and etoposide resistant WERI ETOR reveals new insights to overcome topoisomerase inhibitor resistance in retinoblastoma
Chemotherapy resistance is one of the reasons for the loss of the eye in retinoblastoma (RB) pa-tients. RB chemotherapy resistance has been investigated in different cell culture models like WERI RB1. Furthermore, chemotherapy resistant RB subclones like the etoposide resistant WERI ETOR cell line h...
ORGANISM(S): Homo sapiens (Human) 
2022-05-20 | PXD030924 | Pride
Chemotherapy resistance Mass spectrometry Weri rb1 Weri etor Retinoblastoma 
ProteomicsOxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in pla...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-05-29 | MSV000089567 | MassIVE
ProteomicsThe proteome landscape of genome-wide genetic perturbations
Despite the massive research efforts of the post-genomics era, a significant fraction of genes remain without functional annotation. Proteomics holds the promise to close significant gaps, but has only recently reached the scalability and precision of genome-scale studies. Here we combine large-scal...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2022-08-15 | MSV000090136 | MassIVE
ProteomicsRapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome
UPF1 is a multi-domain RNA helicase that constantly monitors the transcriptome by non-specifically binding to mRNAs, dissociating from non-target transcripts, and initiating degradation on selected target RNAs via multiple proposed pathways such as nonsense-mediated decay (NMD). NMD is a translation...
ORGANISM(S): Homo sapiens (Human) 
2025-09-03 | PXD061797 | Pride
Mrna degradation Nmd Gene expression Nonsense-mediated mrna decay Upf1 Translation 
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