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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 
UnknownDIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.
Not available
S-EPMC6949130 | biostudies-literature
Unknowndia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts.
Not available
S-EPMC9270362 | biostudies-literature
UnknownSpectronaut and DIA-NN: A Comparison of their Performance in the Analysis of Lung Adenocarcinoma Biopsies.
Not available
S-EPMC12903166 | biostudies-literature
UnknownDIAgui: a Shiny application to process the output from DIA-NN.
Not available
S-EPMC10799745 | biostudies-literature
ProteomicsDecoding the impact of isolation window selection and QuantUMS filtering in DIA-NN for DIA quantification of peptides and proteins.
Proteomic studies using Data Independent Acquisition (DIA) have gained momentum in all fields of biology. Search engines are evolving to keep up with the latest developments in instrument technology. DIA-NN is the most popular software for DIA analysis under academic use license. The QuantUMS algori...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2025-12-04 | PXD063416 | Pride
Isolation window Dia Mass spectrometry Quantums Quantification 
ProteomicsEvaluation of the False Discovery Rate in Library-free Search by DIA-NN Using in vitro Human Proteome
In recent years, deep learning-based in silico spectral libraries have gained increasing attention. Several data-independent acquisition (DIA) software tools have integrated this feature, known as library-free search, making DIA analysis more accessible. However, controlling the false discovery rate...
ORGANISM(S): Cellular Organisms 
2025-07-23 | PXD056519 | JPOST Repository
ProteomicsBenchmarking plexDIA analysis with SILAC-labelled Hela cell samples
SILAC labelled Hela cell lysates were mixed in defined ratios and analysed using both DDA and DIA methods, to serve as a benchmark for the novel plexDIA features of DIA-NN.
ORGANISM(S): Homo sapiens (Human) 
2023-10-19 | PXD039578 | Pride
Dia-nn Dia Hela Silac Plexdia 
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 
ProteomicsPTMsite-Finder supports DIA-NN-based PTM DIA proteomics
we developed PTMsite-Finder, a user-friendly graphical interface software tool designed to report and quantify multiple PTM sites directly from DIA-NN outputs. We validated PTMsite-Finder’s phosphosite quantification accuracy for phosphoproteomics DIA-MS data and demonstrated its versatility in proc...
ORGANISM(S): Homo Sapiens 
2024-11-11 | PXD057731 |
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