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Enable analysis of data independent acquisition (including SWATH) data.
- [x] peak detection in pockets/isolation windows.
- [x] data structures for identified chromatographic peaks (issue #346).
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Hi,
I'm seeking clarification on the process of determining the 'max' and 'norm' values for NYU patients. These values are crucial for intensity scaling during data analysis. Understanding their or…
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- [ ] [Correlated gene modules uncovered by high-precision single-cell transcriptomics](https://www.pnas.org/doi/abs/10.1073/pnas.2206938119)
- [x] [Dynamics of single-cell protein covariation during…
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Hi, is it possible to generate the PDF report while running DIANN from command line? I'm using this version:
```
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2…
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Tools needed for Data Independent Acquisition Swath Workflow using DIA-UmpireSE for signal extraction:
msconvert .wiff -> mzXML
DIA-Umpire SE mzXML -> *.mgf
msconvert .mgf -> mzXML
Xtandem mzXML -> pe…
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Hi,
Could the protein abundance values shown in the ‘Results’ tab for DDA (Data Dependent Analysis) proteomics baseline experiments include **ppb** (parts per billion) as the unit displayed next to…
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Many papers on mass-spectrometry based proteomics have shown the use of deep learning for intensity prediction, combining scores across search algorithms, retention time, collision corss section predi…
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Hi,
I have a lot of doubts when reading the scoring principle in the Sumpplementary Note 4 of the OpenSWATH paper named “OpenSWATH enables automated, targeted analysis of data-independent acquisition…
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In your manuscript entitled "Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry" you state that:
"The pipeline generated decoys for FDR calculations, whic…
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Hello,
I am new to using DIA-NN. The log file showed the below message:
DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 15 2022 08:45:18
Current date and time: Thu…