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[iBAQ protein quantification](https://www.nature.com/articles/nature10098) excludes missed cleavages and normalizes intensities by the number of theoretical peptides, which correlates with length.
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My raw files were searched with DIA-NN 1.8.1 and the output table "report.pg_matrix.tsv" was used for further analysis. I was confused with the two columns "Protein.Group" and "Protein.Ids". The colu…
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how to do label-free quantification and I cannot find the value from pBulid and the result files. I am wondering if the pfind is capable to do LFQ, and if yes, is the "match between runs" applied and…
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Hi. I got the following errors in the quantification step.
> IRFinder-1.2.5/bin/IRFinder: line 562: 49201 Broken pipe gzip -cd "$1"
49202 Aborted (core dumped) | "…
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I am trying to direct-search HeLa raw file in DIA-NN 18. There is no searched data at the end. Below is the report.log which says
[25:57] Loading run D:\Jae_DIA_practice\1_200 ng HeLa digest (3 file…
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I am trying to compare results between library-free search
[report.pg_matrix.tsv.txt](https://github.com/vdemichev/DiaNN/files/11439840/report.pg_matrix.tsv.txt)
```
diann.exe --f "C:\Users\anim…
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Hi,
I'm running into a repeated issue in which DIA-NN (I'm using v1.8 for an intercomparison project) is exited before it finishes. It seems to fail after trying to load the spectral library. I end …
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I am trying to compare MaxQuant v 2.4 [mqpar..xml.txt](https://github.com/vdemichev/DiaNN/files/11358777/mqpar.xml.txt) with DIA-NN v 1.8.1
```
diann.exe --f "C:\Users\animeshs\230421_plasma\New\…
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There is any possibility of a relative cuantification and doing a heatmap in case of having just one replicate of each sample? How can I fix this to achieve the report without errors like:
- Error i…
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Dear FragPipe team,
I am currently processing some phophoenrichment samples using FragPipe. I was wondering whether there is not only the option to filter out modified peptides for protein quantifica…