column mapping issue for DIANN output files

[mhmd-tarek]

Hi,
I am using a DIA-NN (version 1.9.1) output report.tsv file. After uploading the file, the dataset summary shows: Number of Proteins = 1, Number of Peptides = 111,966, and Number of Features = 1,663,571. It seems for some reason all rows have been mapped to a single protein. Anyone knows how to fix that?

[tonywu1999]

@mhmd-tarek

Hi I haven't seen this issue before. Would you be able to share a subset of your dataset and I can look to debug further?

Thanks
Tony

[mhmd-tarek]

Hi Tony, thanks for the quick response. Here's a subset of my data, I get the following

Number of Proteins | 1
Number of Peptides | 783
Number of Features | 10573

Note that my annotation file is missing a run that I don't want to include in my analysis, but I still get the same problem even if I included it. Thanks!

subset_report.tsv

annotation_2.csv

[tonywu1999]

@mhmd-tarek

Thank you for sharing the file. So MSstatsShiny uses the Protein.Names column from the DIANN report for the protein ID. I'm not sure why it's not populated in your report (there is likely an additional setting in DIANN to enable this)

For now, you can copy and paste the Protein.Group column into the Protein.Names column of your report, and MSstatsShiny should run smoothly.

Let me know if you encounter any additional issues.

Tony

[mhmd-tarek]

That worked. Thanks so much!