MSStats with DIA-NN. DIANNtoMSstatsFormat input file.

Ramon Diaz

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Apr 1, 2024, 7:04:50 PM4/1/24

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Hi there!

I´m just starting to use MSStats with DIA-NN, and I'm wondering what DIA-NN output file I need to use in DIANNtoMSstatsFormat.

Thanks!

Devon Kohler

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Apr 4, 2024, 9:23:35 AM4/4/24

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Hello,

You need the DIA-NN PSM report. It should be named "diann_report.tsv". Additionally, you will need to create an annotation file that maps the run names in DIA-NN to your experimental design. For more information on this check out the MSstats v4 paper supplementary.

Best,

Devon

Ramon Diaz

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Apr 4, 2024, 12:00:38 PM4/4/24

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Thanks, Devon!

Ramon Diaz

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Apr 4, 2024, 12:09:53 PM4/4/24

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By the way. Is this diann_report.tsv only generated by fragpipe or by DIA-NN standalone version as well?

Thanks again!

El jueves, 4 de abril de 2024 a las 15:23:35 UTC+2, devonj...@gmail.com escribió:

Devon Kohler

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Apr 4, 2024, 1:01:34 PM4/4/24

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I think by both tools. On a side note, if you are using FragPipe you can also generate the FragPipe msstats report (named msstats.csv for label free).

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