Data cleanup prior to file conversion?

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Marvin Altamia

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May 22, 2025, 8:14:32 AMMay 22
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Hi MSstats Team,

I have the PSM output from Proteome Discoverer, which I am converting to MSstatsTMT format. Is it necessary to remove contaminants (see attached PNG) manually, or is this step handled automatically during file conversion?

Thanks!

-marvin
Contampng.png

Devon Kohler

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May 22, 2025, 10:33:58 AMMay 22
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Hi Marvin,

The PD TMT converter does not currently filter out contaminants. I would recommend filtering them out before inputting the PSM file into the converter.

Devon 

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