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optimal parameters for mgf's from TimsTOF-Pro #53

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KurtBo opened this issue Sep 28, 2020 · 1 comment
Open

optimal parameters for mgf's from TimsTOF-Pro #53

KurtBo opened this issue Sep 28, 2020 · 1 comment

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@KurtBo
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KurtBo commented Sep 28, 2020

Hi,

When analyzing TimsTOF-Pro data with pfind, the number of identified proteins and peptides seems to be too low. I use mgf's that are made by the Bruker software itself and also checked mgf's made with msconvert. These mgf's are sometimes quite large (500Mb +). I do also get an error message:
image
Do you know which parameters are best used for Tims-TOF data? Are there known issues with these files?
Kind regards,

Kurt
@zengxinlei0
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I met same problems. Have you resolved it?

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@KurtBo @zengxinlei0