Proteome Discoverer input

[FloraMika]

Hi Matthew,

I would like to run your proteomics pipeline but my input is from Proteome Discoverer and is quite different from triqler input.

Do you have any way to convert it as you did for MaxQuant ?

Regards,

Flora

[percolator]

The short answer is no. However, it might be of interest to us to implement such a feature. Do you have any insight into which file formats to best access to get quantitative information from LFQ experiments in PD?

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On Wed, Nov 20, 2019 at 4:25 PM FloraMika ***@***.***> wrote: Hi Matthew, I would like to run your proteomics pipeline but my input is from Proteome Discoverer and is quite different from triqler input. Do you have any way to convert it as you did for MaxQuant ? Regards, Flora — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11?email_source=notifications&email_token=AAAXKAA46H3F5FHRWE4KQJLQUVJFPA5CNFSM4JPUKT32YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H2YGLKQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXKAELEKN2PKONZPIN3BDQUVJFPANCNFSM4JPUKT3Q> .

[FloraMika]

Infortunatly, I am not a user of the program myself but I have to work with output file. PD output differ in the score (no negative values) and there is no decoy column...

[MatthewThe]

No negative scores should not be an issue, but we do need some decoy hits to estimate error rates. Could you perhaps share a PD output file, so that we can figure out what will be possible?

[FloraMika]

Yes, of course, here is the first lines of a PD output...

example_PD.xlsx

[percolator]

Is this the direct output from PD? Or did you specifically export your results as an Excel file?

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--Lukas

On Thu, Nov 21, 2019 at 11:44 AM FloraMika ***@***.***> wrote: Yes, of course, here is the first lines of a PD output... example_PD.xlsx <https://github.com/statisticalbiotechnology/triqler/files/3874224/example_PD.xlsx> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11?email_source=notifications&email_token=AAAXKAHRNVOV7CWY6E6UL2TQUZRBLA5CNFSM4JPUKT32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEZZBBQ#issuecomment-557027462>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXKABIOEFL3WQM4Z5WP6DQUZRBLANCNFSM4JPUKT3Q> .

[MatthewThe]

Thanks for the file, is it correct that this is a TMT (or other isobaric labeling) experiment? Triqler currently does not support such modes at the moment, though it is definitely something we want to include in the future.

[FloraMika]

Honestlty I am just doing the downstream analysis I guess it is PD output as excel file... Yes this is TMT experiment. I guess there is a huge need for tools adapted to proteomics and I hear great recommendations about your program.