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statisticalbiotechnology / triqler

The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code
Apache License 2.0
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Proteome Discoverer input #11

Open FloraMika opened 4 years ago

FloraMika commented 4 years ago

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 commented 4 years ago

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?

On Wed, Nov 20, 2019 at 4:25 PM FloraMika notifications@github.com 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

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FloraMika commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

example_PD.xlsx

percolator commented 4 years ago

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

--Lukas

On Thu, Nov 21, 2019 at 11:44 AM FloraMika notifications@github.com 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

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MatthewThe commented 4 years ago

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 commented 4 years ago

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.