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Vitek-Lab / MSstatsPTM

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments
https://vitek-lab.github.io/MSstatsPTM/
Artistic License 2.0
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converter for MetaMorpheus output to MSstatsPTM #48

Open ofleitas opened 1 year ago

ofleitas commented 1 year ago

Hello

Could be possible to add a dedicated converter for MetaMorpheus output in MSstatsPTM?

Best regards,

tonywu1999 commented 9 months ago

@ofleitas

Hello,

I'll be working on adding a converter for Metamorpheus output into MSstatsPTM. To assist us with implementation, could you provide sample datasets, i.e. one Metamorpheus dataset from a regular label free experiment and one Metamorpheus dataset from a PTM experiment?

If you have privacy restrictions for your dataset, you could anonymize the proteins, the conditions, etc. We'd also be happy to work with a subset of your dataset. You can find an example at SampleMetamorpheus.zip

Thanks, Tony

ofleitas commented 9 months ago

Hello

Great that you going to implement a converter for metamorpheus output into MSstatsPTM. The Metamorpheus output data that I have is from the global PTM discovery (G-PTM-D) strategy. Does this data work for you?

On Mon, Dec 11, 2023 at 1:30 PM tonywu1999 @.***> wrote:

@ofleitas https://github.com/ofleitas

Hello,

I'll be working on adding a converter for Metamorpheus output into MSstatsPTM. To assist us with implementation, could you provide sample datasets, i.e. one Metamorpheus dataset from a regular label free experiment and one Metamorpheus dataset from a PTM experiment?

If you have privacy restrictions for your dataset, you could anonymize the proteins, the conditions, etc. We'd also be happy to work with a subset of your dataset.

Thanks, Tony

— Reply to this email directly, view it on GitHub https://github.com/Vitek-Lab/MSstatsPTM/issues/48#issuecomment-1850747940, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NFMVJQ6WG4ON22YVF3YI5NMTAVCNFSM6AAAAAAWMOUQHKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJQG42DOOJUGA . You are receiving this because you were mentioned.Message ID: @.***>

tonywu1999 commented 9 months ago

Yes, from my understanding, output data from the global PTM discovery (G-PTM-D) strategy should work.

Thanks.

Hello

Great that you going to implement a converter for metamorpheus output into MSstatsPTM. The Metamorpheus output data that I have is from the global PTM discovery (G-PTM-D) strategy. Does this data work for you?

ofleitas commented 9 months ago

Can I share it with you by drive? The data is too big to share here.

tonywu1999 commented 9 months ago

Yes, you can share by drive.

You can either share with my gmail anthonywu92@gmail.com

tonywu1999 commented 6 months ago

@ofleitas

Hi, I published code to github for the Metamorpheus converter (function name is MetamorpheusToMSstatsPTMFormat). Could you try it out and provide any feedback / difficulties you encounter? You can install the code using the command devtools::install_github("Vitek-Lab/MSstatsPTM", build_vignettes = TRUE) on RStudio.

In the meantime, our team will be performing beta testing on the converter before pushing to Bioconductor.

ofleitas commented 5 months ago

Great news!!!!! Sorry for the late reply. At the moment it will be almost impossible for me to test but as soon as I have some free time I will do it. Best regards, Osmel

On Wed, Mar 6, 2024 at 2:34 PM tonywu1999 @.***> wrote:

@ofleitas https://github.com/ofleitas

Hi, I published code to github for the Metamorpheus converter. Could you try it out and provide any feedback / difficulties you encounter? You can install the code using the command devtools::install_github("Vitek-Lab/MSstatsPTM", build_vignettes = TRUE) on RStudio.

In the meantime, our team will be performing beta testing on the converter before pushing to Bioconductor.

— Reply to this email directly, view it on GitHub https://github.com/Vitek-Lab/MSstatsPTM/issues/48#issuecomment-1981736389, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NH5LR66X3HFG46D3LTYW54WTAVCNFSM6AAAAAAWMOUQHKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBRG4ZTMMZYHE . You are receiving this because you were mentioned.Message ID: @.***>