search

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
8 stars 2 forks source link

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 11 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 11 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 11 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 11 months ago

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

tonywu1999 commented 11 months ago

Yes, you can share by drive.

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

tonywu1999 commented 9 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 8 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: @.***>