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lgatto / synapter

Label-free data analysis pipeline for optimal identification and quantitation
https://lgatto.github.io/synapter/
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Not sure an issue #138

Open BaylorSci opened 4 years ago

BaylorSci commented 4 years ago

I'm just playing around with MSe (and not HDMSe) data and was excited to find your package on R. However, as the latest progenesis release has integrated PLGS into so that it is no longer run separately, i was wondering if there were plans to update the vignette/package to account for this?

lgatto commented 4 years ago

Unfortunately, we (the synapter authors) don't acquire any MSe data any more, nor de we collaborate with researchers that do. We aren't in a position (and don't plan) to make any changes to the package. If you would be willing to contribute an update or new documentation, we would be happy to consider it and help if necessary.

BaylorSci commented 4 years ago

Many thanks for your quick reply. If you are not working with MSe data anymore, that makes sense. I am not sure i am proficient enough to contribute an update to the documentation, but maybe someone reading this in the future would be willing to take this on as i know a lot of people do not like the rigidity of Progenesis. By any chance do you know if there are others working on MSe specific proteomics packages within R? I know XCMS has recently added MSe handling for metabolomics.

lgatto commented 4 years ago

Handling of raw data in xcms is likely relying on MSnbase, but I don't know how they convert it. This would unfortunately not be directly compatible with synatper.