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lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
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intact protein - MW determination #520

Closed cbroeckl closed 3 years ago

cbroeckl commented 4 years ago

Are there any tools within MSnbase that can perform spectrum deconvolution of charge state determination/isotope envelope deconvolution?
i.e. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838638/

Thanks! Corey

lgatto commented 4 years ago

No, and I can't think of any package that can do that. May be @jorainer or @sgibb know of any.

cbroeckl commented 4 years ago

@lgatto - thanks, and any suggestions are appreciated. I can try to hack one together if need be but would rather not if it exists!

jorainer commented 4 years ago

We were playing around to identify and match isotopes in a MS spectrum - but never really finished that.

I would love to have an isotope envelope deconvolution algorithm implemented - maybe you could then contribute it to the MsCoreUtils (or MetaboCoreUtils) packages? That would be great 👍

cbroeckl commented 4 years ago

https://github.com/cbroeckl/RAMClustR/blob/master/R/assign.z.R

I had implemented a partial solution in RAMClustR for this. given a spectrum of centroids, infer charge state of the ions. Once charge is assigned, calcluate m. I could see one additional step being of value - aggregation of similar masses (i.e. if we have charge state of 3 and 4, the produce nearly identical m values which we would want to merge). I can try to work on this and document a function, but would probably need a bit of support on ensuring the function is up-to-standards.

cbroeckl commented 4 years ago

An isotope abundance check (averagine) would probably also be useful.

sgibb commented 4 years ago

Does this be of any value?

Based on poison distribution: https://github.com/sgibb/MALDIquant/blob/master/R/monoisotopic-functions.R

Based on averagine: https://github.com/sgibb/MALDIquantTools/blob/master/R/monoisotopic-methods.R

Both methods would need some work. 18.08.2020 16:43:30 Corey Broeckling notifications@github.com:

An isotope abundance check (averagine) would probably also be useful.

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