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PaulBrack / Yamato

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m/z is not a unit of measurement in UO #25

Closed marinaPauw closed 5 years ago

marinaPauw commented 5 years ago

Still have to figure out what to do about this.

PaulBrack commented 5 years ago

UO?

Ozzard commented 5 years ago

m/z is measured in Daltons, which should be a unit of measure in the ontology?

marinaPauw commented 5 years ago

The problem is that at this stage of the data analysis we don't know the charge states of the fragment ions, which with ESI or even with very giant peptides in MALDI can be multiply charged. The charge state is not contained in the mzml files and I am still trying to figure out how skyline calculates it, but my initial thoughts are that they used the spectral library, which is not suited to our needs. So it may still be possible for us to calculate the charge state, but I am not sure if we want to go that route.

marinaPauw commented 5 years ago

UO = unit ontology sorry, I've been writing UO so much in the last while I've forgotton that not everyone calls it that.

Ozzard commented 5 years ago

Correct: Skyline - like any other tool - calculates the charge state via the spectral library. A fragment has two variables: m and z; the instrument is only capable of measuring the ratio of the two, m/z, so we need another piece of information to go from one variable to two.

marinaPauw commented 5 years ago

HUPO-psi dev team said I could use the MS ontology for cases that do not appear in the UO.