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PRECURSOR_TYPE for isotopologues #210

Open meowcat opened 1 year ago

meowcat commented 1 year ago

We currently do not have a way to specify spectra from "higher isotopologue" precursors. For example, for a brominated compound we could be fragmenting the 81Br-isotopologue, i.e. 2 "isotopes" above [M+H]+.

NIST uses [M+H+2i]+ notation. MzSpecLib don't specifically speak about how to label the precursor; but are copying this convention in the peak annotation format for fragments.

This is different from a deuterated/other isotope labelled standard, where the isotope position can be clearly specified in the SMILES, whereas here we are looking at a natural abundance with unknown position (as there may be one or multiple Br in the molecule).

schymane commented 1 year ago

I would vote for using the notation consistent with NIST ...

sneumann commented 1 year ago

There is an upcoming PSI standard mzPAF, I'll have a look if they say anything about that. Steffen

takaakin commented 1 year ago

Hi. We don't need any additional definition for the spectral data of isotologues. The one difference is "the value of MS$FOCUSED_ION: PRECURSOR_M/Z is that of the most abondant isotopologue". For an example, MSSJ deposited the ESI-MS and ESI-MS/MS data of Tetrabromobisphenol A. This has a molecular form, C15H12Br4O2 (exact mass is 539.75708 Da). Most abondant isotopologue consists of C15H12(79Br2)(81Br2)O2 (exact mass is 543.75299 Da). MSBNK-MSSJ-MSJ00475 is ESI-MS spectrum of negative ion of Tetrabromobisphenol A. It shows the typical Br4 isotopic pattern that shows the max intensity at m/z 542.7527. MSBNK-MSSJ-MSJ00476 - 482 are ESI-MS/MS data of the MS$FOCUSED_ION: PRECURSOR_M/Z: 542.745711.

Takaaki Nishioka

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