From email conversation with Rich Johnson. He was working with a file that looks like this:

file    scan    charge    adduct    inchikey    chemicalformula    moleculename    hmdb or cas    retentiontime    width    MW    MolecularIon    frag1comp    frag1calc    frag2comp    frag2calc
QEP1_2021_0823_RJ_21_2ab55prm.raw    3423    1    [M+H]    QQVDJLLNRSOCEL-UHFFFAOYSA-N      C2H8NO3P    (2-AMINOETHYL)PHOSPHONATE    HMDB11747    5    2    125.0241796    126.0320046    CH6O3P    97.0054556    H4O4P    98.9847214
QEP1_2021_0823_RJ_31_2ef55prm.raw    5909    1    [M+H]    XFNJVJPLKCPIBV-UHFFFAOYSA-N    C3H10N2    "1,3-DIAMINOPROPANE"    HMDB00002    8.9    2    74.0844    75.09222333    C3H8N    58.0656708    na    na

Note that the header line has two pairs of [fragment formula, fragment m/z] (obviously there could be any number of pairs in practice). Notice also that the second data line has "na" for its second pair values - only one fragment for that precursor.

It's **very** inconvenient to smith this kind of file into a "one transition per line" format that Skyline currently insists upon. We should be willing to consume more than one fragment per line, and I think we could reasonably insist that they be at the tail of the line, and that they each have a consistent set of descriptors. And of course we have to deal with different lines potentially leaving some of those sets empty since not all precursors have the same fragment count.

Another request for this: https://skyline.ms/announcements/home/support/thread.view?rowId=68715

In this case (compound discoverer), it looks like this:

CompoundName,ExperimentType,Compound Type,ChemicalFormula,Ionization,ResponseThreshold,PrecursorMass,ProductMass,Adduct,Polarity,ChargeState,RT,Fragment,Fragment,Fragment,Fragment,Fragment,Fragment,Fragment,Fragment,Fragment,Fragment
Glutamate,XIC,eTargetCompound,C5 H9 N O4,ESI,0,146.0458984375,146.0458984375,M-H,-,1,0.1366550515314679,146.04674,102.05665,128.03595,74.0251,84.04614,72.04605,103.04063,85.03022,78.95964,116.03696
Glutamine,XIC,eTargetCompound,C5 H10 N2 O3,ESI,0,145.06190490722656,145.06190490722656,M-H,-,1,0.10541853986230618,145.06279,146.04677,127.05203,128.03613,102.05656,101.02505,145.0154,109.04119,74.02509,101.07263
Creatine,XIC,eTargetCompound,C4 H9 N3 O2,ESI,0,130.06221008300781,130.06221008300781,M-H,-,1,0.06642901923823144,88.04092,130.0517,130.08804,61.98866,131.03571,87.04551,131.07211,112.04086,128.05103,130.88982