|Title||»||Support more than one fragment specification per line in transition list column picker, for small molecules at least|
|Assigned To||»||Brian Pratt|
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.