I'm new to msgfplus. Is the following understanding correct:
For orbitrap instruments:
For incorporating the benefits attributed to high-res spectra when generating a raw score (and e-value calculations), msgfplus will only take into account the high-res aspect of "y ions only" (ie ignore b ions and all other non-y ions completely) and even for those y ions, it will only consider those y ions that are adjacent to each other.
If that's correct, wouldn't that mean that msgfplus is not taking into account nearly as much information as other search engines, such as say X!Tandem or Sequest, that do take into account the high-res information for every fragment (whether b ion or y ion, or whether they're adjacent or not)? (I know that msgfplus will still "count" those non-adjacent y ions, but it will not consider it's high-res tolerance when it scores all ions, I believe.) Or, is the assumption that orbitraps primarily produce y ions and those y ions are almost always adjacent, and so "everything works out" in the end? (From what I can tell, I think that may be true for abundant peptides, but for the lower abundant peptides, many fragments may be missing, and some/many of them may be ones which cause a gap in the "y ion" sequence; and for lower abundant ions, one may not be able to afford to ignore a whole class of ions, eg b ions, since every ion produces potentially critical info to narrow down the possibilities of potential peptides?)
I'm new to msgfplus. Is the following understanding correct:
For orbitrap instruments:
For incorporating the benefits attributed to high-res spectra when generating a raw score (and e-value calculations), msgfplus will only take into account the high-res aspect of "y ions only" (ie ignore b ions and all other non-y ions completely) and even for those y ions, it will only consider those y ions that are adjacent to each other.
If that's correct, wouldn't that mean that msgfplus is not taking into account nearly as much information as other search engines, such as say X!Tandem or Sequest, that do take into account the high-res information for every fragment (whether b ion or y ion, or whether they're adjacent or not)? (I know that msgfplus will still "count" those non-adjacent y ions, but it will not consider it's high-res tolerance when it scores all ions, I believe.) Or, is the assumption that orbitraps primarily produce y ions and those y ions are almost always adjacent, and so "everything works out" in the end? (From what I can tell, I think that may be true for abundant peptides, but for the lower abundant peptides, many fragments may be missing, and some/many of them may be ones which cause a gap in the "y ion" sequence; and for lower abundant ions, one may not be able to afford to ignore a whole class of ions, eg b ions, since every ion produces potentially critical info to narrow down the possibilities of potential peptides?)