alchemistmatt
commented
4 years ago Sorry, but MS-GF+ does not support filtering MS2 fragmentation ions by charge state. You can filter precursor ions by charge, but not fragmentation ions. I looked around in the code and it was not obvious to me where the theoretical b/y/etc. ions are computed, so you would need to find a developer to implement this feature, then submit the update as a pull request.
We have a routine to do charge deconvolution on our spectra such that all the fragments are set to be +1 ms2 fragmention ions only (ie no +2 or +3 ms2 fragments etc.). However, we couldn't determine in msgfplus what option, if any, we could set in msgfplus to limit the theoretical ions to also be ONLY +1 fragment ions. (In msfragger, a new tool, one can limit the theoretical fragments to be only +1, though I'm not clear if it's working well in msfragger....). Is there an option in msgfplus to limit the theoretical fragments to only +1 charge fragments? If not, could you point me in the right direction in the source code where I can (temporarily) hack msfplus to limit fragments to only +1 fragment ions? (As an alternative, I considered "hacking" my spectrum itself to make it look as if the precursor itself was only +1, which I presume would trick msgfplus (and any other search engine) in only considering +1 theoretical fragments; but, my concern was that would be less ideal, since msgfplus may model +1 precursor peptides differently than +2 or +3 etc and the same may be true for any post-processing tools, eg percolator or peptideprophet/iprophet etc., so "faking/hacking" all spectra to look like the precursor was +1 would lose some important information.) Thoughts?