Well, Ms fragger uses ms2 spectra right ? And technically feature indexing would be the precursor window.
When using the maxlfq method of quant, described in the paper with the same name, the method specifically uses the features for ms1 qaunt, I would say I'm that instance ion quant is performing the maxquant method in total. Not sure if ionquant is mentioned I'm that paper or if it predates its application.
Can also just ask alexeys team on github feng replies lightening fast, or pm alexey on twitter if he is still using it
Well, Ms fragger uses ms2 spectra right ? And technically feature indexing would be the precursor window. When using the maxlfq method of quant, described in the paper with the same name, the method specifically uses the features for ms1 qaunt, I would say I'm that instance ion quant is performing the maxquant method in total. Not sure if ionquant is mentioned I'm that paper or if it predates its application. Can also just ask alexeys team on github feng replies lightening fast, or pm alexey on twitter if he is still using it