list of matched b/y ions from psm

[letung1992]

I'm interested in extracting the list of matched b/y ions (not just total number of matched ions) for each PSM identified by MSFragger. Could you kindly instruct me on how to do it? Thank you so much for your time.

[fcyu]

PDV (https://github.com/wenbostar/PDV) can match the peaks. If you want to have a column with matched ions in the output table, we don't have that yet. Will add this feature when we have time.

Best,

Fengchao

[Mirjamva]

Hi! Just wondering if this is available yet? Would be really nice to have! (not just b/y ions, but also the neutral loss ions & a, c, x, z etc, with respective masses and intensities, like in the MQ msms.txt).

[fcyu]

Not yet. But the latest FragPipe (version 18.0) has a visualization module that can show annotated MS/MS spectrum.

Best,

Fengchao