Increasing throughput in mass spec proteomics requires new ways to model the increased complexity of the spectra. To model highly multiplexed mass spectra, we developed JMod. JMod enables new multiplexing approaches in the time and mass domains. biorxiv.org/content/10.110…

By modeling both MS1 and MS2 spectra as linear superpositions of library precursors, JMod can identify and quantify highly similar precursors within the same spectrum as well as decovolve overlapping isotopes introduced by plexDIA.

In the context of plexDIA, JMod uniquely supports channel offsets of <4 Da. Using 2 Da offsets, it enables almost 2-fold more throughput for any given tag. We demonstrate this using PSMtag parallelsq.org/psmtags, which was newly developed here at PTI!

JMod can also provide highly accurate quantitation for these highly multiplexed samples, regardless of isotopic overlap