JMod is open source and available on GitHub. If you are interested in collaborating or contributing to the project, please feel free to reach out!

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github.com/ParallelSqua...

We would also like to thank everyone at PTI for contributing to the project, it has been a huge team effort and a wonderful environment to work in!

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JMod also uniquely supports multiplexing in the time domain as demonstrated in timePlex [link] by Derks et al. This orthogonal dimension can be combined with plexDIA, providing multiplicative increases in throughput!

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www.biorxiv.org/content/10.1...

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

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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, which was newly developed here at PTI, enabling 9-plexDIA!

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www.biorxiv.org/content/10.1...

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 deconvolve overlapping isotopes introduced by plexDIA.

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