JMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics

Parallelization of data acquisition substantially increases the throughput of mass spectrometry-based proteomics. However, parallelization also increases the density of mass spectra and consequently the overlap between ions, frustrating their analysis. To improve sequence identification and quantification from such spectra, we developed an open-source software for Joint Modeling of mass spectra (JMod). JMod models overlapping peaks as linear superpositions of their components in both MS1 and MS2 space, which permits multiplexed DIA with smaller mass offsets to increase the multiplexing capacity and thus proteomics throughput for a given plexDIA tag. This enables 9-plexDIA using 2 Da offset PSMtags, increasing throughput 9-fold while preserving quantitative accuracy and coverage depth. Furthermore, we use JMod to deconvolve simultaneous labeling by mass tags and heavy amino acids, thus increasing the throughput of metabolic pulse experiments measuring protein synthesis and degradation rates in single cells from mouse liver. By supporting enhanced decoding of highly multiplexed DIA spectra, JMod provides an open and flexible software that increases the throughput of sensitive proteomics.