Fu, Y.; Yuan, Z.-F.; Byrum, S. D.; Wu, L.; Peng, J.; Wang, X.; High, A. A.

Incomplete quantification remains a persistent challenge in data-independent acquisition (DIA) mass spectrometry (MS), particularly in low-input and single-cell analyses. In identification-driven workflows, missing protein quantities often arise not from true absence of the corresponding peptides, but from failure to retain low-abundance signals from precursor or product ions for quantification. Here we present JUMPlion (local inference of ion-level missingness), a DIA quantification framework that re-examines MS raw files to recover missing values at the ion level before protein quantification. JUMPlion re-extracts precursor- and product-ion signals directly from raw data, infers ion-level measurements within precursor-specific local quantitative neighborhoods, and combines complementary precursor- and product-ion signals into downstream quantification. Using benchmark datasets acquired on multiple DIA platforms, JUMPlion increased protein-level completeness, improved fold-change accuracy, and enhanced detection of differentially abundant proteins while maintaining low differential-abundance false discovery rates. These gains were most evident in low-input and single-cell DIA datasets. Together, these results show that addressing missingness at the ion level before protein-level summarization can improve DIA quantification in diverse acquisition settings.