Data-independent acquisition (DIA) mass spectrometry (MS) has introduced deter-ministic, periodic and simultaneous acquisition of all fragment ions. Despite the chimeric side-effects associated with this unprecedented data integrity, DIA data analysis approaches still use conventional spectra and extracted ion chromatograms (XICs) that represent individual precursors and fragments. Here, we introduce ion-networks, an alternative data format wherein nodes correspond to reproducible fragment ions from multiple runs and edges correspond to consistent co-elution. Each ion-network represents a complete experiment and computationally eliminates chimericy based on reproducibility without sacrificing data integrity.*   t  D     :   drift time    t  R     :   retention time    m/z     :   mass-to-charge ratio    cRAP    :   common repository of adventitious proteins    CV    :   coefficient of variation    DDA    :   data-dependent acquisition    DIA    :   data-independent acquisition    diaPASEF    :   parallel accumulation – serial fragmentation combined with data-independent acquisition    FDR    :   false discovery rate    HDMS e     :   high definition Mse    HE    :   high energy    IMS    :   ion mobility separation    IQR    :   interquartile range    LC    :   liquid chromatography    LE    :   low energy    logFC    :   logarithmic fold change    MRM    :   multiple-reaction-monitoring    MS    :   mass spectrometry    PIM    :   peptide-fragment-to-ion-neighborhood match    ppm    :   parts per million    PSM    :   peptide-to-spectrum match    QC    :   quality control    RANSAC    :   random sample consensus    SNR    :   signal-to-noise ratio    SONAR    :   scanning quadrupole DIA    SWATH    :   sequential window acquisition of all theoretical mass spectra    SWIM    :   single window ion mobility    ToF    :   time of flight    XIC    :   extracted ion chromatogram

Ion-networks: a sparse data format capturing full data integrity of data independent acquisition mass spectrometry