The chromatogram analysis workflows in Byos (using Byomap node) show color-coded MS1 scans in each individual elution peak. The spectrum in the MS1 plot is associated with the elution time designated by the black bar in the Chromatogram pane. The elution time of the MS1 spectra can be changed by dragging the vertical black bar to a different time. Doing so can help increase understanding of the elution of peptides or glycans within the elution peak. The colors for the m/z peaks reflect the degree of time correlation of their intensity time profile with the shape of the highlighted elution peak’s profile. Green is highly correlated, magenta somewhat correlated, and grey poorly correlated.
In the example below, the green m/z ions are the 2+ and 3+ charge state of the same peptide: TPE… (id:1758). These ions are green because their elution profile is highly correlated with peak #79 in the chromatogram. On the other hand, the ion at m/z=993.512 (id:1743) is magenta colored, thus is poorly correlated and remains unassigned. All background ions are grey.
We can see in the Candidates table below that the magenta ion (id:1743) matches to sequence AAP… which is actually assigned to peak #78. What we see in peak #79 is the trailing of the AAP... peptide, hence the low correlation is expected in peak #79. The same ion is highly correlated with peak #78, and is green in the MS1 spectrum of that peak (not shown).