The Tool Buttons - Pairing
With the pairing feature in MassAI, you can hunt for scans that have similar fragmentation patterns, but differ in mass.

In the below example, we search for scans that have a mass difference of 4 Da. We have further specified that the
peptide in at least ONE of the scans involved must have been identified.

The high-scoring scan 106 in the reference has been identified as the peptide DKGLQTSQDAR. Several scans also
present in the dataset match this scan, only 4Da heavier.

The selected matching scan pairs are drawn in the chart. The reference is coloured blue, while the 4Da heavier
counterpart is coloured in red and mirrored around the X-axis.

( The 4Da difference is due to the fact that the LYS in the peptide is modified with a dead-end BS3-d0 cross-linker,
whilst the counterpart has been modified with the 4Da heavier BS3-d4).