The single ion quantitation algorithm as implemented in PyMS. Shown is a hypothetical alignment table with three peak positions (peak UIDs "149-61-82.3-499.8", "155-101-52.5-561.2", and "161-11-49.8-433.2"), with nine individual peaks detected in three different experiments (shown as columns). For each individual peak, PyMS keeps track of the full mass spectrum and all m/z ions from the peak begin and end scans. In the single ion quantitation algorithm, the N most intensive ions are extracted for each peak (by default, N = 5). For each peak position, a single common ion present in all peaks is found. If multiple such ions may exits, the first found is used. This procedure aims to find at least one that will be used for consistent quantitation at this peak position across all experiments. In the example shown, for the first and second peak the selected common ions are m/z = 149 and m/z = 134, respectively (underlined). For the third peak position (UID = "161-11-49.8-433.2"), none of the ions present in both experiments #1 and are found in the top five ions of the experiment #3, suggesting the misalignment for this peak position (peak cell highlighted).