msalign2

The software tool 'msalign2' is a solution for addressing the poor migration time reproducibility of Capillary Electrophoresis-Mass Spectrometry (CE-MS) data. CE-MS is a widely-used technique for analyzing small soluble compounds in biological fluids. However, CE's poor migration time reproducibility poses a significant challenge for combining data from different experiments and correctly assigning compounds. To address this issue, several alignment algorithms have been developed. However, not all these algorithms can cope with large and irregular time shifts between CE-MS runs.

The 'msalign2' tool is a genetic algorithm that aligns CE-MS data using accurate mass information. The algorithm's utility has been demonstrated through real data, showing a significant reduction of elution time variation in the aligned datasets. Moreover, the importance of mass accuracy for the algorithm's performance has been demonstrated by comparing alignments of datasets from a standard Time-of-Flight (TOF) instrument with those from the new ultrahigh-resolution TOF maXis (Bruker Daltonics).