Does the mass spectrometer define the marker? A comparison of global metabolite profiling data generated simultaneously via UPLC-MS on two different mass spectrometers.

By coupling a single UPLC separation to two different types of mass spectrometer an unbiased comparison of the metabolite profiles produced by each instrument for a set of rat urine samples was obtained. The flow from the UPLC column was split equally and both streams of eluent were simultaneously directed to the inlets of the two mass spectrometers. Mass spectrometry on the eluent was undertaken using a triple quadrupole linear ion trap and a hybrid quadrupole time-of-flight mass spectrometer using both positive and negative ESI. Data from both mass spectrometers were subjected to multivariate statistical analysis, after applying the same data extraction software, and showed the same general pattern of correlation between the samples using both unsupervised and supervised methods of statistical analysis. Based on orthogonal partial least-squares discriminant analysis models a number of ions were recognized as "responsible" for the separation of the animal groups. From the peaks detected, and denoted as significant by the statistical analysis a number of ions were found to be unique to one data set or the other, a result which may have consequences for biomarker discovery and interlaboratory comparisons. The software package used for data analysis also had an effect on the outcome of the statistical analysis.