I have LC-MS/MS data files from a lipidomics experiment were each sample was injected and analyzed 4 times as follows:

Positive polarity, low m/z range Positive polarity, high m/z range Negative polarity, low m/z range Negative polarity, high m/z range

I would like to know if it's possible to merge the scan ranges and polarities with XCMS prior to alignment, so that I have a single aligned feature table for each sample that is an amalgamation of the 4 LC-MS/MS analyses performed. I have the same question about MZmine 2, as well. If neither of these packages are capable of this I'd greatly appreciate suggestions if anyone knows of another solution.

I've been able to accomplish the task using LipidSearch, by Thermo, and am now trying to achieve the same outcome with open source software.

Short answer: no, in the xcms workflow it is not possible to merge the 4 data sets into one which would be required for alignment.

A workaround would be if you managed to combine/safe/export the high and low m/z per sample into one mzML file. Then it would be possible to align them against each other. What I would however not do is to merge the positive and negative polarity data. You can not expect to have all compounds ionized in both positive and negative polarity and I would thus always perform the pre-processing separately for the two runs.