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.