How to combine MS level 1 and 2?

[FangYangUW]

The chromatogram() only can separately run MS level 1 and 2. How to combine MS level 1 and 2 after chromatogram() for peak detection and alignment? chromatogram(object, rt, mz, aggregationFun = "sum", missing = NA_real_, msLevel = 1L, BPPARAM = bpparam(), adjustedRtime = hasAdjustedRtime(object), filled = FALSE)

Thank you so much for your help in advance.

Fang

[jorainer]

With the chromatogram function you want to extract an ion chromatogram from the data. It makes only sense to extract such a chromatogram from either MS1 data or MS2 data, but not both.

In xcms the main object is the XCMSnExp that contains the link to the raw mass spec data as well as all xcms results. In that object you will also have MS1 and MS2 spectra. chromatogram is only used to extract certain data from that XCMSnExp object for data visualization purposes. You should keep the XCMSnExp and work only with that.