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XCMS Online / peak lists m/z value difference generated by different software
I just started metabolic analysis. Recently, I need to comparing peak lists generated by different softwares from same raw file include XCMS, MZmine2, QI. And I found the m/z value of XCMS has no overlap from the other two softwares peak lists m/z value, while MZmine2 and QI peaklist have some overlap.
I wonder if the different m/z value from different software is abnormal and affect downstream analysis? Could it be caused by the XCMS parameters I used, or other data processing problems, such as during the raw data converting?
Here is the detailed for processing using XCMS and MZmine2:
First I use msconvert to convert raw data into centroid mzXMl file.
For XCMS, I use the following parameters: xset <- xcmsSet(my_file, ppm=0.5, method= "centWave", peakwidth=c(5, 20), prefilter=c(2, 1000)); xset1 <- group(xset1, bw = 2, mzwid=0.015).
For MZmine2, I use noise level = 1E3 for mass detecter(centroid); min time span = 0.01, min height = 1.0E3, m/z tolerance = 1.0E-12 or 2.5 ppm.
And XCMS thinks it’s a profile data, and gave me a warning, while for MZmine2 thinks it’s a centroid file. So I use a second converter named RawConverter, and didn't get warning from XCMS, but the m/z value still has no overlap with the other two software.
Thanks for your answer!
Lucy