Thanks a lot Jan! Your suggestions really help! I modified the parameter according to your suggestion, and a package called IPO which can find best parameters of xcmsSet, and the result looks better now. Now xcms, qi, and mzmine detect similar peaks, and each of them have around 2000 to 4000 overlap peaks under 5 ppm.
Sorry for the late reply! I checked the first suggestion under m/z tollerance = 0.0005. And then XCMS detected 16238 peaks on positive mode and has 935 overlap peaks with QI's list, while XCMS has 16009 overlap peaks with MZmine's list. But under tollerance = 0.0025, XCMS has 3183 overlap m/z with QI's list. Would it be the too low ppm setting in XCMS cause the problem?( I paste the parameters below) And for the second suggestion, I try to set the ppm higher and higher, till at ppm=15 got a peak merge warning, but there is still profile mode warning. So it might be orbitrap shoulder peaks problems? I paste some screenshot of one sample as follow, would it be help for expressing the question! Thank you for your precious time! Any comments will be much appreciated!
Parameters and Samples I used: machine : Acquity UPLC(Waters) / LTQ Orbitrap XL from Thermo samples: all pool samples(15 in total), on positive mode XCMS parameters : ppm = 2.5, peakwidth = c(5, 20), prefilter = c(2, 1000), bw = 2, mzwid=0.015. Mzmine parameters: noise level : 1000, m/z tollerance : 0.0005 or 2.5ppm.
Pictures: picture1 : intensity-retention time plot from one m/z
picture2 : intensity-retention time plot from one m/z( In a step called chromatograms deconvolution in mzmine, this m/z has been recognized as many separate peaks, and produce many peaks with same m/z value but different RT in mzmine, I don't know why but in xcms and qi there is few or no peaks with same m/z.)
picture 3 : some peaks have m/z difference less than 0.005:
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.