Why does xcms takes into account only the base peak across different scans?

June 26, 2018, 05:12:51 AM

Hello everyone,

I have performed untargeted global metabolic profiling on the mammalian cells using Thermo Scientific™ Orbitrap Fusion™ Tribrid™ mass spectrometer.

The machine has performed both positive and negative polarization scans in sequential order followed by MS2 fragmentation.

This is how the data structure looks when I open the raw files in Mzmine for visualization.

#1 @0.00 MS1 P + (this is a profile spectra in positive polarization with base peak 445.139, which corresponds to acetonitrile the
mobile phase)

#2 @0.02 MS1 P - (this is a profile spectra with negative polarization with base peak 220.1460)

#3 @0.03 MS2 C+ (This is a centroid spectra in positive polarization)
#4 @0.03 MS2 C+ (This is a centroid spectra in positive polarization)
.
.
.
.
#22 @0.05 MS1 P+ (this is a profile spectra in positive polarization with base peak 445.139, which corresponds to acetonitrile the
mobile phase)

#23 @0.05 MS2 C- (This is a centroid spectra in negative polarization)
#24 @0.06 MS2 C- (This is a centroid spectra in negative polarization)
.
.
.

#37 @0.07 MS1 P - (this is a profile spectra with negative polarization with base peak 220.1464)
.
.
.
#22257 @120.01 MS2 C+ (This is a centroid spectra in positive polarization)
#22258 @120.02 MS2 C+ (This is a centroid spectra in positive polarization)

This is a high-resolution data each individual profile scans consist of several peaks that correspond to metabolites (unfortunately, they are not the base peaks).

XCMS takes into account only the base peaks when it generates the TIC vs retention time but doesn't take into consideration the rest of the peaks which are important for my analysis.

Which means I am already losing 99 % of my data. Is there any other software that could help me with this problem?

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