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Topic: Why does xcms takes into account only the base peak across different scans? (Read 69 times) previous topic - next topic

  • Naresh
  • [*]
Why does xcms takes into account only the base peak across different scans?
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?

  • Sorbonne Université
Naresh Rambabu
Doctorant
Centre de Recherche des Cordeliers U1138
Equipe lacroix-Desmazes(16) : Immunopathologie et Immuno-Intervention Thérapeutique
Escalier E 4e étage
15 rue de l'Ecole de Médecine
75006 Paris CEDEX 06
France