I have got MS1 and MS2 raw files of test sample and solvent blanks from QExactive mass spec. How can I subtract the solvent blank from test samples? When we set up the Q Exactive MS we have included a mass exclusion list observed in blanks before setting up the methods. Is this enough to exclude the signal coming from the blank? I am hopping to run my data in untargeted lipidomics using Lipidsearch for analysis.
Dear Kaushalya,
To the best of my memory, there is a special function for spectra subtraction in Q Exactive software. However, to obtain more reliable results I would recommend you using the background subtraction function in XCalibur selecting two background ranges - before and after chromatographic peak of interest. If you use direct injection without chromatographic separation, this is best done in the solvent flow from the chromatographic pump. In this case, you will get an analog of the chromatogram and you can subtract the background obtaining clean mass spectra. The advantage of this method compared to the syringe injection is also the reduction of the ion source contamination.
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