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It is advisable to turn both the LC system and the MS system on for at least 30 minutes prior to analysis. This time can usually be spent running 1 or more solvent or matrix blanks.

Perform loop injections of your analyte using isocractic elution through a short column at the flow rate and approximate mobile phase composition. Use a concentration where the signal to noise is approximately 10:1. Record the raw data file and integrate the peaks, comparing peak areas at different source positions (i.e. left and right, up and down, fore and aft). Ensure that the background noise is not increasing more than the peak area.

Note: The needle position on the Thermo Scientific ™ TSQ Altis MS, TSQ Quantis MS and TSQ Fortis MS instruments is set and should not be adjusted.

  • The Ion Transfer Tube should be removed and sonicated in 50:50 solution of methanol/water that contains 20% formic acid for 30 minutes. Rinse thoroughly with water. Then sonicate in methanol for 15 minutes. Dry with nitrogen gas.
  • The same procedure can be applied to the Ion Sweep Cone
  • Refer to the Instrument Manual for more detailed instructions.
  • The mass calibration should ideally be performed every 3 months and definitely performed at least every 6 months.
  • Refer to the Instrument Manual for detailed instructions on how to do mass calibration.
  • For short periods (less than 24 hours) the system can just be put into standby. However, it is good practice to flush the system with 50:50 solvent/water (where the solvent is either methanol or acetonitrile) to remove buffers or additives and stop microbial growth.
  • For longer periods, flush the LC system with 50:50 solvent/water. Then flush with 100% solvent. Put the system into standby.

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