Dear all,
I have a couple of questions for LC-MS users. We are experiencing some noise problems with our new qTof mass spectrometer (Waters Xevo G2-XS). In detail, the instrument is connected to a Waters UPLC Acquity I Class and a PDA. The noise signals are very high: 10^7 of TIC in positive and 10^6 in negative. In this way, we cannot perform metabolomics analysis since the most abundant molecules are in saturation state and we suspect that many compounds are not visible due to the noise suppression effect. Initially, we thought that the solvent bottles and cylinders were dirty, so we bought new glassware, but the noise still remained high. Therefore, we tried the cleaning procedures suggested by Waters, i.e. cleaning UPLC tubes and lines with a “Magic Solution” and then with acid and basic solutions, followed by an overnight cleaning with isopropanol. These procedures were repeated twice. I want to specify that the solvents were all LC-MS grade (Honeywell) and the additive was formic acid (UPLC-MS grade) purchased by Biosolv. Unfortunately, we did not assist to any noise reduction. Three days ago, we added a carbon filter (specific for MS application) for the nitrogen, just before the mass spectrometer. Waters technicians suggested to wait for one week, but we are not seeing any improvements in noise reduction. So, could anyone help us with an advice to reduce the noise?
Finally, the few experiments we performed originated files with high dimensions: one chromatographic run of 15 min, in positive MSe and with 0.1 as scan time, gives rise to 6 Gb of data. Is this file size normal? Thanks in advance
Dear Mauro
Did you try to disassemble the spray unit and clean the chamber?
Have you tried to wash LC line and MS with alternate Water and Organic phase? Or maybe with magic mix
If the noise is still high could be contamination of ion optics.
Dear Eduardo,
thanks for the prompt answer. I only cleaned the UPLC system with different solutions. As I wrote, I used a magic mix including solvents with different polarity, then I washed with an acid solution (25% acetonitrile + 25% isopropanol + 25% methanol + 22.5% water and 2.5% formic acid), a basic solution (water plus ammonia solution) and also with isopropanol. I carefully avoided the introduction of these wash solvents in the Xevo G2-XS. The mass spectrometer is new and I only cleaned the cone in front of the ion block. After the last cleaning procedure I observed a changing in the noise profile and some peaks appeared while other disappeared.
From first principles, your sample flow is too high, leading to incomplete evaporation of your solvent, leading to injection of too much neutral material into the MS, leading to signal saturation. UPLC-MS systems can be very capricious. I suggest you start with simple mixtures of easygoing low-mass compounds that you can easily identify. Do invest some money for a proper Waters training course (even that may not be good enough, from practical experience). Try the same sample mixture by direct injection into the MS (if you have enough) and optimize the conditions of the MS source before going to LC-MS analysis.
Dear Pavlov,
thanks for your suggestions but I don't think that the problem is the incomplete solvent evaporation since we set up the ion source parameters as specified by Waters for the proper flow rate.
Hello Mauro! Just curious to know whether you solved your problem with G2XS? The file sizes are unfortunately huge when you acquire data in profile mode.
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