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We recently purchased a Thermo Vanquish Neo (nanoflow) LC coupled to an Exploris 240 mass spectrometer for use in bottom-up proteomics. This very nice system has not yet passed system specification for peak shape and appearance.  The Cytochrome C digest that came with the instrument gives noisy peaks.  Similarly, the standard Thermo digest of HeLa gives both noisy TIC and BPI. TIC is really ugly through most of the gradient. Presale tests with the same HeLa that we had done for us at the Thermo apps lab on Exploris and Exploris/Vanquish Neo did not have that problem, nor do we see it on another older Thermo system in our lab using similar columns, gradient and identically prepared solvents.

Thermo is in the process of elevating this problem to higher technical support levels and have been very supportive.  We do not know whether the issue resides in the LC or MS.  While it is nice to have these engineers around the lab, it tends to consume a lot of time for us. We suspect some factory defect on this particular unit. Does anyone out there have experience with this exact problem on this system?  It is a quite new design, especially, the LC which as extensive self-tests. While Thermo is very supportive and dedicated to fixing this system, I wanted to post this question on the forum, to perhaps save some time.  Maybe somebody has seen this or knows of someone who quietly solved the problem on their own new system. Different columns have been tried. Please post or reply privately to me directly if you have similar experience on this system.  It will save us time and relieve the service engineers of a headache,

Thanks, 
Lewis Brown Ph.D.

Director, Quantitative Proteomics and Metabolomics Center
Columbia University