Chromatography Forum

Every time I run a blank injection on my Varian 1200L LCMS, I get the same series of contaminant peaks/background ions, and I'm curious as to whether anyone has seen anything like these spectra before. They aren't really interfering with my analysis, this is more a curiosity than anything else, as I normally run in MS/MS mode, and have almost no analyses which require a full scan mode. I've made new mobile phase, changed bottles, and have done a cursory wipe of the spray chamber. I haven't bothered to break vacuum and clean the source, nor have I tried to use a different source of water yet. If anyone has an idea as to what these contaminants are, that might give me some insight into where they're coming from and how to possibly remove them from my system.

I'm injecting 10uL (in microliter pickup mode with my Varian ProStar 410 autosampler, with DI water as my co-injected solvent) of 96:4 Methanol:DI Water out of a polypropylene vial with an aluminum crimp cap and polyethylene septa onto a Waters dC18 2.1x150mm 3um column. I'm running 5mM Sigma LCMS grade ammonium acetate in DI water (filtered through a 0.2um GHP membrane filter) on pump B, and 100% Macron LC/MS methanol on pump A (both pumps are Varian ProStar 210s), running 0.25mL/min at 45C. Gradient is as follows: 5:95 A:B at t0, linear gradient to 100:0 A:B at 40 min, hold 100:0 to 60 min.

I'm running in profile mode, scanning 50-450 m/z. Parameters are as follows: Positive - needle at 5000V, shield at 600V, negative - needle = -4500V, shield = -600V, drying gas temperature = 400C, nebulizing gas = 56psi, drying gas =36psi, CID gas = 2 mTorr. detector at 1800V.

Positive TIC




Negative TIC




Negative spectrum at ~40min, roughly the maxima of the negative TIC.




Positive spectrum at ~40 min




Positive ion spectrum of peak in positive TIC at 31.1 min

Positive ion spectrum @ RT 31.1min
m/z Assignmt
437.2 [M+Na]
432.3 [M+NH4]
415.3 [M+H]

MW = 414.3 (N count is even, 0, 2,4,....); my memory suggests that is a sulfur-containing anti-oxidant derived from polypropylene, possibly published in a paper by R.S. Bahktiar et al, although I cannot find the ref. quickly.

Positive ion spectrum @ RT 40 min
m/z Assignmt
381.4 [M+Na]
376.5 [M+NH4]
359.4 [M+H]
341.4 [M+H - H2O]

MW = 358.4 (N count is even, 0, 2, 4,...); my memory bank is blank !!

Negative ion spectrum @ RT 40 min
m/z Assignmt
389.4 [M-H]:MeOH adduct ??

MW =358.4 possibly,

Di-t-Butyl-phenol-(CH2)7-COOH ?????

That proposal needs another -CH2- and two >C=C< to get to MW 358.

Might you contaminants in positive ion mode be PEG and PPG? (see reference http://www.sciencedirect.com/science/ar ... 7008007605)

However I would still be worried of strong background because MS2 will remove all of the background noise but won't do anything to correct any variability due to ionization suppression at the electrospray tip!

Thanks for the replies. I'll try a different electrospray needle and grounding union to see if the capillary or the union have PPG contamination. This system was giving me some problems recently with turbo issues, but those have been recently resolved so I can get back to using it with some regularity.