Dear experts across the world, today I am looking for advice on a new field my lab is starting to work on: LC/MS. We are using an Agilent 1260 Infinity system, with a 6120 Quadrupole LC/MS. We do not use a column for our studies. Lately, we ran a full SCAN (100 to 1000 m/z) of a single sample of urine extract (based on MeOH, CHCl3 and H2O mixture) in our LC/MS (5 minutes the first run, and then 3 more runs of 1 minute ea), with a mobile phase solvent of ACN:H2O (50:50 v:v) obtaining the following spectra: (IMG_0924).
We assumed this reading made sense, since the masses observed are small, and this is usually normal in urine samples. However, we made a series of scans of pure water and methanol afterwards, obtaining the following spectra: (IMG_0923).
Readings of pure water did not show those results before, and clearly something was wrong. Since then, we have attempted several cleaning methods thinking it may be a contamination problem. We have tried cleaning and sonnicating the injection, corona and nebulization needle, and needle port, flushing the needle with water and the mobile phase used (we are using Acetonitrile + Water, 50:50), flushing and purging the entire system with water, acetonitrile, methanol, isopropanol (in that order), and cleaning the vials. We have ran at least 20 scans of water, methanol and mobile phase (Acetonitrile + Water, 50:50) since then, obtaining the same spectra results.
We would like to know if any of you have experienced something similar and how you handled it. Thankyou, any advice regarding this matter will be greatly appreciated. :)
I don't know the Agilent 1260/6120 system well but it seems there can be many possibilities. One of them is deposition in the APCI or ESI spray chambers. These need to be cleaned out periodically with IPA . Another possibility is gas contamination - I am not sure whether you are using zero air or nitrogen at the interface to blow out the mobile phase, or whether you have a gas generator or bottled (cylinder) gas. Impurities in the gas can also show low level persistent peaks. You might want to call an MS tech to go through the unit systematically along the process flow diagram until the problem is eliminated. If the problem is upstream in the HPLC (you said you were not using a column, but there can still be some impurities), you can try running the sample on only the mass spec using a syringe infusion pump - you might have to remove the water from your sample before you can do this.
My analytical lab work was years ago, and some excellent advice on potential contamination areas or solutions already. I would take some of your prepared samples in your glassware, etc. to another lab, analyze with same procedures. If contaminants do not show up with their equipment, then likely something associated with yours. If it does show up in their system also using your mixed samples, contamination somewhere in mixing or dilution, cleaning, etc.
It could be something simple or complex. We have all used those pipette bulbs for example. If you or one of your assistants pull in too much sample, or raise pipette into air while withdrawing sample, contamination of bulb is possible, perhaps unnoticed or poor work quality control ethics to throw contaminated bulb away and get a new one. There are all sorts of possible contamination issues in labs. Using another lab may help identify better identify the area of contamination, or by deduction, areas not contaminated. It is a thankless task and potentially expensive and time consuming to figure out. As suggested, the MS tech or equipment quality control expert might offer some advice, low cost or complementary quality testing or control. One desires a trustworthy equipment advisor, rather than one that just replaces parts or want to sell new analytical equipment.
If research is time sensitive, securing services in another respected and certified lab may help solve the sort term demand. Collaboration, partnerships or cost-shared resources is sometimes the way to go.
But are ghost peaks reproducible from one run to another? Are they always the same? How pure is the water? Which is the purification system for water?
When you use MS, you see all, that's the problem, and it is rather impossible to ahve a "clean" background. Also nitrogen purity i very critical.
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