Chromatography Forum

Hi,
I am using a commonly used binary gradient system for lipid LC-MS.

Mobile phase A: Water: Acetonitrile (40:60)
Mobile phase B: Isopropanol: Acetonitrile (90:10)

To make sure I cleaned line with those solvent separately (LC run with acetonitrile, isopropanol separately). The spectra were clean with very minimal noise. I also made sure that the solvent were clean by running them separately. Once I started running the above binary solvent system, I saw the noisy spectra. The sample ran was blank (Mobile phase A) with above binary solvent system. I could not understand how the mixing of solvent gave me a significantly noisy spectra.
Is there anything off with the above solvent system? I am running qtrap 5500 with LC.

When you initially checked the solvents and lines, did you have the column fitted?

Hi lmh,
I did with column and then without column after detecting the noise. Now I am flushing the line without column and still noise is there. I can see the noise coming after increasing the organic percentage. I used both individual solvents (polar to non polar) and gradient cleaning. Still the unwanted peaks show up. The amazing thing is, the intensity or peak is constant after cleaning too. SO I am kind of upset. I was just wondering if something happened after mixing of A and B. But the gradient system I used is commonly used for lipid analysis.
Until now, I know the noise shows up once you increase the percentage of organic (B). It showed up with different other gradient system (ACN and water) too. The noise is coming throughout the gradient like impurities in the solvent (with or without column no difference). So I was thinking if something happened when organic percentage was increased in the gradient.

How does the noise look like? Is it noise in the spectra, or in the TIC? Can you post a chromatogram/spectrum?

Can you use a syringe pump to infuse the solvents directly into the source without passing them through the HPLC? This would help to determine if the noise is coming from the solvent, the source, or the HPLC.